#------------------------------------------------------------------------------
#$Date: 2018-07-18 23:53:05 +0300 (Wed, 18 Jul 2018) $
#$Revision: 209108 $
#$URL: file:///home/coder/svn-repositories/cod/cif/1/54/69/1546928.cif $
#------------------------------------------------------------------------------
#
# This file is available in the Crystallography Open Database (COD),
# http://www.crystallography.net/. The original data for this entry
# were provided by IUCr Journals, http://journals.iucr.org/.
#
# The file may be used within the scientific community so long as
# proper attribution is given to the journal article from which the
# data were obtained.
#
data_1546928
loop_
_publ_author_name
'Bull, Craig L.'
'Flowitt-Hill, Giles'
'de Gironcoli, Stefano'
'Küçükbenli, Emine'
'Parsons, Simon'
'Pham, Cong Huy'
'Playford, Helen Y.'
'Tucker, Matthew G.'
_publ_section_title
;
 ζ-Glycine: insight into the mechanism of a polymorphic phase transition
;
_journal_issue                   5
_journal_name_full               IUCrJ
_journal_page_first              569
_journal_page_last               574
_journal_paper_doi               10.1107/S205225251701096X
_journal_volume                  4
_journal_year                    2017
_chemical_absolute_configuration rm
_chemical_formula_moiety         'C2 D5 N O2'
_chemical_formula_sum            'C2 D5 N O2'
_chemical_formula_weight         80.097
_chemical_name_systematic        zeta-glycine-d5
_space_group_crystal_system      triclinic
_space_group_IT_number           1
_space_group_name_Hall           'I 1'
_space_group_name_H-M_alt        'I 1'
_cell_angle_alpha                85.815(5)
_cell_angle_beta                 114.456(5)
_cell_angle_gamma                104.136(5)
_cell_formula_units_Z            2
_cell_length_a                   5.1000(4)
_cell_length_b                   6.2850(3)
_cell_length_c                   5.4295(3)
_cell_measurement_pressure       0
_cell_measurement_temperature    100
_cell_volume                     153.545(18)
_diffrn_ambient_temperature      100
_diffrn_detector                 'ZnS scintillator'
_diffrn_detector_type            custom
_diffrn_measurement_device_type  'PEARL, ISIS'
_diffrn_radiation_type           Neutron
_diffrn_source                   'Pulsed neutron source'
_exptl_absorpt_correction_type   empirical
_exptl_absorpt_process_details
;
Calculated using custom ISIS software.
;
_exptl_crystal_density_diffrn    1.732
_pd_block_diffractogram_id       100K
_pd_char_colour                  Colourless
_pd_char_particle_morphology     Block
_pd_instr_dist_spec/detc         600
_pd_instr_dist_src/spec          12600
_pd_instr_location               'ISIS, Rutherford Appleton Laboratory'
_pd_meas_2theta_fixed            90
_pd_meas_scan_method             Time-of-flight
_pd_proc_info_data_reduction
;
Custom ISIS software
;
_pd_proc_info_excluded_regions
;
excluded short TOF region above

;
_pd_proc_ls_background_function  'Chebychev polynomial'
_pd_proc_ls_pref_orient_corr
; 
Modelling of preferred orientation was found to be unnecessary.
;
_pd_proc_ls_profile_function
;
Voigt function convoluted with a back-to-back double exponential.
;
_pd_proc_ls_prof_R_factor        2.86617175
_pd_proc_ls_prof_wR_factor       3.08785325
_pd_spec_mounting                'TiZr Capsule'
_pd_spec_mount_mode              transmission
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_all   1.36489139
_refine_ls_hydrogen_treatment    refxyz
_refine_ls_matrix_type           sparse
_refine_ls_number_constraints    22
_refine_ls_number_parameters     65
_refine_ls_number_restraints     0
_refine_ls_shift/su_max          <0.001
_refine_ls_weighting_scheme      sigma
_iucr_refine_instructions_details
;
####Topas .inp file for final refinement cycle:####

'T=100K

    r_exp  2.26234356         
    r_exp_dash  6.58399481  
    r_wp  3.08785837      
    r_wp_dash  8.98645274       
    r_p  2.86626696          
    r_p_dash  8.70026087      
    weighted_Durbin_Watson  0.268373933
    gof  1.36489365        




'do_errors

#define INCLUDE_ZETA
#define INCLUDE_EPSILON
'#define INCLUDE_GAMMA_RIETVELD  'Rwp = 3.10
#define INCLUDE_GAMMA_PAWLEY    'Rwp = 3.09 ...for fewer parameters

 
xdd PRL91270_91274_tof_xye-0.xye xye_format
      
    neutron_data
    x_calculation_step = Yobs_dx_at(Xo);
  weighting =  1/SigmaYobs^2;


'############################################################

 TOF_LAM(0.001)
     TOF_x_axis_calibration(!t0, 2.90479, !difc, 4837.35127, !difa,-0.36636)
   
   prm !exp1  5.57911 min 1 max 10
  
      TOF_Exponential(!p1, 30.84298,!p2, 47.23187, exp1, difc, +)
   push_peak        
      TOF_Exponential(!p3, 16.25530,!p4,  2.29958, exp1, difc, +)
   bring_2nd_peak_to_top      
      TOF_Exponential(!p5, 9167.96334,!p6,  639.11639_LIMIT_MIN_57.5204755, exp1, difc, -)
      scale_top_peak  !p7  1180.69154 min .001 del = Val .05 + 1; 
   add_pop_1st_2nd_peak    

'############################################################


    bkg @   1.19184042` -0.139525814`  0.13540451` -0.0727958297`  0.0114285286`  0.0578136407`  0.0751317602`  0.0658448697`  0.0449697553`  0.013309265`  0.0313281806`  0.0131293007` '-0.0263619341  0.00825125166 -0.00837490529
   

   scale_pks = D_spacing^4;         

   start_X 3000
   'finish_X 19000
   
    prm !dnh  1.05          ' from Acta B36 115 1980
    prm !dch  1.09
    prm !dcn  1.48
    prm !dcc  1.53
    prm !dco  1.25
    prm !acch  109
    prm !acnh  109
    prm !ancc  112 
    prm !acco1 117
    prm !acco2 117     

#ifdef INCLUDE_ZETA
    str     
      phase_name zeta
            space_group I1       'choose this setting to make relationship with epsilon phase clearer
      a  @  5.099988`
      b  @  6.285048`
      c  @  5.429506`
      al @  85.81511`
      be @  114.45608`
      ga @  104.13649`
        MVW( 150.133, 153.545`, 2.547`)
    TOF_PV(@,  588.79220`, @  ,   0.502833094`, difc)
        scale @  0.0809039733`
    
    
    'geometric parameters:
          prm ztors  35.12777` min -180.0 max 180.0   ' torsion N1C2C1O2
            prm ztornh3 -169.98392` min -180.0 max 180.0   ' NH3+ torsion
    
     rigid
            load z_matrix
            {
            N1
            C2   N1  =dcn;
            C1   C2  =dcc;  N1 =ancc;
            O1   C1  =dco;  C2 =acco1; N1  =180+ztors;    
            O2   C1  =dco;  C2 =acco2; N1  =ztors;        
            H1   C2  =dch;  C1 =acch;  O2  =120+ztors;
            H2   C2  =dch;  C1 =acch;  O2  =-120+ztors;
            H3   N1  =dnh;  C2 =acnh;  C1  =ztornh3;     
            H4   N1  =dnh;  C2 =acnh;  C1  =ztornh3-120; 
            H5   N1  =dnh;  C2 =acnh;  C1  =ztornh3+120; 
            }    

            rotate @  -139.91735` min -180 max 180  qa 1        
            rotate @  -137.03733` min -180 max 180  qb 1        
            rotate @   90.00848` min -180 max 180  qc 1         
            
            translate    'not refined to fix origin
              ta   0.71144        
              tb   0.68132             
              tc   0.77926   

          prm b1z  0.57881` 'overall isotropic thermal parameter 
          site  N1   x   0.71144` y  0.68132` z  0.77926` occ  N  1.0  beq  =b1z;
          site  C1   x   0.53980` y  0.77702` z  1.11658` occ  C  1.0  beq  =b1z;
          site  C2   x   0.51771` y  0.79952` z  0.82654` occ  C  1.0  beq  =b1z;
          site  O1   x   0.30817` y  0.76597` z  1.14913` occ  O  1.0  beq  =b1z;
          site  O2   x   0.78781` y  0.77139` z  1.29918` occ  O  1.0  beq  =b1z;
          site  H1   x   0.28933` y  0.73160` z  0.68652` occ  D  1.0  beq  =1.2*b1z;
          site  H2   x   0.58432` y  0.97278` z  0.78860` occ  D  1.0  beq  =1.2*b1z;
          site  H3   x   0.71779` y  0.72440` z  0.59095` occ  D  1.0  beq  =1.5*b1z;
          site  H4   x   0.62523` y  0.51163` z  0.77997` occ  D  1.0  beq  =1.5*b1z;
          site  H5   x   0.92554` y  0.72602` z  0.93410` occ  D  1.0  beq  =1.5*b1z;

       
    Out_CIF_STR(zeta.cif)

#endif  'include zeta

   
#ifdef  INCLUDE_EPSILON  
    str     
    phase_name epsilon
         space_group Pn   
         a  @   5.023025`
        b  @   5.984642`
        c  @   5.494603`
        al   90.0
        be @    114.65393`
        ga    90.0
        scale @   0.0603698008`
        MVW( 150.133, 150.117`, 1.858`)
    TOF_PV(,  552.99587,  ,   0.765214829, difc)
 
    'geometric parameters:
          prm etors  16.03732` ' torsion N1C2C1O2
            prm etornh3  180.82427` ' NH3+ torsion

          rigid
            load z_matrix
            {
            N1
            C2   N1  =dcn;
            C1   C2  =dcc;  N1 =ancc;
            O1   C1  =dco;  C2 =acco1; N1  =180+etors;    
            O2   C1  =dco;  C2 =acco2; N1  =etors;        
            H1   C2  =dch;  C1 =acch;  O2  =120+etors;
            H2   C2  =dch;  C1 =acch;  O2  =-120+etors;
            H3   N1  =dnh;  C2 =acnh;  C1  =etornh3;     
            H4   N1  =dnh;  C2 =acnh;  C1  =etornh3-120; 
            H5   N1  =dnh;  C2 =acnh;  C1  =etornh3+120; 
            }    

            rotate  @ -164.24494` qa 1
            rotate  @  212.83090` qb 1
            rotate  @  129.03909` qc 1
            

            translate   'x and z not refined to fix origin
              ta      0.73400
              tb   @  0.69268`
              tc      0.7800

    prm b1e  0.41810` 'overall isotropic thermal parameter
        site O1   x  0.29248` y  0.79475` z   1.14715` occ O  1 beq =b1e;
        site O2   x  0.74724` y  0.66707` z   1.27310` occ O  1 beq =b1e;
        site N1   x  0.73400` y  0.69268` z   0.78000` occ N  1 beq =b1e;
        site C1   x  0.51446` y  0.75130` z   1.10730` occ C  1 beq =b1e;
        site C2   x  0.49991` y  0.80627` z   0.83008` occ C  1 beq =b1e;
        site H1   x  0.28869` y  0.75223` z   0.67817` occ D  1 beq =1.2*b1e;
        site H2   x  0.52460` y  0.98609` z   0.81555` occ D  1 beq =1.2*b1e;
        site H3   x  0.71634` y  0.73756` z   0.58911` occ D  1 beq =1.5*b1e;
        site H4   x  0.70940` y  0.51912` z   0.78968` occ D  1 beq =1.5*b1e;
        site H5   x  0.93847` y  0.74264` z   0.92650` occ D  1 beq =1.5*b1e;

       
    Out_CIF_STR(epsilon.cif)

#endif  'include espilon


#ifdef INCLUDE_GAMMA_RIETVELD
    str 
       phase_name gamma_glycine
        space_group P31
        Trigonal(@  6.932681, @  5.632331)
        MVW( 225.200, 234.434, 2.118)
        scale @  0.00542616989
    TOF_PV(@,  1433.83137, @ ,   7.62922635e-005_LIMIT_MIN_0, difc)
    PO_Spherical_Harmonics(sg2, 2 load sh_Cij_prm {
            y00   !sg2_c00  1.00000
            y20   sg2_c20  -2.62473
            } )

    'geometric parameters:
          prm !tors  13.23157    ' torsion N1C2C1O2
            prm !tornh3  180.60355 ' NH3+ torsion

          rigid
            load z_matrix
            {
            N1
            C2   N1  =dcn;
            C1   C2  =dcc;  N1 =ancc;
            O1   C1  =dco;  C2 =acco1; N1  =180+tors;    
            O2   C1  =dco;  C2 =acco2; N1  =tors;        
            H1   C2  =dch;  C1 =acch;  O2  =120+tors;
            H2   C2  =dch;  C1 =acch;  O2  =-120+tors;
            H3   N1  =dnh;  C2 =acnh;  C1  =tornh3;     
            H4   N1  =dnh;  C2 =acnh;  C1  =tornh3-120; 
            H5   N1  =dnh;  C2 =acnh;  C1  =tornh3+120; 
            }    
    
            rotate @   41.63351 qx 1
            rotate @ -31.89513 qy 1
            rotate @ -153.21747 qz 1

            translate
              ta @  0.96993
              tb @  0.21058
              tc   0.49270 
        
        prm bg  5.81734
        site O1 num_posns  3 x  0.97472 y  0.55423 z  0.98003 occ O  1 beq =bg;
             site O2 num_posns  3 x  0.74172 y  0.20105 z  0.88078 occ O  1 beq =bg;
             site N1 num_posns  3 x  0.96993 y  0.21058 z  0.49270 occ N  1 beq =bg;
             site C1 num_posns  3 x  0.91723 y  0.38386 z  0.85709 occ C  1 beq =bg;
             site C2 num_posns  3 x  1.07632 y  0.40065 z  0.65944 occ C  1 beq =bg;
             site H1 num_posns  3 x  1.12895 y  0.55388 z  0.55994 occ D  1 beq =1.5*bg;
             site H2 num_posns  3 x  1.22068 y  0.40253 z  0.73870 occ D  1 beq =1.5*bg;
             site H3 num_posns  3 x  1.08606 y  0.22906 z  0.36210 occ D  1 beq =1.5*bg;
             site H4 num_posns  3 x  0.83211 y  0.20897 z  0.41328 occ D  1 beq =1.5*bg;
             site H5 num_posns  3 x  0.91791 y  0.06203 z  0.58718 occ D  1 beq =1.5*bg;
#endif 'INCLUDE_GAMMA_RIETVELD


#ifdef INCLUDE_GAMMA_PAWLEY
hkl_Is
       phase_name gamma_glycine
        space_group "P31"
        Trigonal(@  6.940308`, @  5.647138`)
        MVW( 225.200, 235.568`, 72.440`)
    TOF_PV(@,  1931.62611`,  ,   0, difc)
        load hkl_m_d_th2 I 
        {
               1   1   1   6    2.956555     14301.59804  @  2.66606`
               1   1   0   6    3.470154     16784.84691  @  1.32589`
        }
#endif 'INCLUDE_GAMMA_PAWLEY

      str
      space_group "Fm-3m"
      phase_name lead  'pressure marker. Note T=100K
      MVW( 828.800, 119.114`, 2.779`)
      Cubic( @  4.920252`)
      site Pb1 x  0.00  y 0.00  z 0.00 occ Pb 1 beq @  0.67425`
      scale  @  0.0206167103`
      TOF_PV( @ ,  424.90247` ,@ ,  9.3907089e-008`_LIMIT_MIN_0 , difc)        

      str
      space_group "R-3c"
      phase_name Al2O3  'part of PE cell, not centred in beam.
      Hexagonal( @  4.746449`,  @  12.962343`)  
      TOF_PV(@ ,  921.40990` ,@ ,  0.509195187`, difc)        
      site  Al1  x    0.        y   0.      z @  0.35302` occ  Al   1   beq  @ -0.44834`
      site  O1   x  @  0.30676` y   0.      z    0.25     occ  O    1   beq  @ -0.28428`
      scale @  0.0234226202`

      str
      space_group "P42/nmc"
      phase_name ZrO2  'part of PE cell, not centred in beam.
      Tetragonal(  @  3.609716` , @  4.963445`)
      TOF_PV(@  ,  1568.01754` , ,  0, difc)
      site   Zr1  x   0.75   y   0.25   z     0.75     occ  Zr   1   beq @  19.99934`_LIMIT_MAX_20
      site   O1   x   0.25   y   0.25   z  @  0.61849` occ  O    1   beq @  16.60614`
      scale @  0.177219278`


'end of Topas input file.
;
_cod_data_source_file            lq5008.cif
_cod_data_source_block           zeta_glycine_100K
_cod_original_cell_volume        153.545(17)
_cod_original_sg_symbol_Hall     I1
_cod_original_sg_symbol_H-M      I1
_cod_database_code               1546928
_pd_proc_ls_prof_r_expected      2.26234356
loop_
_space_group_symop_id
_space_group_symop_operation_xyz
1 x,y,z
2 x+1/2,y+1/2,z+1/2
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
_atom_site_B_iso_or_equiv
N1 N 2 0.71144 0.68132 0.77926 1 0.58(3)
C1 C 2 0.540(2) 0.777(2) 1.1166(9) 1 0.58(3)
C2 C 2 0.518(2) 0.7995(16) 0.8265(8) 1 0.58(3)
O1 O 2 0.308(3) 0.766(4) 1.1491(13) 1 0.58(3)
O2 O 2 0.788(2) 0.7714(17) 1.2992(6) 1 0.58(3)
H1 D 2 0.2893(15) 0.732(3) 0.6865(9) 1 0.69(4)
H2 D 2 0.584(4) 0.9728(15) 0.7886(14) 1 0.69(4)
H3 D 2 0.7178(14) 0.7244(11) 0.5909(7) 1 0.87(5)
H4 D 2 0.625(2) 0.5116(2) 0.7800(17) 1 0.87(5)
H5 D 2 0.9255(5) 0.7260(15) 0.9341(9) 1 0.87(5)
loop_
_geom_angle_atom_site_label_1
_geom_angle_atom_site_label_2
_geom_angle_atom_site_label_3
_geom_angle
_geom_angle_publ_flag
O1 C1 O2 126.00 yes
O1 C1 C2 117.00 yes
O2 C1 C2 117.00 yes
C2 N1 H5 109.00 yes
C2 N1 H3 109.00 yes
C2 N1 H4 109.00 yes
H4 N1 H5 110.00 yes
H3 N1 H4 110.00 yes
H3 N1 H5 110.00 yes
N1 C2 C1 112.00 yes
N1 C2 H1 108.00 yes
N1 C2 H2 108.00 yes
C1 C2 H1 109.00 yes
C1 C2 H2 109.00 yes
H1 C2 H2 110.00 yes
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_publ_flag
O1 C1 1.2500 yes
O2 C1 1.2500 yes
N1 C2 1.4800 yes
C1 C2 1.5300 no
N1 H3 1.0500 yes
N1 H4 1.0500 yes
N1 H5 1.0500 yes
C2 H1 1.0900 yes
C2 H2 1.0900 yes
loop_
_geom_torsion_atom_site_label_1
_geom_torsion_atom_site_label_2
_geom_torsion_atom_site_label_3
_geom_torsion_atom_site_label_4
_geom_torsion
_geom_torsion_publ_flag
O1 C1 C2 N1 -144.9(4) no
O2 C1 C2 N1 35.1(4) no
