#==============================================================================
data_global
#==============================================================================
_publ_contact_author 'Harry L. Anderson'
_publ_contact_author_email
harry.anderson@chem.ox.ac.uk
loop_
_publ_author_name
_publ_author_address
'Scriven, Lorel M.'
;
Department of Chemistry,
University of Oxford,
Chemistry Research Laboratory,
Oxford OX1 3TA. UK.
;
'Kaiser, Katharina'
;
IBM Research-Zurich,
S\"aumerstrasse 4,
8803 R\"uschlikon,
Switzerland.
;
'Schulz, Fabian'
;
IBM Research-Zurich,
S\"aumerstrasse 4,
8803 R\"uschlikon,
Switzerland.
;
'Sterling, Alistair J.'
;
Department of Chemistry,
University of Oxford,
Chemistry Research Laboratory,
Oxford OX1 3TA. UK.
;
'Woltering, Steffen L.'
;
Department of Chemistry,
University of Oxford,
Chemistry Research Laboratory,
Oxford OX1 3TA. UK.
;
'Gawel, Przemyslaw'
;
Department of Chemistry,
University of Oxford,
Chemistry Research Laboratory,
Oxford OX1 3TA. UK.
;
'Christensen, Kirsten E.'
;
Chemical Crystallography Department,
Chemistry Research Laboratory,
University of Oxford,
Mansfield Road,
Oxford OX1 3TA. UK.
;
'Anderson, Harry L.'
;
Department of Chemistry,
University of Oxford,
Chemistry Research Laboratory,
Oxford OX1 3TA. UK.
;
'Gross, Leo.'
;
IBM Research-Zurich,
S\"aumerstrasse 4,
8803 R\"uschlikon,
Switzerland.
;
_publ_requested_journal
'Journal of American Chemical Society'
_journal_volume '?'
_journal_page_first '?'
_journal_page_last '?'
_journal_year '2020'
_ccdc_journal_depnumber '?'
_publ_section_title
;
Synthesis of cyclo[18]carbon via debromination of C~18~Br~6~
;
_publ_section_abstract
;
Cyclo[18]carbon (C~18~, a molecular carbon allotrope) can be synthesized by
dehalogenation of a bromocyclocarbon precursor, C~18~Br~6~, in 50% yield, by
atomic manipulation on a sodium chloride surface at 5 K, and imaged by high
resolution atomic force microscopy (AFM). This method of generating C~18~ gives
a higher yield and cleaner images than the method reported previously, elimination
of CO from the cyclocarbon oxide, C~24~O~6~. The experimental images of C~18~
were compared with calculated images for four theoretical model geometries:
D~9h~ polyyne, D~18h~ cumulene, D~9h~ cumulene and C~9h~ polyyne. The
results fit well with the two polyyne models, but do not distinguish between
D~9h~ and C~9h~ geometries: there is evidence for bond-length alternation, and
some degree of bond-angle alternation cannot be excluded.
;
#==============================================================================
data_C18Br6
#==============================================================================
_audit_creation_date "2020-04-14"
_audit_creation_method 'CRYSTALS_ver_14.61_build_7491 '
_oxford_structure_analysis_title '7256-c Fdd2-cba'
_chemical_name_systematic .
_chemical_melting_point 'not measured'
_diffrn_special_details
;
The crystals of this compound quickly loose solvent and
becomes amorphous. Several attempts at measuring these
crystals were made. For one particular sample the solvent was
very slowly evaporated in the fridge. A small hexagonal plate
crystal was seen and mounted. This particular sample did not
seem to suffer from solvent loss in the same way as the
others.
The crystal was mounted using our in-house diffractometor and
collected over the weekend. Unfortunately the crystal
diffracted weakly and a hemisphere of data were collected to
1\%.
;
_refine_special_details
;
Data were carefully examined for symmetry, beam damage and
other issues. The collected data were weak but would solve in
Fdd2 using SHELXT. Due to the resolution of the data the data
to parameter ratio is low, which is why a disordered model is
not appropriate though the thermal ellipsoids clearly indicate
that disorder is present in the structure.
;
_cell_length_a 21.6885(16)
_cell_length_b 13.647(4)
_cell_length_c 12.5084(11)
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_cell_volume 3702(1)
_symmetry_cell_setting 'orthorhombic'
_symmetry_space_group_name_H-M 'F d d 2 '
_symmetry_space_group_name_Hall 'F 2 -2d'
loop_
_symmetry_equiv_pos_as_xyz
'x,y,z'
'x,y+1/2,z+1/2'
'x+1/2,y,z+1/2'
'x+1/2,y+1/2,z'
'-x,-y,z'
'-x,-y+1/2,z+1/2'
'-x+1/2,-y,z+1/2'
'-x+1/2,-y+1/2,z'
'-x+1/4,y+1/4,z+1/4'
'-x+1/4,y+3/4,z+3/4'
'-x+3/4,y+1/4,z+3/4'
'-x+3/4,y+3/4,z+1/4'
'x+1/4,-y+1/4,z+1/4'
'x+1/4,-y+3/4,z+3/4'
'x+3/4,-y+1/4,z+3/4'
'x+3/4,-y+3/4,z+1/4'
loop_
_atom_type_symbol
_atom_type_scat_dispersion_real
_atom_type_scat_dispersion_imag
_atom_type_scat_Cromer_Mann_a1
_atom_type_scat_Cromer_Mann_b1
_atom_type_scat_Cromer_Mann_a2
_atom_type_scat_Cromer_Mann_b2
_atom_type_scat_Cromer_Mann_a3
_atom_type_scat_Cromer_Mann_b3
_atom_type_scat_Cromer_Mann_a4
_atom_type_scat_Cromer_Mann_b4
_atom_type_scat_Cromer_Mann_c
_atom_type_scat_source
C 0.0181 0.0091 2.3100 20.8439 1.0200 10.2075 1.5886 0.5687
0.8650 51.6512 0.2156 'International Tables Vol C 4.2.6.8 and 6.1.1.4'
Br -0.6763 1.2805 17.1789 2.1723 5.2358 16.5796 5.6377 0.2609
3.9851 41.4328 2.9557 'International Tables Vol C 4.2.6.8 and 6.1.1.4'
_cell_formula_units_Z 8
# Given Formula = C18 Br6
# Dc = 2.50 Fooo = 2544.00 Mu = 156.48 M = 695.62
# Found Formula = C18 Br6
# Dc = 2.50 FOOO = 2544.00 Mu = 156.48 M = 695.62
_chemical_formula_sum 'C18 Br6'
_chemical_formula_moiety 'C18 Br6'
_chemical_compound_source .
_chemical_formula_weight 695.62
_cell_measurement_reflns_used 408
_cell_measurement_theta_min 5.20
_cell_measurement_theta_max 47.67
_cell_measurement_temperature 150
_exptl_crystal_description 'plate'
_exptl_crystal_colour 'clear_intense_red'
_exptl_crystal_size_min 0.01
_exptl_crystal_size_mid 0.04
_exptl_crystal_size_max 0.04
_exptl_crystal_density_diffrn 2.496
_exptl_crystal_density_meas 'not measured'
_exptl_crystal_density_method 'not measured'
# Non-dispersive F(000):
_exptl_crystal_F_000 2544
_exptl_absorpt_coefficient_mu 15.648
# Sheldrick geometric approximatio 0.53 0.86
_exptl_absorpt_correction_type multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro (Rigaku Oxford Diffraction, 2017)
;
_exptl_absorpt_correction_T_min 0.27
_exptl_absorpt_correction_T_max 0.86
_diffrn_measurement_device_type 'Oxford Diffraction SuperNova'
_diffrn_measurement_device 'Area'
_diffrn_radiation_monochromator 'focussing mirrors'
_diffrn_radiation_type 'Cu K\a'
_diffrn_radiation_wavelength 1.54184
_diffrn_measurement_method \w
# If a reference occurs more than once, delete the author
# and date from subsequent references.
_computing_data_collection 'SuperNova, (Oxford Diffraction, 2010)'
_computing_cell_refinement
;
CrysAlisPro (Rigaku Oxford Diffraction, 2017)
;
_computing_data_reduction
;
CrysAlisPro (Rigaku Oxford Diffraction, 2017)
;
_computing_structure_solution 'SHELXT '
_computing_structure_refinement 'CRYSTALS (Betteridge et al., 2003)'
_computing_publication_material 'CRYSTALS (Betteridge et al., 2003)'
_computing_molecular_graphics 'CAMERON (Watkin et al., 1996)'
_diffrn_standards_interval_time .
_diffrn_standards_interval_count .
_diffrn_standards_number 0
_diffrn_standards_decay_% .
_diffrn_ambient_temperature 150
_diffrn_reflns_number 906
_diffrn_reflns_av_unetI/netI 0.099
_reflns_number_total 906
_diffrn_reflns_av_R_equivalents 0.1301
_diffrn_reflns_av_sigmaI/netI 0.1830
# Number of reflections without Friedels Law is 906
# Number of reflections with Friedels Law is 514
# Theoretical number of reflections is about 480
_diffrn_reflns_theta_min 5.212
_diffrn_reflns_theta_max 50.225
_diffrn_measured_fraction_theta_max 1.000
_diffrn_reflns_theta_full 50.225
_diffrn_measured_fraction_theta_full 1.000
_diffrn_reflns_limit_h_min 0
_diffrn_reflns_limit_h_max 21
_diffrn_reflns_limit_k_min 0
_diffrn_reflns_limit_k_max 13
_diffrn_reflns_limit_l_min -11
_diffrn_reflns_limit_l_max 12
_reflns_limit_h_min 0
_reflns_limit_h_max 21
_reflns_limit_k_min 0
_reflns_limit_k_max 13
_reflns_limit_l_min -11
_reflns_limit_l_max 12
_oxford_diffrn_Wilson_B_factor 7.04
_oxford_diffrn_Wilson_scale 550.43
_atom_sites_solution_primary other #heavy,direct,difmap,geom,iterative
# _atom_sites_solution_secondary difmap
_atom_sites_solution_hydrogens difmap
_refine_diff_density_min -1.61
_refine_diff_density_max 2.87
# The current dictionary definitions do not cover the
# situation where the reflections used for refinement were
# selected by a user-defined sigma threshold
# Explicitly named reflections are ALWAYS excluded from R&wR
# The values actually used during refinement
# These are labelled "all" for compatibility with PLATON
_oxford_refine_reflns_threshold_expression_ref I>-10.0\s(I)
_refine_ls_number_restraints 219
_refine_ls_number_parameters 110
_refine_ls_number_reflns 902
_oxford_refine_ls_R_factor_ref 0.2032
_refine_ls_R_factor_all 0.2032
_refine_ls_wR_factor_ref 0.3720 #Calculated the Oxford way
_refine_ls_wR_factor_all 0.3720
_refine_ls_goodness_of_fit_ref 0.9687
_refine_ls_shift/su_max 0.0000615
_refine_ls_shift/su_mean 0.0000117
# Computed with no filters except I/sigma = -10
_oxford_reflns_number_all 902
_oxford_refine_ls_R_factor_all 0.2032
_oxford_refine_ls_wR_factor_all 0.3720
# Computed with no filters except I/sigma = +2 a la SHELX
_reflns_threshold_expression I>2.0\s(I)
_reflns_number_gt 460
_refine_ls_R_factor_gt 0.1297
_refine_ls_wR_factor_gt 0.2958
# For an explanation, see Cooper & Watkin, Acta Cryst. (2016). B72, 661-683
_oxford_Hooft_y -0.1(3) # for 169 Friedel pairs
_oxford_Bijvoet_difference -0.1(2) # for 169 Friedel pairs
# (Similar to the Parsons(q).)
_oxford_refined_Flack_x 0.2(4) # for 392 Friedel pairs
_refine_ls_abs_structure_Flack -0.1(2)
_refine_ls_abs_structure_details
;
Parsons, Flack & Wagner (2013),
169 Friedel Pairs
;
# choose from:
# rm (reference molecule of known chirality),
# ad (anomolous dispersion - Flack), rmad (rm and ad),
# syn (from synthesis), unk (unknown) or . (not applicable).
_chemical_absolute_configuration 'ad'
_refine_ls_structure_factor_coef Fsqd
_refine_ls_matrix_type full
_refine_ls_hydrogen_treatment noref #undef, noref, refall,
# refxyz, refU, constr or mixed
_refine_ls_weighting_scheme calc
_refine_ls_weighting_details
;
Method= Modified Sheldrick
w=1/[\s^2^(F^2^) + ( 0.20P)^2^ + 0.00P]
,where P=(max(Fo^2^,0) + 2Fc^2^)/3
;
# Insert your own references if required - in alphabetical order
_publ_section_references
;
User-defined structure solution reference
Betteridge, P.W., Carruthers, J.R., Cooper, R.I.,
Prout, K. & Watkin, D.J. (2003). J. Appl. Cryst. 36, 1487.
Oxford Diffraction, (2010). Supernova User Manual.
Parsons,S., Flack, H.D. and Wagner, T. Acta Cryst. (2013). B69, 249?59
Rigaku Oxford Diffraction (2017). CrysAlisPro.
Watkin, D.J., Prout, C.K. & Pearce, L.J. (1996). CAMERON, Chemical
Crystallography Laboratory, Oxford, UK.
;
# Uequiv = arithmetic mean of Ui i.e. Ueqiv = (U1+U2+U3)/3
# Replace last . with number of unfound hydrogen atoms attached to an atom.
# ..._refinement_flags_...
# . no refinement constraints S special position constraint on site
# G rigid group refinement of site R riding atom
# D distance or angle restraint on site T thermal displacement constraints
# U Uiso or Uij restraint (rigid bond) P partial occupancy constraint
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_occupancy
_atom_site_adp_type
_atom_site_refinement_flags_posn
_atom_site_refinement_flags_adp
_atom_site_refinement_flags_occupancy
_atom_site_disorder_assembly
_atom_site_disorder_group
_atom_site_attached_hydrogens
Br1 Br 0.4230(3) 0.4901(6) 0.9029(7) 0.1281 1.0000 Uani . U . . . .
C2 C 0.469(2) 0.487(6) 0.776(5) 0.1174 1.0000 Uani . U . . . .
C3 C 0.434(2) 0.498(6) 0.679(5) 0.1165 1.0000 Uani . U . . . .
C4 C 0.408(2) 0.492(6) 0.595(4) 0.1150 1.0000 Uani . U . . . .
C5 C 0.373(2) 0.498(7) 0.504(4) 0.1146 1.0000 Uani . U . . . .
C6 C 0.349(3) 0.501(5) 0.416(4) 0.1189 1.0000 Uani . U . . . .
C7 C 0.318(2) 0.496(6) 0.313(4) 0.1216 1.0000 Uani . U . . . .
Br8 Br 0.2319(2) 0.5004(7) 0.3250(8) 0.1263 1.0000 Uani . U . . . .
Br9 Br 0.3066(3) 0.5085(7) 0.0931(7) 0.1259 1.0000 Uani . U . . . .
C10 C 0.351(3) 0.503(6) 0.225(4) 0.1199 1.0000 Uani . U . . . .
C11 C 0.410(2) 0.506(6) 0.215(4) 0.1190 1.0000 Uani . U . . . .
C12 C 0.465(2) 0.513(6) 0.214(4) 0.1169 1.0000 Uani . U . . . .
loop_
_atom_site_aniso_label
_atom_site_aniso_U_11
_atom_site_aniso_U_22
_atom_site_aniso_U_33
_atom_site_aniso_U_23
_atom_site_aniso_U_13
_atom_site_aniso_U_12
Br1 0.061(3) 0.265(8) 0.058(3) 0.000(5) -0.000(2) -0.008(5)
C2 0.062(8) 0.23(2) 0.057(5) 0.001(8) -0.001(2) -0.008(19)
C3 0.061(12) 0.23(2) 0.059(4) 0.009(13) 0.000(6) -0.008(18)
C4 0.060(13) 0.23(2) 0.057(10) 0.018(15) 0.002(9) -0.011(17)
C5 0.055(12) 0.24(2) 0.052(8) 0.022(17) 0.007(8) -0.011(18)
C6 0.059(7) 0.25(2) 0.052(5) 0.019(16) 0.006(7) -0.007(18)
C7 0.060(3) 0.251(19) 0.054(4) 0.021(15) 0.003(4) -0.000(17)
Br8 0.060(3) 0.268(8) 0.051(3) -0.001(4) 0.004(2) 0.004(6)
Br9 0.066(3) 0.260(7) 0.052(3) 0.004(5) -0.000(2) 0.000(6)
C10 0.060(4) 0.25(2) 0.052(5) 0.018(15) 0.003(3) 0.008(19)
C11 0.060(5) 0.24(2) 0.052(12) 0.014(14) 0.004(4) 0.01(2)
C12 0.060(5) 0.24(3) 0.047(16) 0.005(8) -0.002(7) 0.01(2)
_refine_ls_extinction_method
'None'
_oxford_refine_ls_scale 0.04987(7)
loop_
_geom_bond_atom_site_label_1
_geom_bond_site_symmetry_1
_geom_bond_atom_site_label_2
_geom_bond_site_symmetry_2
_geom_bond_distance
_geom_bond_publ_flag
Br1 . C2 . 1.87(6) yes
C2 . C2 5_665 1.38(10) yes
C2 . C3 . 1.45(8) yes
C3 . C4 . 1.19(7) yes
C4 . C5 . 1.37(7) yes
C5 . C6 . 1.21(7) yes
C6 . C7 . 1.47(8) yes
C7 . Br8 . 1.87(4) yes
C7 . C10 . 1.32(7) yes
Br9 . C10 . 1.91(5) yes
C10 . C11 . 1.29(7) yes
C11 . C12 . 1.19(6) yes
C12 . C12 5_665 1.55(11) yes
loop_
_geom_angle_atom_site_label_1
_geom_angle_site_symmetry_1
_geom_angle_atom_site_label_2
_geom_angle_site_symmetry_2
_geom_angle_atom_site_label_3
_geom_angle_site_symmetry_3
_geom_angle
_geom_angle_publ_flag
Br1 . C2 . C2 5_665 121(2) yes
Br1 . C2 . C3 . 115(4) yes
C2 5_665 C2 . C3 . 119(4) yes
C2 . C3 . C4 . 169(9) yes
C3 . C4 . C5 . 171(9) yes
C4 . C5 . C6 . 171(6) yes
C5 . C6 . C7 . 175(7) yes
C6 . C7 . Br8 . 113(4) yes
C6 . C7 . C10 . 119(4) yes
Br8 . C7 . C10 . 128(4) yes
Br9 . C10 . C7 . 116(4) yes
Br9 . C10 . C11 . 115(4) yes
C7 . C10 . C11 . 129(5) yes
C10 . C11 . C12 . 174(8) yes
C12 5_665 C12 . C11 . 162(11) yes
_iucr_refine_instructions_details
;
#
# Punched on 14/04/20 at 11:01:23
#
#LIST 12
BLOCK SCALE X'S U'S
CONT ENANTIO
END
#
# Punched on 14/04/20 at 11:01:23
#
#LIST 16
NO
REM HREST START (DO NOT REMOVE THIS LINE)
REM HREST END (DO NOT REMOVE THIS LINE)
REM DELU START (DO NOT REMOVE THIS LINE)
VIBR .0, 0.00100 = BR(1) TO C(2)
VIBR .0, 0.00100 = C(2) TO C(2,2,1,1,1)
VIBR .0, 0.00100 = C(2) TO C(3)
VIBR .0, 0.00300 = C(2,2,1,1,1) TO BR(1)
VIBR .0, 0.00300 = C(3) TO BR(1)
VIBR .0, 0.00300 = C(3) TO C(2,2,1,1,1)
VIBR .0, 0.00100 = C(3) TO C(4)
VIBR .0, 0.00300 = C(4) TO C(2)
VIBR .0, 0.00100 = C(4) TO C(5)
VIBR .0, 0.00300 = C(5) TO C(3)
VIBR .0, 0.00100 = C(5) TO C(6)
VIBR .0, 0.00300 = C(6) TO C(4)
VIBR .0, 0.00100 = C(6) TO C(7)
VIBR .0, 0.00300 = C(7) TO C(5)
VIBR .0, 0.00100 = C(7) TO BR(8)
VIBR .0, 0.00100 = C(7) TO C(10)
VIBR .0, 0.00300 = BR(8) TO C(6)
VIBR .0, 0.00300 = C(10) TO C(6)
VIBR .0, 0.00300 = C(10) TO BR(8)
VIBR .0, 0.00100 = BR(9) TO C(10)
VIBR .0, 0.00100 = C(10) TO C(11)
VIBR .0, 0.00300 = C(7) TO BR(9)
VIBR .0, 0.00300 = C(11) TO BR(9)
VIBR .0, 0.00300 = C(11) TO C(7)
VIBR .0, 0.00100 = C(11) TO C(12)
VIBR .0, 0.00300 = C(12) TO C(10)
VIBR .0, 0.00100 = C(12) TO C(12,2,1,1,1)
VIBR .0, 0.00300 = C(11) TO C(12,2,1,1,1)
REM DELU END (DO NOT REMOVE THIS LINE)
REM THERMSIM START (DO NOT REMOVE THIS LINE)
U(IJ) .0, 0.04000 = BR(1) TO C(2)
U(IJ) .0, 0.02000 = C(2) TO C(2,2,1,1,1)
U(IJ) .0, 0.02000 = C(2) TO C(3)
U(IJ) .0, 0.02000 = C(3) TO C(4)
U(IJ) .0, 0.02000 = C(4) TO C(5)
U(IJ) .0, 0.02000 = C(5) TO C(6)
U(IJ) .0, 0.02000 = C(6) TO C(7)
U(IJ) .0, 0.04000 = C(7) TO BR(8)
U(IJ) .0, 0.02000 = C(7) TO C(10)
U(IJ) .0, 0.04000 = BR(9) TO C(10)
U(IJ) .0, 0.02000 = C(10) TO C(11)
U(IJ) .0, 0.02000 = C(11) TO C(12)
U(IJ) .0, 0.02000 = C(12) TO C(12,2,1,1,1)
REM THERMSIM END (DO NOT REMOVE THIS LINE)
REM SHIFTLIMIT START (DO NOT REMOVE THIS LINE)
LIMIT 0.20000000 U[ISO]
LIMIT 0.20000000 X
LIMIT 0.20000000 Y
LIMIT 0.20000000 Z
LIMIT 0.20000000 U[11]
LIMIT 0.20000000 U[22]
LIMIT 0.20000000 U[33]
LIMIT 0.20000000 U[12]
LIMIT 0.20000000 U[13]
LIMIT 0.20000000 U[23]
LIMIT 0.20000000 OCC
REM SHIFTLIMIT END (DO NOT REMOVE THIS LINE)
END
;
# Manually omitted reflections
loop_
_oxford_refln_omitted_index_h
_oxford_refln_omitted_index_k
_oxford_refln_omitted_index_l
_oxford_refln_omitted_flag
_oxford_refln_omitted_details
0 4 0 x .
2 10 4 x .
0 8 0 x .
0 12 0 x .
# start Validation Reply Form
_vrf_THETM01_I
;
PROBLEM: The value of sine(theta_max)/wavelength is less than 0.550
RESPONSE: The best crystal obtained were small and did not
diffract to high angle. The emphasis was on collecting as
intense data as possible. Data were collected to 1\%A.
;
_vrf_PLAT084_I
;
PROBLEM: High wR2 Value (i.e. > 0.25)
RESPONSE: Data were carefully examined to determine space
group and any potential twinning. Reflections were broad along
certain directions but no obvious indications of twinning were
observed.
;
_vrf_PLAT090_I
;
PROBLEM: Poor Data / Parameter Ratio (Zmax > 18)
RESPONSE: Due to size of crystal and diffraction intensity
data were only collected to 1\%A which gives rise to a
poor data to parameter ratio.
;
_vrf_PLAT250_I
;
PROBLEM: Large U3/U1 Ratio for Average U(i,j) Tensor
RESPONSE: Due to the poor data to parameter ratio it is not
reasonable to model the disorder for this compound. Initial
attemps were made to check if the disorder could easily be
resolved.
;
# end Validation Reply Form
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