#------------------------------------------------------------------------------ #$Date: 2020-06-05 13:22:57 +0300 (Fri, 05 Jun 2020) $ #$Revision: 252747 $ #$URL: file:///home/coder/svn-repositories/cod/cif/1/55/80/1558014.cif $ #------------------------------------------------------------------------------ # # This file is available in the Crystallography Open Database (COD), # http://www.crystallography.net/ # # All data on this site have been placed in the public domain by the # contributors. # data_1558014 loop_ _publ_author_name 'M\"uller, Matthias' 'Karttunen, Antti J.' 'Buchner, Magnus R.' _publ_section_title ; Speciation of Be2+ in acidic liquid ammonia and formation of tetra- and octanuclear beryllium amido clusters ; _journal_issue 21 _journal_name_full 'Chemical Science' _journal_page_first 5415 _journal_paper_doi 10.1039/D0SC01112F _journal_volume 11 _journal_year 2020 _chemical_formula_moiety 'Be4 H42 N22' _chemical_formula_sum 'Be4 H42 N22' _chemical_formula_weight 386.59 _space_group_crystal_system monoclinic _space_group_IT_number 15 _space_group_name_Hall '-C 2yc' _space_group_name_H-M_alt 'C 1 2/c 1' _atom_sites_solution_hydrogens difmap _audit_creation_method SHELXL-2018/3 _audit_update_record ; 2020-02-06 deposited with the CCDC. 2020-05-04 downloaded from the CCDC. ; _cell_angle_alpha 90 _cell_angle_beta 111.134(2) _cell_angle_gamma 90 _cell_formula_units_Z 4 _cell_length_a 13.4543(3) _cell_length_b 10.5289(3) _cell_length_c 16.9967(4) _cell_measurement_reflns_used 14461 _cell_measurement_temperature 100(2) _cell_measurement_theta_max 152.26 _cell_measurement_theta_min 10.97 _cell_volume 2245.79(10) _computing_structure_refinement 'SHELXL-2018/3 (Sheldrick, 2018)' _diffrn_ambient_temperature 100(2) _diffrn_measured_fraction_theta_full 1.000 _diffrn_measured_fraction_theta_max 0.989 _diffrn_measurement_device_type 'STOE STADIVARI' _diffrn_radiation_type CuK\a _diffrn_radiation_wavelength 1.54178 _diffrn_reflns_av_R_equivalents 0.0156 _diffrn_reflns_av_unetI/netI 0.0136 _diffrn_reflns_Laue_measured_fraction_full 1.000 _diffrn_reflns_Laue_measured_fraction_max 0.989 _diffrn_reflns_limit_h_max 16 _diffrn_reflns_limit_h_min -16 _diffrn_reflns_limit_k_max 13 _diffrn_reflns_limit_k_min -12 _diffrn_reflns_limit_l_max 14 _diffrn_reflns_limit_l_min -21 _diffrn_reflns_number 11750 _diffrn_reflns_point_group_measured_fraction_full 1.000 _diffrn_reflns_point_group_measured_fraction_max 0.989 _diffrn_reflns_theta_full 67.679 _diffrn_reflns_theta_max 75.650 _diffrn_reflns_theta_min 5.484 _diffrn_source 'GeniX 3D HF Cu' _exptl_absorpt_coefficient_mu 0.695 _exptl_absorpt_correction_T_max 0.9687 _exptl_absorpt_correction_T_min 0.3649 _exptl_absorpt_correction_type multi-scan _exptl_absorpt_process_details ; STOE LANA, absorption correction by scaling of reflection intensities. J. Koziskova, F. Hahn, J. Richter, J. Kozisek, "Comparison of different absorption corrections on the model structure of tetrakis(\m~2~-acetato)- diaqua-di-copper(II)", Acta Chimica Slovaca, vol. 9, no. 2, 2016, pp. 136 - 140. Afterwards a spherical absorption correction was performed within STOE LANA. ; _exptl_crystal_colour colorless _exptl_crystal_density_diffrn 1.143 _exptl_crystal_description needle _exptl_crystal_F_000 848 _exptl_crystal_size_max 0.05 _exptl_crystal_size_mid 0.02 _exptl_crystal_size_min 0.01 _refine_diff_density_max 0.225 _refine_diff_density_min -0.192 _refine_diff_density_rms 0.038 _refine_ls_extinction_method none _refine_ls_goodness_of_fit_ref 1.047 _refine_ls_hydrogen_treatment refall _refine_ls_matrix_type full _refine_ls_number_parameters 203 _refine_ls_number_reflns 2312 _refine_ls_number_restraints 0 _refine_ls_restrained_S_all 1.047 _refine_ls_R_factor_all 0.0480 _refine_ls_R_factor_gt 0.0367 _refine_ls_shift/su_max 0.000 _refine_ls_shift/su_mean 0.000 _refine_ls_structure_factor_coef Fsqd _refine_ls_weighting_details 'w=1/[\s^2^(Fo^2^)+(0.0640P)^2^+0.7085P] where P=(Fo^2^+2Fc^2^)/3' _refine_ls_weighting_scheme calc _refine_ls_wR_factor_gt 0.1005 _refine_ls_wR_factor_ref 0.1079 _reflns_Friedel_coverage 0.000 _reflns_number_gt 1887 _reflns_number_total 2312 _reflns_threshold_expression 'I > 2\s(I)' _cod_data_source_file d0sc01112f2.cif _cod_data_source_block 5_CCDC1 _cod_depositor_comments 'Adding full bibliography for 1558013--1558021.cif.' _cod_original_sg_symbol_H-M 'C 2/c' _cod_database_code 1558014 _shelx_shelxl_version_number 2018/3 _shelx_space_group_comment ; The symmetry employed for this shelxl refinement is uniquely defined by the following loop, which should always be used as a source of symmetry information in preference to the above space-group names. They are only intended as comments. ; _shelx_res_file ; TITL 1_a.res in C2/c 5.res created by SHELXL-2018/3 at 18:22:05 on 06-Dec-2018 REM Old TITL 1 in C2/c REM SHELXT solution in C2/c: R1 0.171, Rweak 0.002, Alpha 0.013 REM 0.583 for 129 systematic absences, Orientation as input REM Formula found by SHELXT: Be2 N11 CELL 1.54178 13.4543 10.5289 16.9967 90.000 111.134 90.000 ZERR 4.000 0.0003 0.0003 0.0004 0.000 0.002 0.000 LATT 7 SYMM -X, Y, 1/2-Z SFAC BE H N UNIT 16 168 88 L.S. 10 BOND LIST 4 ACTA TEMP -173.15 FMAP 2 PLAN 20 HTAB EQIV $2 x+1/2, y-1/2, z HTAB N5 N12_$2 HTAB N5 N7 EQIV $3 -x+1/2, -y+3/2, -z+1 HTAB N5 N8_$3 HTAB N5 N9_$3 HTAB N6 N10_$2 EQIV $4 -x+1, y-1, -z+3/2 HTAB N6 N9_$4 HTAB N6 N11 HTAB N10 N7 EQIV $5 -x, -y+2, -z+1 HTAB N10 N12_$5 HTAB N12 N9 HTAB N11 N7_$2 HTAB N11 N8_$2 EQIV $1 -x+1, y, -z+3/2 HTAB N11 N10_$1 EQIV $6 -x+3/2, y-1/2, -z+3/2 HTAB N11 N7_$6 EQIV $7 -x+1/2, -y+5/2, -z+1 HTAB N12 N9_$7 EQIV $8 -x+1, y+1, -z+3/2 HTAB N12 N11_$8 REM EXTI 0.000000 WGHT 0.064000 0.708500 FVAR 0.41716 N1 3 0.569399 0.406126 0.664677 11.00000 0.02218 0.02634 = 0.02440 -0.00134 0.00934 -0.00177 N2 3 0.500000 0.597035 0.750000 10.50000 0.02134 0.02160 = 0.02855 0.00000 0.00721 0.00000 N3 3 0.640235 0.410860 0.840916 11.00000 0.01900 0.02655 = 0.02439 0.00095 0.00501 -0.00048 N4 3 0.500000 0.220991 0.750000 10.50000 0.02430 0.02276 = 0.02557 0.00000 0.00790 0.00000 N5 3 0.426299 0.599843 0.568509 11.00000 0.02784 0.02891 = 0.02749 0.00521 0.00879 0.00108 N6 3 0.716068 0.213191 0.762413 11.00000 0.02328 0.02877 = 0.03047 -0.00049 0.00852 0.00302 N7 3 0.319837 0.826541 0.622679 11.00000 0.04436 0.04329 = 0.05260 0.00626 0.02089 0.00790 N8 3 0.296841 0.932117 0.602524 11.00000 0.02834 0.04199 = 0.02941 -0.00193 0.00889 0.00182 N9 3 0.273641 1.036680 0.582768 11.00000 0.05230 0.03820 = 0.04260 -0.00384 0.01217 0.00323 N10 3 0.136701 0.613561 0.569422 11.00000 0.04184 0.03755 = 0.03547 0.00306 0.01562 0.00624 N11 3 0.921577 0.392284 0.822271 11.00000 0.03643 0.04149 = 0.04353 -0.00359 0.01825 -0.00173 N12 3 0.107110 1.263253 0.512753 11.00000 0.03299 0.04462 = 0.03770 -0.00930 0.00905 -0.00122 BE1 1 0.465969 0.503314 0.661923 11.00000 0.02116 0.02529 = 0.02257 0.00194 0.00539 0.00080 BE2 1 0.605789 0.314629 0.753910 11.00000 0.01992 0.02534 = 0.02576 0.00076 0.00715 0.00203 H2 2 0.450093 0.643248 0.746632 11.00000 0.03360 H1A 2 0.616340 0.445931 0.662856 11.00000 0.03229 H1B 2 0.553046 0.358238 0.625046 11.00000 0.03354 H4 2 0.482783 0.171455 0.708363 11.00000 0.03541 H3A 2 0.664363 0.366099 0.886247 11.00000 0.03294 H3B 2 0.684556 0.451151 0.842310 11.00000 0.03742 H5A 2 0.477163 0.627193 0.557668 11.00000 0.03670 H5B 2 0.391619 0.659788 0.576549 11.00000 0.03111 H5C 2 0.383374 0.555673 0.523304 11.00000 0.04770 H6A 2 0.706648 0.175308 0.716623 11.00000 0.03572 H6B 2 0.724058 0.159956 0.801174 11.00000 0.03390 H6C 2 0.767168 0.253120 0.770756 11.00000 0.03409 H10A 2 0.185188 0.678697 0.574008 11.00000 0.04207 H10B 2 0.144256 0.559380 0.534347 11.00000 0.06773 H10C 2 0.071525 0.647698 0.547489 11.00000 0.05211 H12 2 0.149376 1.197374 0.530147 11.00000 0.03595 H11A 2 0.900017 0.407190 0.768847 11.00000 0.04278 H11B 2 0.912433 0.462057 0.843223 11.00000 0.02987 H11C 2 0.991170 0.380606 0.842045 11.00000 0.04418 H12A 2 0.128148 1.316122 0.481869 11.00000 0.03806 H12B 2 0.113823 1.301314 0.556224 11.00000 0.04618 HKLF 4 REM 1_a.res in C2/c REM wR2 = 0.1079, GooF = S = 1.047, Restrained GooF = 1.047 for all data REM R1 = 0.0367 for 1887 Fo > 4sig(Fo) and 0.0480 for all 2312 data REM 203 parameters refined using 0 restraints END WGHT 0.0635 0.7155 REM Instructions for potential hydrogen bonds HTAB N5 N12_$2 HTAB N5 N7 HTAB N5 N8_$3 HTAB N5 N9_$3 HTAB N6 N10_$2 HTAB N6 N9_$4 HTAB N6 N11 HTAB N10 N7 HTAB N10 N12_$5 HTAB N12 N9 HTAB N11 N7_$2 HTAB N11 N8_$2 HTAB N11 N10_$1 HTAB N11 N7_$6 HTAB N12 N9_$7 HTAB N12 N11_$8 REM Highest difference peak 0.225, deepest hole -0.192, 1-sigma level 0.038 Q1 1 0.6270 0.3704 0.7974 11.00000 0.05 0.22 Q2 1 0.5856 0.3683 0.7063 11.00000 0.05 0.22 Q3 1 0.5188 0.4489 0.6647 11.00000 0.05 0.22 Q4 1 0.4875 0.5508 0.7097 11.00000 0.05 0.21 Q5 1 0.5990 0.4585 0.8465 11.00000 0.05 0.20 Q6 1 0.3423 1.0039 0.5903 11.00000 0.05 0.19 Q7 1 0.4537 0.2630 0.7460 11.00000 0.05 0.18 Q8 1 0.6690 0.2651 0.7645 11.00000 0.05 0.18 Q9 1 0.3425 1.0599 0.5799 11.00000 0.05 0.17 Q10 1 0.4499 0.5674 0.6095 11.00000 0.05 0.16 Q11 1 0.0855 1.2948 0.4670 11.00000 0.05 0.14 Q12 1 0.0437 1.2481 0.5103 11.00000 0.05 0.13 Q13 1 0.2011 1.1240 0.5714 11.00000 0.05 0.13 Q14 1 0.1122 1.1966 0.4988 11.00000 0.05 0.13 Q15 1 0.1291 0.5574 0.6104 11.00000 0.05 0.11 Q16 1 0.1397 1.3826 0.4609 11.00000 0.05 0.11 Q17 1 0.9065 0.3157 0.8472 11.00000 0.05 0.11 Q18 1 0.2718 0.9932 0.5607 11.00000 0.05 0.11 Q19 1 0.0819 1.3634 0.4972 11.00000 0.05 0.10 Q20 1 0.2352 0.9933 0.5934 11.00000 0.05 0.10 ; _shelx_res_checksum 59718 loop_ _space_group_symop_operation_xyz 'x, y, z' '-x, y, -z+1/2' 'x+1/2, y+1/2, z' '-x+1/2, y+1/2, -z+1/2' '-x, -y, -z' 'x, -y, z-1/2' '-x+1/2, -y+1/2, -z' 'x+1/2, -y+1/2, z-1/2' 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_adp_type _atom_site_occupancy _atom_site_site_symmetry_order _atom_site_calc_flag _atom_site_refinement_flags_posn _atom_site_refinement_flags_adp _atom_site_refinement_flags_occupancy _atom_site_disorder_assembly _atom_site_disorder_group N1 N 0.56940(8) 0.40613(11) 0.66468(7) 0.0240(2) Uani 1 1 d . . . . . N2 N 0.500000 0.59703(13) 0.750000 0.0243(3) Uani 1 2 d S T P . . N3 N 0.64024(8) 0.41086(10) 0.84092(7) 0.0241(2) Uani 1 1 d . . . . . N4 N 0.500000 0.22099(14) 0.750000 0.0245(3) Uani 1 2 d S T P . . N5 N 0.42630(9) 0.59984(11) 0.56851(7) 0.0284(3) Uani 1 1 d . . . . . N6 N 0.71607(9) 0.21319(11) 0.76241(8) 0.0278(3) Uani 1 1 d . . . . . N7 N 0.31984(10) 0.82654(13) 0.62268(9) 0.0458(3) Uani 1 1 d . . . . . N8 N 0.29684(9) 0.93212(12) 0.60252(7) 0.0337(3) Uani 1 1 d . . . . . N9 N 0.27364(11) 1.03668(13) 0.58277(9) 0.0457(3) Uani 1 1 d . . . . . N10 N 0.13670(11) 0.61356(13) 0.56942(8) 0.0378(3) Uani 1 1 d . . . . . N11 N 0.92158(11) 0.39228(13) 0.82227(10) 0.0394(3) Uani 1 1 d . . . . . N12 N 0.10711(10) 1.26325(14) 0.51275(10) 0.0395(3) Uani 1 1 d . . . . . Be1 Be 0.46597(11) 0.50331(14) 0.66192(10) 0.0237(3) Uani 1 1 d . . . . . Be2 Be 0.60579(11) 0.31463(15) 0.75391(10) 0.0240(3) Uani 1 1 d . . . . . H2 H 0.4501(12) 0.6432(16) 0.7466(10) 0.034(4) Uiso 1 1 d . . . . . H1A H 0.6163(14) 0.4459(16) 0.6629(11) 0.032(4) Uiso 1 1 d . . . . . H1B H 0.5530(13) 0.3582(17) 0.6250(12) 0.034(4) Uiso 1 1 d . . . . . H4 H 0.4828(13) 0.1715(16) 0.7084(10) 0.035(4) Uiso 1 1 d . . . . . H3A H 0.6644(13) 0.3661(16) 0.8862(11) 0.033(4) Uiso 1 1 d . . . . . H3B H 0.6846(15) 0.4512(17) 0.8423(11) 0.037(5) Uiso 1 1 d . . . . . H5A H 0.4772(14) 0.6272(16) 0.5577(11) 0.037(4) Uiso 1 1 d . . . . . H5B H 0.3916(13) 0.6598(17) 0.5765(10) 0.031(4) Uiso 1 1 d . . . . . H5C H 0.3834(15) 0.5557(18) 0.5233(13) 0.048(5) Uiso 1 1 d . . . . . H6A H 0.7066(13) 0.1753(16) 0.7166(12) 0.036(4) Uiso 1 1 d . . . . . H6B H 0.7241(13) 0.1600(17) 0.8012(11) 0.034(4) Uiso 1 1 d . . . . . H6C H 0.7672(14) 0.2531(16) 0.7708(11) 0.034(4) Uiso 1 1 d . . . . . H10A H 0.1852(14) 0.6787(18) 0.5740(11) 0.042(5) Uiso 1 1 d . . . . . H10B H 0.1443(18) 0.559(2) 0.5343(15) 0.068(7) Uiso 1 1 d . . . . . H10C H 0.0715(17) 0.6477(19) 0.5475(12) 0.052(5) Uiso 1 1 d . . . . . H12 H 0.1494(14) 1.1974(16) 0.5301(11) 0.036(4) Uiso 1 1 d . . . . . H11A H 0.9000(15) 0.4072(17) 0.7688(14) 0.043(5) Uiso 1 1 d . . . . . H11B H 0.9124(13) 0.4621(17) 0.8432(11) 0.030(4) Uiso 1 1 d . . . . . H11C H 0.9912(16) 0.3806(16) 0.8420(12) 0.044(5) Uiso 1 1 d . . . . . H12A H 0.1281(13) 1.3161(17) 0.4819(12) 0.038(4) Uiso 1 1 d . . . . . H12B H 0.1138(14) 1.3013(17) 0.5562(13) 0.046(5) Uiso 1 1 d . . . . . 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 N1 0.0222(5) 0.0263(5) 0.0244(6) -0.0013(4) 0.0093(4) -0.0018(4) N2 0.0213(7) 0.0216(7) 0.0286(8) 0.000 0.0072(6) 0.000 N3 0.0190(5) 0.0265(5) 0.0244(6) 0.0010(4) 0.0050(4) -0.0005(4) N4 0.0243(7) 0.0228(7) 0.0256(8) 0.000 0.0079(6) 0.000 N5 0.0278(5) 0.0289(6) 0.0275(6) 0.0052(4) 0.0088(5) 0.0011(4) N6 0.0233(5) 0.0288(6) 0.0305(6) -0.0005(5) 0.0085(5) 0.0030(4) N7 0.0444(7) 0.0433(7) 0.0526(8) 0.0063(6) 0.0209(6) 0.0079(6) N8 0.0283(5) 0.0420(7) 0.0294(6) -0.0019(5) 0.0089(5) 0.0018(5) N9 0.0523(8) 0.0382(7) 0.0426(8) -0.0038(6) 0.0122(6) 0.0032(6) N10 0.0418(7) 0.0376(7) 0.0355(7) 0.0031(5) 0.0156(6) 0.0062(5) N11 0.0364(7) 0.0415(7) 0.0435(8) -0.0036(6) 0.0182(6) -0.0017(5) N12 0.0330(6) 0.0446(7) 0.0377(7) -0.0093(6) 0.0090(5) -0.0012(5) Be1 0.0212(7) 0.0253(7) 0.0226(7) 0.0019(6) 0.0054(6) 0.0008(5) Be2 0.0199(6) 0.0253(7) 0.0258(8) 0.0008(6) 0.0071(6) 0.0020(5) loop_ _atom_type_symbol _atom_type_description _atom_type_scat_dispersion_real _atom_type_scat_dispersion_imag _atom_type_scat_source Be Be 0.0038 0.0014 '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' N N 0.0311 0.0180 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' loop_ _geom_angle_atom_site_label_1 _geom_angle_atom_site_label_2 _geom_angle_atom_site_label_3 _geom_angle _geom_angle_site_symmetry_1 _geom_angle_site_symmetry_3 _geom_angle_publ_flag Be2 N1 Be1 109.27(9) . . ? Be1 N2 Be1 109.59(13) 2_656 . ? Be2 N3 Be1 110.37(9) . 2_656 ? Be2 N4 Be2 109.72(13) . 2_656 ? N9 N8 N7 179.62(16) . . ? N2 Be1 N1 111.20(9) . . ? N2 Be1 N3 108.01(10) . 2_656 ? N1 Be1 N3 108.77(10) . 2_656 ? N2 Be1 N5 110.32(10) . . ? N1 Be1 N5 109.96(10) . . ? N3 Be1 N5 108.49(9) 2_656 . ? N1 Be2 N4 108.74(9) . . ? N1 Be2 N3 109.50(10) . . ? N4 Be2 N3 109.65(10) . . ? N1 Be2 N6 111.77(10) . . ? N4 Be2 N6 108.21(10) . . ? N3 Be2 N6 108.94(10) . . ? loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_distance _geom_bond_site_symmetry_2 _geom_bond_publ_flag N1 Be2 1.7125(19) . ? N1 Be1 1.7143(17) . ? N2 Be1 1.7117(18) 2_656 ? N2 Be1 1.7118(18) . ? N3 Be2 1.7129(19) . ? N3 Be1 1.7152(18) 2_656 ? N4 Be2 1.7129(17) . ? N4 Be2 1.7129(17) 2_656 ? N5 Be1 1.7966(18) . ? N6 Be2 1.7912(18) . ? N7 N8 1.1715(18) . ? N8 N9 1.1605(18) . ? loop_ _geom_hbond_atom_site_label_D _geom_hbond_atom_site_label_H _geom_hbond_atom_site_label_A _geom_hbond_distance_DH _geom_hbond_distance_HA _geom_hbond_distance_DA _geom_hbond_angle_DHA _geom_hbond_site_symmetry_A _geom_hbond_publ_flag N5 H5A N12 0.822(19) 2.580(19) 3.3821(19) 165.6(15) 3_545 yes N5 H5B N7 0.825(18) 2.275(18) 3.0899(18) 169.5(15) . yes N5 H5C N8 0.91(2) 2.59(2) 3.3591(16) 142.6(15) 7_566 yes N5 H5C N9 0.91(2) 2.43(2) 3.3055(18) 162.2(16) 7_566 yes N6 H6A N10 0.842(19) 2.42(2) 3.2365(19) 162.6(15) 3_545 yes N6 H6B N9 0.842(19) 2.352(19) 3.1835(19) 169.4(15) 2_646 yes N6 H6C N11 0.774(18) 2.433(19) 3.1949(18) 168.5(16) . yes N10 H10A N7 0.930(19) 2.304(19) 3.211(2) 164.8(16) . yes N10 H10C N12 0.90(2) 2.44(2) 3.3301(19) 179.0(18) 5_576 yes N12 H12 N9 0.878(18) 2.319(18) 3.194(2) 174.6(15) . yes N11 H11A N7 0.86(2) 2.47(2) 3.242(2) 148.7(16) 3_545 yes N11 H11A N8 0.86(2) 2.68(2) 3.5246(19) 168.5(16) 3_545 yes N11 H11B N10 0.845(18) 2.428(18) 3.236(2) 160.5(14) 2_656 yes N11 H11C N7 0.88(2) 2.46(2) 3.333(2) 170.9(16) 4_646 yes N12 H12A N9 0.879(19) 2.530(19) 3.395(2) 168.0(15) 7_576 yes N12 H12B N11 0.82(2) 2.47(2) 3.262(2) 162.5(17) 2_666 yes