# -*- coding: latin-1 -*- # This program is in the public domain # Author: Paul Kienzle """ This module adds the following fields to the periodic table * covalent_radius * covalent_radius_uncertainty * covalent_radius_units = 'angstrom' Use :func:`init` to initialize a private table. Data is taken from Cordero et al., 2008 [#Cordero2008]_. Bond specific values (single, double, or triple) are available from Pyykkö et al., 2009 [#Pyykko2009]_, but they are generally smaller. The CRC Handbook uses the average of Cordero and Pyykkö. Note that the combined Cordero/Pyykkö tables are included herein as *periodictable.covalent_radius.CorderoPyykko*, but are not yet parsed. The abstract of Cordero reads as follows: A new set of covalent atomic radii has been deduced from crystallographic data for most of the elements with atomic numbers up to 96. The proposed radii show a well behaved periodic dependence that allows us to interpolate a few radii for elements for which structural data is lacking, notably the noble gases. The proposed set of radii therefore fills most of the gaps and solves some inconsistencies in currently used covalent radii. The transition metal and lanthanide contractions as well as the differences in covalent atomic radii between low spin and high spin configurations in transition metals are illustrated by the proposed radii set. .. Note:: #. Values are averages only. The particular radius can be highly dependent on oxidation state and chemical compound. #. The paper lists values for multiple spin states on select elements. We are using sp3 for carbon and low spin for manganese, iron and cobalt. #. Elements with zero or one measurements of covalent radius are assigned an uncertainty of 0.00. These are He, Ne, Pm, At, Rn, Fr, Ac, Pa. #. Elements above 96 are assigned a covalent radius and uncertainty of None. #. Radii are measured from bonds to C, N or O. The choice of which compound was used is element dependent. Details are available in the references. .. [#Cordero2008] Beatriz Cordero, Verónica Gómez, Ana E. Platero-Prats, Marc Revés, Jorge Echeverría, Eduard Cremades, Flavia Barragán and Santiago Alvarez. Covalent radii revisited. Dalton Trans., 2008, 2832-2838. `doi:10.1039/b801115j `_ .. [#Pyykko2009] P. Pyykkö and M. Atsumi. Molecular Double-Bond Covalent Radii for Elements Li-E112. Chemistry, A European Journal, 15, 2009, 12770-12779. `doi:10.1002/chem.200901472 `_ """ from .core import Element def init(table, reload=False): """ Add the covalent radius property to a private table. Use *reload = True* to replace the covalent radius property on an existing table. """ if 'covalent_radius' in table.properties and not reload: return table.properties.append('covalent_radius') # neutron covalent radius of 0.20 A ? Not sure where that value came from # table[0].covalent_radius = 0.20 Element.covalent_radius_units = 'angstrom' Element.covalent_radius = None Element.covalent_radius_uncertainty = None for line in Cordero.split('\n'): fields = line.split() if len(fields) == 3: fields += ['0', '0'] # Fill in uncertainties if fields[0] == '-': continue # Skip alternate spin states Z = int(fields[0]) #el = fields[1] r = float(fields[2]) dr = float(fields[3])*0.01 #n = int(fields[4]) table[Z].covalent_radius = r table[Z].covalent_radius_uncertainty = dr # Table of radii from Cordero. Note that in cases where there are # multiple spin states (C, Mn, Fe, Co) only the first spin state is used. # #Z, Symbol, radius(A), uncertainty (0.01A), number of measurements Cordero = """\ 1 H 0.31 5 129 2 He 0.28 3 Li 1.28 7 5789 4 Be 0.96 3 310 5 B 0.84 3 1770 6 Csp3 0.76 1 10000 - Csp2 0.73 2 10000 - Csp 0.69 1 171 7 N 0.71 1 2200 8 O 0.66 2 10000 9 F 0.57 3 10000 10 Ne 0.58 11 Na 1.66 9 1629 12 Mg 1.41 7 3234 13 Al 1.21 4 3206 14 Si 1.11 2 10000 15 P 1.07 3 10000 16 S 1.05 3 10000 17 Cl 1.02 4 1987 18 Ar 1.06 10 9 19 K 2.03 12 435 20 Ca 1.76 10 2647 21 Sc 1.70 7 32 22 Ti 1.60 8 231 23 V 1.53 8 389 24 Cr 1.39 5 916 25 Mnl.s. 1.39 5 321 - Mnh.s. 1.61 8 929 26 Fel.s. 1.32 3 336 - Feh.s. 1.52 6 1540 27 Col.s. 1.26 3 5733 - Coh.s. 1.50 7 780 28 Ni 1.24 4 1030 29 Cu 1.32 4 1149 30 Zn 1.22 4 443 31 Ga 1.22 3 1330 32 Ge 1.20 4 1013 33 As 1.19 4 2015 34 Se 1.20 4 1717 35 Br 1.20 3 2140 36 Kr 1.16 4 5 37 Rb 2.20 9 23 38 Sr 1.95 10 1500 39 Y 1.90 7 30 40 Zr 1.75 7 93 41 Nb 1.64 6 18 42 Mo 1.54 5 97 43 Tc 1.47 7 96 44 Ru 1.46 7 1032 45 Rh 1.42 7 458 46 Pd 1.39 6 1892 47 Ag 1.45 5 1728 48 Cd 1.44 9 19 49 In 1.42 5 546 50 Sn 1.39 4 2999 51 Sb 1.39 5 609 52 Te 1.38 4 692 53 I 1.39 3 451 54 Xe 1.40 9 2 55 Cs 2.44 11 24 56 Ba 2.15 11 3076 57 La 2.07 8 190 58 Ce 2.04 9 47 59 Pr 2.03 7 58 60 Nd 2.01 6 96 61 Pm 1.99 62 Sm 1.98 8 53 63 Eu 1.98 6 167 64 Gd 1.96 6 178 65 Tb 1.94 5 55 66 Dy 1.92 7 59 67 Ho 1.92 7 48 68 Er 1.89 6 66 69 Tm 1.90 10 15 70 Yb 1.87 8 122 71 Lu 1.87 8 61 72 Hf 1.75 10 53 73 Ta 1.70 8 88 74 W 1.62 7 219 75 Re 1.51 7 476 76 Os 1.44 4 99 77 Ir 1.41 6 131 78 Pt 1.36 5 1768 79 Au 1.36 6 114 80 Hg 1.32 5 137 81 Tl 1.45 7 291 82 Pb 1.46 5 112 83 Bi 1.48 4 51 84 Po 1.40 4 4 85 At 1.50 86 Rn 1.50 87 Fr 2.60 88 Ra 2.21 2 3 89 Ac 2.15 0 1 90 Th 2.06 6 11 91 Pa 2.00 0 1 92 U 1.96 7 57 93 Np 1.90 1 22 94 Pu 1.87 1 9 95 Am 1.80 6 11 96 Cm 1.69 3 16\ """ # Cordero/Pyykko combined table. # rC are the Cardero radii with uncertainty. # r# are the single/double/triple bonded Pyykko radii. # Entries starting with # are for specific species mentioned in Cardero. # The CRC tables are obtained by averaging Cordero rC and Pyykko r1. #Z Symbol rC(A) r1(A) r2(A) r3(A) CorderoPyykko = """\ 1 H 0.31(5) 0.32 2 He 0.28 0.46 3 Li 1.28(7) 1.33 1.24 4 Be 0.96(3) 1.02 0.90 0.85 5 B 0.84(3) 0.85 0.78 0.73 6 C 0.76(1) 0.75 0.67 0.60 #sp3: 0.76(1) #sp2: 0.73(2) #sp: 0.69(1) 7 N 0.71(1) 0.71 0.60 0.54 8 O 0.66(2) 0.63 0.57 0.53 9 F 0.57(3) 0.64 0.59 0.53 10 Ne 0.58 0.67 0.96 11 Na 1.66(9) 1.55 1.60 12 Mg 1.41(7) 1.39 1.32 1.27 13 Al 1.21(4) 1.26 1.13 1.11 14 Si 1.11(2) 1.16 1.07 1.02 15 P 1.07(3) 1.11 1.02 0.94 16 S 1.05(3) 1.03 0.94 0.95 17 Cl 1.02(4) 0.99 0.95 0.93 18 Ar 1.06(10) 0.96 1.07 0.96 19 K 2.03(12) 1.96 1.93 20 Ca 1.76(10) 1.71 1.47 1.33 21 Sc 1.70(7) 1.48 1.16 1.14 22 Ti 1.60(8) 1.36 1.17 1.08 23 V 1.53(8) 1.34 1.12 1.06 24 Cr 1.39(5) 1.22 1.11 1.03 25 Mn 1.39(5) 1.19 1.05 1.03 #low spin: 1.39(5) #high spin: 1.61(8) 26 Fe 1.32(3) 1.16 1.09 1.02 #low spin: 1.32(3) #high spin: 1.52(6) 27 Co 1.26(3) 1.11 1.03 0.96 #low spin: 1.26(3) #high spin: 1.50(7) 28 Ni 1.24(4) 1.10 1.01 1.01 29 Cu 1.32(4) 1.12 1.15 1.20 30 Zn 1.22(4) 1.18 1.20 31 Ga 1.22(3) 1.24 1.17 1.21 32 Ge 1.20(4) 1.21 1.11 1.14 33 As 1.19(4) 1.21 1.14 1.06 34 Se 1.20(4) 1.16 1.07 1.07 35 Br 1.20(3) 1.14 1.09 1.10 36 Kr 1.16(4) 1.17 1.21 1.08 37 Rb 2.20(9) 2.10 2.02 38 Sr 1.95(10) 1.85 1.57 1.39 39 Y 1.90(7) 1.63 1.30 1.24 40 Zr 1.75(7) 1.54 1.27 1.21 41 Nb 1.64(6) 1.47 1.25 1.16 42 Mo 1.54(5) 1.38 1.21 1.13 43 Tc 1.47(7) 1.28 1.20 1.10 44 Ru 1.46(7) 1.25 1.14 1.03 45 Rh 1.42(7) 1.25 1.10 1.06 46 Pd 1.39(6) 1.20 1.17 1.12 47 Ag 1.45(5) 1.28 1.39 1.37 48 Cd 1.44(9) 1.36 1.44 49 In 1.42(5) 1.42 1.36 1.46 50 Sn 1.39(4) 1.40 1.30 1.32 51 Sb 1.39(5) 1.40 1.33 1.27 52 Te 1.38(4) 1.36 1.28 1.21 53 I 1.39(3) 1.33 1.29 1.25 54 Xe 1.40(9) 1.31 1.35 1.22 55 Cs 2.44(11) 2.32 2.09 56 Ba 2.15(11) 1.96 1.61 1.49 57 La 2.07(8) 1.80 1.39 1.39 58 Ce 2.04(9) 1.63 1.37 1.31 59 Pr 2.03(7) 1.76 1.38 1.28 60 Nd 2.01(6) 1.74 1.37 61 Pm 1.99 1.73 1.35 62 Sm 1.98(8) 1.72 1.34 63 Eu 1.98(6) 1.68 1.34 64 Gd 1.96(6) 1.69 1.35 1.32 65 Tb 1.94(5) 1.68 1.35 66 Dy 1.92(7) 1.67 1.33 67 Ho 1.92(7) 1.66 1.33 68 Er 1.89(6) 1.65 1.33 69 Tm 1.90(10) 1.64 1.31 70 Yb 1.87(8) 1.70 1.29 71 Lu 1.87(8) 1.62 1.31 1.31 72 Hf 1.75(10) 1.52 1.28 1.22 73 Ta 1.70(8) 1.46 1.26 1.19 74 W 1.62(7) 1.37 1.20 1.15 75 Re 1.51(7) 1.31 1.19 1.10 76 Os 1.44(4) 1.29 1.16 1.09 77 Ir 1.41(6) 1.22 1.15 1.07 78 Pt 1.36(5) 1.23 1.12 1.10 79 Au 1.36(6) 1.24 1.21 1.23 80 Hg 1.32(5) 1.33 1.42 81 Tl 1.45(7) 1.44 1.42 1.50 82 Pb 1.46(5) 1.44 1.35 1.37 83 Bi 1.48(4) 1.51 1.41 1.35 84 Po 1.40(4) 1.45 1.35 1.29 85 At 1.50 1.47 1.38 1.38 86 Rn 1.50 1.42 1.45 1.33 87 Fr 2.60 2.23 2.18 88 Ra 2.21(2) 2.01 1.73 1.59 89 Ac 2.15 1.86 1.53 1.40 90 Th 2.06(6) 1.75 1.43 1.36 91 Pa 2.00 1.69 1.38 1.29 92 U 1.96(7) 1.70 1.34 1.18 93 Np 1.90(1) 1.71 1.36 1.16 94 Pu 1.87(1) 1.72 1.35 95 Am 1.80(6) 1.66 1.35 96 Cm 1.69(3) 1.66 1.36 97 Bk - 1.66 1.39 98 Cf - 1.68 1.40 99 Es - 1.65 1.40 100 Fm - 1.67 101 Md - 1.73 1.39 102 No - 1.76 1.59 103 Lr - 1.61 1.41 104 Rf - 1.57 1.40 1.31 105 Db - 1.49 1.36 1.26 106 Sg - 1.43 1.28 1.21 107 Bh - 1.41 1.28 1.19 108 Hs - 1.34 1.25 1.18 109 Mt - 1.29 1.25 1.13 110 Ds - 1.28 1.16 1.12 111 Rg - 1.21 1.16 1.18 112 Cn - 1.22 1.37 1.30 113 Uut - 1.36 114 Uuq - 1.43 115 Uup - 1.62 116 Uuh - 1.75 117 Uus - 1.65 118 Uuo - 1.57\ """