1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
|
# -*- 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 <http://dx.doi.org/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 <http://dx.doi.org/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\
"""
|
