[Ifeffit] Cobalamin XANES: experiments and simulations do not match

Mon May 15 17:59:31 CDT 2017

Dear all,

I have been working on simulating for the K-edge XANES spectra of
methylcobalamin (MeCbl) and cyanocobalamin (CNCbl). The only change in the
two materials is one bond (the upper axial bond in an octahedral
coordination at the Cobalt site) from CH3 to CN. The molecule consists of
about 180 atoms in total. We, however, use a truncated (50 atom) structure
and more recently, an extended (90 atom) structure. But neither of them
seem to predict the relative changes in peak positions and edge chemical
shifts accurately.

As a quick summary:

Experimental XANES spectra show:
1. CNCbl has a 1 eV blue-shifted absorption edge as compared to MeCbl.
2. The shoulder peak in CNCbl (about 6-7 eV lower than the main-peak) is
much stronger (than MeCbl) and comparable in intensity to the main
(strongest) peak.

We use Gaussian to identify the optimized structure and then feed it to
FEFF 8.4 to simulate for the XANES. When we do the simulations we note -

1. CNCbl has an approx. 0.1-0.2 eV red-shifted absorption edge as compared
to MeCbl.
2. The shoulder peak intensity is comparable to the main peak intensity in
CNCbl. However, in comparing with MeCbl, the shoulder peak intensity is
still lower.

Incidentally, we see the exact same problem repeat with hydroxocobalamin
OHCbl as we see with CNCbl as well ! (I do not present that here, since I
assume the origin of the problem is same).

I thought, maybe truncation is affecting the the optimized geometry when we
perform DFT and hence increased the cluster size to about 90 atoms but
noticed no significant change. (We did this quite sometime back just with
MeCbl to actually justify the use of a truncated structure. But now we are
not sure where the error is).
Now I wonder if I am performing the FEFF accurately and not missing
something here.

I attach the input feff files for the truncated and the more elongated
structures of both MeCbl and CNCbl. I also attach the (ATHENA deglitched,
merged and normalized) experimental XAFS for MeCbl and CNCbl.

Any help in identifying the issue is greatly appreciated ! (Sorry for the
long email).

Thanks,

Ganesh Subramanian
Post Doctoral Research Scholar,
Spence Group,
Arizona State University
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e	I_MeCbl
7623.9	7.50E-04
7628.9	3.95E-03
7633.9	-3.40E-03
7638.9	-2.92E-03
7643.9	-2.29E-03
7648.9	-1.35E-03
7653.9	2.87E-04
7658.9	2.50E-04
7663.9	-1.33E-04
7668.9	-5.76E-04
7673.9	2.88E-04
7678.9	9.37E-04
7683.9	-1.27E-03
7688.9	5.01E-04
7693.9	7.35E-04
7698.9	4.41E-04
7703.9	3.27E-03
7704.9	5.39E-03
7705.9	4.37E-03
7706.9	6.84E-03
7707.9	9.53E-03
7708.3	1.02E-02
7708.7	1.22E-02
7709.1	1.16E-02
7709.5	1.71E-02
7709.9	2.02E-02
7710.3	2.75E-02
7710.7	3.96E-02
7711.1	5.96E-02
7711.5	8.68E-02
7711.9	0.1162463
7712.3	0.12487077
7712.7	0.10726144
7713.1	7.74E-02
7713.5	5.85E-02
7713.9	4.89E-02
7714.3	4.84E-02
7714.7	5.27E-02
7715.1	5.95E-02
7715.5	6.80E-02
7715.9	7.84E-02
7716.3	8.75E-02
7716.7	9.54E-02
7717.1	0.10286444
7717.5	0.11558012
7717.9	0.1290066
7718.3	0.14642104
7718.7	0.16739954
7719.1	0.19141217
7719.5	0.21947034
7719.9	0.25047521
7720.3	0.28430166
7720.7	0.32319028
7721.1	0.36457837
7721.5	0.40909176
7721.9	0.45381781
7722.3	0.50197888
7722.7	0.55267322
7723.1	0.60096726
7723.5	0.65085262
7723.9	0.70062996
7724.3	0.74980775
7724.7	0.79497818
7725.1	0.84023154
7725.5	0.88137795
7725.9	0.91656001
7726.3	0.95163771
7726.7	0.97715321
7727.1	0.99742338
7727.5	1.0128584
7727.9	1.0172814
7728.3	1.0174923
7728.7	1.0160896
7729.1	1.0155665
7729.5	1.0156945
7729.9	1.0235909
7730.3	1.0252836
7730.7	1.0417814
7731.1	1.0588335
7731.5	1.0839856
7731.9	1.1103773
7732.3	1.138797
7732.7	1.1653435
7733.1	1.1933882
7733.5	1.2217434
7733.9	1.2460692
7734.3	1.2699837
7734.7	1.2886172
7735.1	1.2958942
7735.5	1.3053271
7735.9	1.3021244
7736.3	1.2934397
7736.7	1.2792
7737.1	1.2580897
7737.5	1.2364309
7737.9	1.2135568
7738.3	1.1923636
7738.7	1.1788081
7739.1	1.158327
7739.5	1.1401025
7739.9	1.1248652
7741.09	1.0847584
7742.28	1.0545379
7743.47	1.0308407
7744.66	1.0043797
7745.85	0.98362241
7747.04	0.96249874
7748.23	0.94319497
7749.42	0.9247655
7750.61	0.91434575
7751.81	0.9024757
7753	0.89029805
7754.19	0.87791662
7755.38	0.86470285
7756.57	0.84877833
7757.76	0.83680428
7758.95	0.84101961
7760.14	0.8339946
7761.33	0.8391244
7762.52	0.85270246
7763.71	0.86560348
7764.9	0.88176337
7766.36	0.90080975
7767.85	0.91275192
7769.35	0.92315846
7770.87	0.93243528
7772.41	0.93971798
7773.97	0.94626632
7775.55	0.94943158
7777.15	0.95962621
7778.76	0.96832667
7780.4	0.98293547
7782.05	0.99128624
7783.73	0.99929861
7785.42	1.0017133
7787.13	1.0050399
7788.86	1.0097698
7790.6	1.0102274
7792.37	1.0130155
7794.16	1.0160214
7795.96	1.0198866
7797.79	1.0196498
7799.63	1.0181578
7801.49	1.0182692
7803.37	1.0179218
7805.27	1.0167892
7807.19	1.0135813
7809.13	1.0087091
7811.09	1.0046227
7813.06	1.0023738
7815.06	1.0009149
7817.07	0.99752902
7819.1	0.99594347
7821.15	0.99227243
7823.22	0.99141185
7825.31	0.99259503
7829.54	0.98785496
7831.69	0.98071402
7833.85	0.97914966
7836.04	0.97062672
7838.24	0.96784454
7840.46	0.96296444
7842.7	0.95915928
7844.96	0.95829632
7847.24	0.95950744
7849.54	0.95787078
7851.85	0.95929802
7854.18	0.96205335
7856.54	0.9674313
7858.91	0.9674025
7861.3	0.97390614
7863.71	0.98073395
7866.14	0.98516042
7868.59	0.98970329
7871.06	0.99549344
7873.54	0.99889273
7876.05	1.0031569
7878.57	1.0039702
7881.11	1.0086429
7883.68	1.0122795
7886.26	1.012958
7888.86	1.0140784
7891.47	1.0147804
7894.11	1.0160259
7896.77	1.0173838
7899.44	1.0165868
7902.14	1.0133085
7904.85	1.0129821
7907.58	1.0120638
7910.33	1.0080228
7913.1	1.004961
7915.89	1.0039379
7918.7	0.99868587
7921.52	0.99724352
7924.37	0.99720085
7927.23	0.99370416
7930.12	0.9919538
7933.02	0.99053144
7935.94	0.99084485
7938.88	0.99290293
7941.84	0.98982586
7944.81	0.99153459
7947.81	0.98994491
7950.83	0.99420113
7953.86	0.99269934
7956.91	0.99182627
7959.99	0.99364704
7963.08	0.99371087
7966.19	0.99360784
7969.32	0.99478123
7972.46	0.99573202
7975.63	0.99442348
7978.82	0.99513978
7982.02	0.99413453
7985.24	0.99554656
7988.49	0.99816984
7991.75	0.9982304
7995.03	0.99803969
7998.33	1.0033624
8001.64	1.0034906
8004.98	1.0028553
8008.34	1.0034294
8011.71	1.0040982
8015.1	1.0060217
8018.52	1.008359
8021.95	1.0059481
8025.4	1.0075777
8028.87	1.0083322
8032.36	1.0084123
8035.86	1.0079553
8039.39	1.006759
8042.93	1.0041479
8046.5	1.0023319
8050.08	1.0015126
8053.68	0.99900329
8057.3	0.99613749
8060.94	0.99586594
8068.28	0.99582289
8071.97	0.99445285
8075.69	0.99508121
8079.42	0.99203591
8083.18	0.99514531
8086.95	0.99492772
8090.74	0.99580382
8094.55	0.99212708
8098.38	0.99823199
8106.09	0.99837227
8109.98	0.99724796
8113.88	0.99682408
8117.8	0.99590215
8121.74	0.99857489
8125.71	0.99928557
8129.69	1.0023402
8133.68	1.0010782
8137.7	1.0016265
8141.74	1.0029265
8145.8	0.99983418
8149.87	1.0011677
8153.96	0.99909503
8158.07	1.0037298
8162.21	1.0013378
8166.36	1.0029593
8170.52	1.0044373
8174.71	1.0017744
8178.92	1.0007285
8183.14	0.99824993
8187.39	1.0000256
8191.65	0.99853179
8195.94	1.0002042
8200.24	0.99730004
8204.56	1.0006886
8208.9	1.0023296
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e	I_CNCbl
7608.9	-6.40E-04
7619.45	-1.52E-03
7630.01	-1.73E-03
7640.57	-1.08E-03
7651.12	-3.65E-03
7661.68	5.52E-04
7672.23	-4.59E-04
7682.79	-7.37E-04
7693.34	6.44E-04
7703.9	3.65E-03
7704.9	4.35E-03
7705.9	5.41E-03
7706.9	6.64E-03
7707.9	7.61E-03
7708.4	9.46E-03
7708.9	1.11E-02
7709.4	1.31E-02
7709.9	1.50E-02
7710.4	1.95E-02
7710.9	2.69E-02
7711.4	4.34E-02
7711.9	6.48E-02
7712.4	7.13E-02
7712.9	5.58E-02
7713.4	4.18E-02
7713.9	3.80E-02
7714.4	3.94E-02
7714.9	4.21E-02
7715.4	4.81E-02
7715.9	5.99E-02
7716.4	7.99E-02
7716.9	0.10038016
7717.4	0.10816922
7717.9	0.10697716
7718.4	0.10705087
7718.9	0.11467326
7719.4	0.12905538
7719.9	0.14968151
7720.4	0.17667361
7720.9	0.20967625
7721.4	0.24614152
7721.9	0.29163317
7722.4	0.34231091
7722.9	0.39905467
7723.4	0.45870855
7723.9	0.52141806
7724.4	0.5896479
7724.9	0.66571725
7725.4	0.74786626
7725.9	0.83817991
7726.4	0.92662663
7726.9	1.0105371
7727.4	1.0797024
7727.9	1.1269398
7728.4	1.15335
7728.9	1.1545514
7729.4	1.1406437
7729.9	1.1196056
7730.4	1.0988037
7730.9	1.0789383
7731.4	1.0694226
7731.9	1.0744902
7732.4	1.0854601
7732.9	1.1059044
7733.4	1.1277512
7733.9	1.1539679
7734.4	1.179068
7734.9	1.2038382
7735.4	1.2255637
7735.9	1.2379509
7736.4	1.2427778
7736.9	1.2405059
7737.4	1.2280045
7737.9	1.2094911
7738.4	1.1864847
7738.9	1.1663612
7739.4	1.1437295
7739.9	1.1233372
7741.15	1.0850279
7742.4	1.0629061
7743.65	1.0447209
7744.9	1.0340853
7746.15	1.0197262
7747.4	0.99961334
7748.65	0.9825913
7749.9	0.96142747
7751.15	0.94725162
7752.4	0.93166241
7753.65	0.91835235
7754.9	0.90342884
7756.15	0.88387243
7757.4	0.86408271
7758.65	0.85061478
7759.9	0.84076065
7761.15	0.83167138
7762.4	0.83273963
7763.65	0.84070263
7764.9	0.85633118
7766.94	0.88022532
7769.02	0.90156777
7771.14	0.91782087
7773.29	0.9285636
7775.48	0.94100128
7777.7	0.95098633
7779.96	0.96486913
7782.26	0.9807418
7784.6	0.99145558
7786.97	1.0005822
7789.38	1.0101745
7791.82	1.0195912
7794.31	1.0276679
7796.82	1.0319624
7799.38	1.0323039
7801.97	1.0313115
7804.6	1.0255083
7807.26	1.0179366
7809.96	1.0085412
7812.7	1.0010759
7815.48	0.99293693
7818.29	0.99034281
7821.13	0.98884822
7824.02	0.98837736
7826.94	0.99165889
7829.89	0.98862463
7832.89	0.9842212
7835.92	0.97966995
7838.98	0.97390883
7842.09	0.96738462
7845.23	0.96409275
7848.4	0.9605542
7851.62	0.9635092
7854.87	0.96619871
7858.15	0.97170333
7861.48	0.97475797
7864.84	0.98071121
7868.23	0.98625228
7871.67	0.99361454
7875.14	0.99957263
7878.64	1.0060794
7882.18	1.0112306
7885.76	1.0128319
7889.38	1.0158644
7893.03	1.0167909
7896.72	1.0198687
7900.44	1.0200849
7904.21	1.0165051
7908	1.0121421
7911.84	1.0103281
7915.71	1.0071586
7919.62	1.003271
7923.56	0.99797491
7927.55	0.99550578
7931.56	0.99017797
7935.62	0.98902458
7939.71	0.98990584
7943.84	0.99108525
7948	0.99273884
7952.2	0.99425095
7956.44	0.99470938
7960.71	0.99701642
7965.03	0.99631886
7969.37	0.99610642
7973.76	0.99595796
7978.18	0.99827721
7982.63	0.99597444
7987.13	0.99789279
7991.66	0.99756199
7996.23	0.9969648
8000.83	0.99902656
8005.47	1.0012235
8010.14	1.0023861
8014.86	1.0041152
8019.61	1.0067463
8024.39	1.0065409
8029.22	1.0067346
8034.08	1.0066193
8038.97	1.0054079
8043.91	1.0040528
8048.87	1.0039881
8053.88	1.0017936
8058.92	1.00085
8069.12	1.0004007
8074.27	0.99868636
8079.46	0.99523768
8084.68	0.99454042
8089.94	0.99558428
8095.24	0.99560161
8100.58	0.99457365
8105.95	0.99393959
8111.36	0.99645418
8116.8	0.99735859
8122.28	0.99650622
8127.8	1.0002356
8133.36	1.0025162
8138.95	1.0012315
8144.58	1.0023736
8150.24	1.0006634
8155.94	1.0003489
8161.68	0.99923316
8167.45	1.0015435
8173.26	1.0004526
8179.11	1.0016487
8184.99	0.99887053
8190.92	1.0011555
8196.87	0.99860918
8202.86	1.0001052
8208.9	1.0039065