Dr Abhijeet Gaur, India

Presentation

on the work done in the field of

X-ray absorption fine structure spectroscopy (XAFS)

1

• Six years of experience of working on synchrotron beamlines. • Performed experiments at the XAFS beamline 11.1 at

ELETTRA Synchrotron Light Laboratory, Basovizza, Italy. • Performed experiments several times at the dispersive EXAFS beamline BL-8 and newly installed DCM EXAFS beamline BL-9

at Indian synchrotron Indus-2 at Raja Ramanna Centre for

Advanced Technology (RRCAT), Indore, India.

Title of Ph.D. thesis - X-ray absorption fine structure (XAFS) studies of copper compounds and complexes of biological significance.

For Ph.D. did research at School of Studies in Physics, Vikram University, Ujjain, India under the supervision of Prof. B. D. Shrivastava, who has worked with Prof. E. A. Stern at the University of Washington, Seattle, USA.

Got fellowship from Madhya Pradesh Council of Science and Technology, Bhopal, India for three years.

Details about experience in the field of XAFS

2

Published nineteen research papers based on the XAFS data recorded at different beamlines including those mentioned earlier and also at EXAFS beamlines X-19A at NSLS, BNL(USA) and 4–1 at the SSRL (USA).

My research work can be categorized into four groups.

1.Three research papers based on the experimental aspects of XAFS beamlines.

2.Five research papers on the XAFS studies of several mixed ligand copper complexes to obtain the local structure.

3.Four research papers on the study of the different methods of speciation using XAFS.

4.A review article on XAFS in Proceedings of the Indian National Science Academy, Vol 79, 2013, 921-966, which is the first review articles on XAFS in India.

Categorization of the work done on XAFS

3

Three research papers based on the experimental aspects of XAFS beamlines.

1.On the method of calibration of the energy dispersive EXAFS beamline at

Indus-2 and fitting theoretical model to the EXAFS spectrum, Sadhana - Academy Proceedings in Engineering Science 36 (2011) 339-

348.

2. A comparative study of the spectra recorded at RRCAT synchrotron BL-8

dispersive EXAFS beamline with other beamlines, Pramana – Journal of Physics 80 (2013) 159-171

3. Performance of BL-8 dispersive and BL-9 scanning EXAFS beamlines at Indus-2 synchrotron, Indian Journal of Physics (published online) DOI - 10.1007/s12648-014-0610-7

These papers provide useful information to any user of these beamlines.4

1. On the method of calibration of the energy dispersive EXAFS beamline at Indus-2 and fitting theoretical model to the EXAFS spectrum

Procedure for calibration of the recently developed BL-8 dispersive EXAFS beamline at the Indus-2 synchrotron source at RRCAT, Indore, India has been developed and this procedure is now being used by research workers on this beamline.

The procedure involves recording of absorption spectra of two standard samples, whose absorption edge energies are well established.

Two methods have been considered for calibration.

• In the first method, the position of the first maximum of the derivative of absorption curve is taken as the position of the edge energy. • In the second method, the position of the point at half edge step in the absorption curve is taken as the position of the edge energy.

5Published in Sadhana 36 (2011) 339-348.

The first method of calibration, i.e., the position of the first maximum of the derivative of absorption curve is taken as the position of the edge energy.

The second method, i.e., the position of the point at half edge step in the absorption curve is taken as the position of the edge energy.

6

Dispersion values determined by the two methods at different beam currents

• It has been shown that only the first method gives same values of dispersion even when the beam current is varied and should be used for calibrating the experimental spectra.

Conclusion

7

2. A comparative study of the spectra recorded at RRCAT synchrotron BL-8 dispersive EXAFS beamline with other beamlines

The quality and reliability of the recorded data and the usefulness of the BL-8 beamline has been evaluated.

• For this purpose, XAFS spectra at Cu K-edge in copper metal have been recorded at (1) EXAFS beamline 11.1 at ELETTRA Synchrotron Light Laboratory, Basovizza, Italy, (2) EXAFS beamline X-19A at National Synchrotron Light Source (NSLS), Brookhaven National Laboratory (BNL), Upton, New York, USA (3) EXAFS wiggler beamline 4–1 at the Stanford Synchrotron Radiation Laboratory (SSRL), Stanford, California, USA.

• Also, the XAFS spectra at Cu K-edge in a copper complex (N,N’-ethylenebis (salicylideneiminato) copper(II)) have been recorded at the BL-8 beamline and beamline 11.1 at ELETTRA.

Published in Pramana – Journal of Physics 80 (2013) 159-171 8

Normalized Cu K-edge EXAFS spectra for metal obtained from four different synchrotron EXAFS beamlines.

k1- weighted χ(k) spectra obtained from normalized μ(E) spectra given in (a).

9

Magnitude of the Fourier transform of experimental data (solid line) along with theoretically modeled fit (dashed line). The data have been fitted using k weight of 1. The fitting parameters are given in the text. 10

Normalized Cu metal K-edge EXAFS spectra k2-weighted χ(k) spectra for copper complex obtained from two different synchrotron EXAFS beamlines.

Magnitude of the Fourier transform of experimental data (solid line) along with theoretically modeled fit (dashed line).

11

Copper foil1st shell 2nd shell 3rd shell 4th shell

Beamlines at

R(Å)

ΔR(Å)

σ2

(Å-2)R(Å)

ΔR (Å)

Σ2

(Å-2)R (Å)

ΔR (Å)

σ2

(Å-2)R(Å)

ΔR (Å)

σ2(Å-2)

ELETTRA

2.55 -0.005 0.0085 ± 0.0005

3.59 -0.022 0.0121 ± 0.0017

4.45 0.030 0.0110 ± 0.0009

5.14 0.039 0.0095 ± 0.0010

BNL 2.54 -0.008 0.0082 ± 0.0006

3.58 -0.025 0.0119 ± 0.0018

4.45 0.026 0.0011 ± 0.0010

5.14 0.032 0.0092 ± 0.0010

SSRL 2.55 -0.003 0.0075 ± 0.0007

3.63 0.018 0.0120 ± 0.0026

4.45 0.032 0.0097 ± 0.0013

5.14 0.040 0.0086 ± 0.0013

RRCAT 2.51 -0.040 0.0078 ± 0.0020

3.53 -0.080 0.0038 ± 0.0028

4.40 -0.018 0.0146 ± 0.0040

5.10 -0.003 0.0073 ± 0.0026

Copper Complex Atomic pair

EXAFS results(ELETTRA)

XRD results

EXAFS results(RRCAT)

N R(Å) ΔR (Å) σ2(Å-2) R N R(Å) ΔR (Å)

σ2(Å-2)

Cu1-O2 1 1.86 -0.04 0.0059 ± 0.0011 1.90 1 1.96 0.06 0.0115 ± 0.0048Cu1-O1 1 1.90 -0.04 0.0059 ± 0.0011 1.94 1 1.99 0.06 0.0115 ± 0.0048Cu1-N1 1 1.95 -0.002 0.0015 ± 0.0003 1.95 1 1.84 -0.11 0.0096 ± 0.0051Cu1-N2 1 1.95 -0.002 0.0015 ± 0.0003 1.95 1 1.84 -0.11 0.0096 ± 0.0051Cu1-Oap 1 2.37 -0.04 0.0055 ± 0.0011 2.41 1 2.47 0.06 0.0115 ± 0.0048

The EXAFS fitting results for copper metal (at T=298 K)

The EXAFS fitting results for the complex. The XRD results for complex (from Bhadbhade et al., 1993) are also given.

12

Conclusions It has been shown that the spectra recorded at the BL-8 beamline can be satisfactorily used to obtain the structural information around the absorbing atom of the sample. The quality of the recorded data has been found to be satisfactory because the noise is less and the beam is stable during the short period of recording of the data. The data has been found to be reliable as it is reproducible.

It is advised that while using this beamline, a large number of spectra should be recorded for a sample and then data should be summed up.

The present work is important in Indian context because the beamline can be used by physicists, chemists and even biologists for determination of molecular structure, specially the environment around the absorbing atom. The beamline is easily accessible to Indian users which otherwise was not possible till now.

13

3. Performance of BL-8 dispersive and BL-9 scanning EXAFS beamlines at Indus-2 synchrotron•The performance and usefulness of the two EXAFS beamlines, BL-8 dispersive and BL-9 scanning, at 2.5 GeV Indus-2 synchrotron source at Raja Ramanna Center for Advanced Technology, Indore (India) have been evaluated.

•From this sample study, it has been found that the range of the EXAFS data is more in BL-9 than BL-8. However, the bond lengths obtained from EXAFS data analysis are comparable for both the beamlines.

•Due to larger damping of EXAFS oscillations at higher energies in BL-8, higher disorder is obtained in BL-8.

•The resolution in the pre-edge and XANES region has been found to be more in BL-9.

•The advantage of BL-8 is that spectra can be recorded very quickly (~300 ms) and hence beamtime is easily available. Further, BL-8 is useful for performing in situ and time resolved studies.

• In BL-9, the time taken to record the spectrum is quite large (~40 min) and hence it takes longer to get access to this beamline.

Published in Indian Journal of Physics (published online) DOI - 10.1007/s12648-014-0610-714

Cu K-edge XAFS spectra for metal recorded at EXAFS beamlines BL-8 and BL-9 (a)Normalized μ(E) versus E spectra (b)k1-weighted χ(k) versus k spectra,(c)Normalized (E) versus E spectra in the XANES region (8970-9050 eV) and (d) Derivative (E) versus E spectra in the XANES region (8970-9050 eV).

15

Cu K-edge XAFS spectra for the copper complex Cu(na)2.4H2O recorded at EXAFS beamlines BL-8 and BL-9, (a)Normalized μ(E) versus E spectra (b)k2-weighted χ(k) versus k spectra, (c) Normalized (E) versus E spectra in the XANES region (8970-9050 eV) and (d) Derivative (E) versus E spectra in the XANES region (8970-9050 eV).

16

The EXAFS fitting results for the cooper complex (at T=298 K).

Beamline BL-9EXAFS results

XRD results

Beamline BL-8EXAFS results

Atomicpair

N R(Å) ΔR(Å) σ2 (Å-2) R(Å) R(Å) ΔR(Å) σ2 (Å-2)

Cu-O1 2 2.02 0.023 0.003±0.002 1.995 1.95 -0.046 0.005±0.004Cu-N1 2 1.90 -0.104 0.004±0.003 2.005 2.21 0.208 0.008±0.007Cu-O2 2 2.41 -0.034 0.019±0.009 2.442 2.46 0.021 0.019±0.006

1st shell 2nd shell 3rd shell 4th shellBeam

lineR

(Å)ΔR(Å)

σ2

(Å-2)R

(Å)ΔR (Å)

σ2

(Å-2)R

(Å)ΔR (Å)

σ2

(Å-2)R (Å)

ΔR (Å)

σ2

(Å-2)BL-8 2.53 -0.027

± 0.0130.0139

± 0.00123.60 -0.012

± 0.0030.0198

± 0.0082

4.42 0.001± 0.040

0.0183± 0.0038

5.22 0.120± 0.047

0.0063± 0.0056

BL-9 2.49 -0.061± 0.003

0.0076± 0.0005

3.53 -0.075± 0.009

0.0101± 0.0014

4.33 -0.085± 0.006

0.0097± 0.0008

5.04 -0.062± 0.026

0.0093± 0.0032

The EXAFS fitting results for copper metal (at T=298 K)

17

Suggestions for improving resolution of the beamline BL-8

As the BL-8 beamline has elliptically bent crystal, the following measures have been suggested for improving the resolution of the beamline –

(i)by reducing the radius of curvature of the polychromator, i.e., by increasing the energy band;

(ii) by reducing the size of the pixels in the CCD detector and

(iii) by reducing the size of the focal spot of the synchrotron beam.

18

Five research papers on the XAFS studies of several mixed ligand copper complexes to obtain the local structure.

1. EXAFS study of binuclear hydroxo-bridged copper (II) complexes Journal of Coordination Chemistry 64 (2011) 1265-1275

2. XAFS investigations of copper(II) complexes with tetradentate Schiff base ligands X-ray Spectrometry 41, (2012) 384–392

3. Extended X-ray absorption fine structure study of mixed-ligand copper(II) complexes having analogous structures Journal of Applied Physics 113 (2013) 073701

4. X-ray absorption fine structure study of multinuclear copper (I) thiourea mixed ligand complexes Journal of Chemical Physics 139 (2013) 034303

5. XAFS study of aqua (diethylenetriamine)(isonicotinato)- copper(II) complex – inference of square pyramidal geometry X-ray Spectrometry 43 (2014) 238

19

1. EXAFS study of binuclear hydroxo-bridged copper (II) complexes

The following four complexes have been studied using EXAFS -

1. Monohydroxo-bridged [(bpy)2Cu-OH-Cu(bpy)2](ClO4)3 (1) its analogous complex [(phen)2Cu-OH-Cu(phen)2](C1O4)3 (2)

2. Dihydroxo-bridged complex [Cu2(µ-OH)2(bipy)2]SO4.5H2O (3) its analogous complex [Cu2(µ OH)2(phen)2]SO4. 5H2O (4)

where bpy is 2,2'-bipyridine and phen is 1,10-phenanthroline.

• These complexes are also of theoretical interest, because they provide examples of the simplest case of magnetic interactions with only two unpaired electrons. • These complexes also exhibit ferromagnetic or antiferromagnetic exchange interactions. • Binuclear hydroxo-bridged copper (II) complexes have been found to be catalytically active for oxidative coupling reactions, a fact that adds to the practical importance of studying the electronic structure of such complexes.

Published in Journal of Coordination Chemistry 64 (2011) 1265-1275.20

• Theoretical models have been generated for the 1 and 3 using the available crystallographic data and fitted to theirexperimental EXAFS data to obtain the structural parameters, which include bond-lengths, coordination numbers and thermal disorders. The results obtained have been found to be comparable with their crystallographic results.

• As the crystallographic data for the 2 and 4 are not available in literature, we have determined their structural parameters by fitting their experimental EXAFS data with the same theoretical models which were generated for their corresponding analogous complexes 1 and 3, respectively. The structural parameters, thus determined have been reported.

21

•On the basis of analysis of the EXAFS data, these four complexes have been shown to be binuclear, i.e., they contain two metal atoms per cluster. This result can be obtained only with EXAFS spectroscopy.

•The values of the chemical shifts suggest that copperis in +2 oxidation state in these complexes.

•On the basis of EXAFS analysis coordination geometry about the copper (II) ions in these complexes are depicted.

Results

22

EXAFS spectra and analysis of complexes

Complex 1

23

Complex 3

24

Complex 2 Complex 4

25

EXAFS fitting results for complexes 1 and 2.

The XRD results [Haddad et al.] for complex 1 are also given.

EXAFS fitting results for complexes 3 and 4. The XRD results [Casey et al.] for complex 3 are also given.

26

Structures suggested on the basis of EXAFS studiesComplex 1

Complex 2

27

Complex 3

Complex 4

28

2. XAFS INVESTIGATIONS OF COPPER(II) COMPLEXES WITH TETRADENTATE SCHIFF BASE LIGANDS

The geometry around Cu centers has been studied using the technique of XAFS in the complexes [Cu(salen)], [Cu(salen)CuCl2].H2O, [Cu(salophen)] and [Cu(salophen)CuCl2].H2O where

salen = N,N’-ethylenebis(salicylideneiminato) dianion salophen = N,N’-o-phenylenediaminebis (salicylideneiminato) dianion.

29 Published in X-ray Spectrometry 41, (2012) 384–392

Complexes 1 and 3 are supposed to have one type of copper centers (called (Cu1)). On the other hand, complexes 2 and 4 are supposed to have two types of copper centers (called (Cu1) and (Cu2)) having different coordination environments and geometries.

Earlier workers (Borghi et al., 2002 & Riggs et al., 1995) have pointed out that the analysis of EXAFS spectra of binuclear metal complexes pose some problems due to the presence of two absorbing atoms, even when the absorbing atoms may be of the same element, and from the fact that the metal–metal contribution in the spectra is superposed to the sample signals.

The geometry about (Cu1) center in all of these complexes and about the (Cu2) center in complexes 2 and 4 has been investigated. The structural parameters determined from the EXAFS spectra, for all the complexes studied have been reported and the coordination geometry has been depicted.

Analysis of the pre-edge region has been used to investigate the binuclear nature of the complexes. XANES features have been used to determine the oxidation state of copper and the coordination geometry about it.

30

Normalized EXAFS spectra at the K-edge of copper in complexes

Derivative XANES spectra

(k) vs. k spectra Fourier transform ((R) vs.R ) spectra 31

Theoretical model for (Cu1) center•Since, 1, 2, 3 and 4 are expected to have similar coordination sphere around the (Cu1) center, the theoretical model for 1 have been generated using its available crystal structure.

•This model for 1 has been fitted to the experimental EXAFS data of 1, 2, 3 and 4 to investigate the geometry about (Cu1) center and to determine their structural parameters.

Theoretical model for (Cu2) center•To estimate the geometry around (Cu2) center in 2 and 4, theoretical model has been generated by taking another standard dichlorobis[2-(o-tolyliminomethyl) phenolato] copper(II), i.e., [Cu(C14H13NO)2Cl2] which has similar geometry and

coordination as (Cu2) center and the crystal structure of which is available.

•As two theoretical models have been generated for the two different types of copper centers present in complexes 2 and 4, one theoretical model has been fitted to the EXAFS data at a time.

32

Complex 1

Fourier transformed EXAFS data for the complexes. Black lines are experimental data and red lines are modeled fit for (Cu1) center.

Complex 2

Complex 3 Complex 4

33

Complex 2 Complex 4

Fourier transformed EXAFS data for complexes 2 and 4. Solid lines are experimental data and dashed lines are modeled fit for (Cu2) center.

34

8974 8976 89780.00

0.01

E (in eV)

Der

(E

)

(a) Complex 1

8974 8976 89780.00

0.01

E (in eV)

Der

(E

)

(b) Complex 2

Area Center Width Height ------------------------------------------------- 0.0099221 8976.4 1.5042 0.0052632

Area Center Width Height --------------------------------------------------- 0.011458 8976.2 1.4760 0.0061940

8974 8976 89780.00

0.01

Der

(E

)

E (in eV)

(c) Complex 3

8974 8976 89780.00

0.01

Der

(E

)

E (in eV)

(d) Complex 4

Area Center Width Height -----------------------------------------------

0.011797 8976.7 1.8933 0.0049715

Area Center Width Height ----------------------------------------------------

0.010306 8976.1 1.7221 0.0047750

Gaussian fitting of ls→3d pre-edge peak for calculating the area under the peak, height and width of the peak for (a) 1, (b) 2, (c) 3 and (d) 4. Solid lines are experimental data and dashed lines are Gaussian fit.

35

Oap

N1 O1 Cu1 N2 O2 (a) Cu1 site

Cl2

Cu2 Cl1 O2 O1 (b) Cu2 site

Coordination geometry about the (a) (Cu1) center in all the complexes and (b) (Cu2) center in binuclear complexes 2 and 4, deduced from the EXAFS data analysis

36

There are different reports regarding the coordination geometry of (Cu1) center in various Cu(salen) and Cu (salophen) complexes using X-ray crystallography. In the present work, using XAFS spectroscopy, we have tried to clarify the situation and concluded that (Cu1) center has square pyramidal geometry in complexes 1- 4.

3. Extended X-ray absorption fine structure study of mixed-ligand copper(II) complexes having analogous structures

X-ray absorption spectroscopic studies of the following five mixed ligand copper complexes have been done.

[Cu(L-glu)(bipy)] , [Cu(L-glu)(o-phen)(H2O)]. 3H2O, [Cu(bipy)(L-tyro)]Cl, [Cu(L-phen)(bpy) H2O (ClO4)] Cu(L-tyr)(phn) 2.5H2O (ClO4) where bipy = 2,2-bipyridine, phen = 1,10-phenanthroline, glu = glutamic acid and tyro = tyrosine

37

•The complexes have analogous structures and their crystallographic data are available in the literature

•By using the crystallographic data of the five complexes, five theoretical models have been generated.

Published in Journal of Applied Physics 113 (2013) 073701

•Firstly, EXAFS data of each complex has been fitted to its own theoretical model to obtain the structural parameters. The results obtained are found to be comparable with the crystallographic results. Thus, after confirming that the generated theoretical models are satisfactory, each theoretical model has been used to fit the EXAFS data of other four complexes.

•In case of each complex, the structural parameters obtained by fitting EXAFS data with theoretical models of the four remaining complexes have been found to be comparable with those obtained by fitting its own theoretical model.

•Thus, it has been shown that the crystal structure of a similar or analogous complex can be used satisfactorily for generating the theoretical model for the EXAFS data analysis of complex.

38

Normalized EXAFS spectra at the K-edge of copper in complexes 1, 2, 3, 4 and 5.

Derivative XANES spectra for complexes 1, 2, 3, 4 and 5.

39

(k) vs. k spectra for complexes 1, 2, 3, 4 and 5.

Fourier transform ((R) vs.R ) spectra for complexes 1, 2, 3, 4 and 5.

40

0 2 4 60

1

2

3

4

5

6

7

(R

)

( Å

-3 )

R (Å )

Expdata O1 N3 N2 N1 O3 C11 C12

The theoretically calculated contribution to ׀χ(R)׀ by the single scattering paths (i) two Cu1-O, (ii) three Cu1-N paths and (iii) two Cu1-C paths , in complex 1 using the theoretical model generated by employing its own crystal structure. The experimental ׀χ(R)׀ is also shown in the figure. This is a representative figure for complex 1. The figures for the other four complexes are similar to this figure and are not shown here.

41

Theoretical model 1 (

2 = 816.97)Theoretical model 2

(2 = 813.04)

Theoretical model 3 (

2 = 742.61)Theoretical model

4 (

2 = 627.59)

Theoretical model 5

(2 = 856.69)

Atomic pair

XRD resul

ts

S02 = 1.06 ± 0.20

E0 = 5.68 ± 1.46 eVS0

2 = 0.85 ± 0.18E0 = 5.08 ± 1.69 eV

S02 = 1.09 ± 0.12

E0 = 4.32 ± 1.29 eVS0

2 = 1.11 ± 0.16E0 = 4.59 ± 1.20

eV

S02 = 0.83 ± 0.16

E0 = 5.09 ± 1.56 eV

R R(Å) ΔR(Å) σ2(Å-2) R(Å) σ2(Å-2) R(Å) σ2(Å-2) R(Å) σ2(Å-2) R(Å) σ2(Å-2)

Cu1-O1 1.96 1.96 0.003 0.0061 ± 0.0015

1.90 0.0038± 0.0010

1.96 0.0070 ± 0.0011

1.94 0.0046 ± 0.0014

1.97 0.0045 ± 0.0031

Cu1-N1 2.02 2.02 0.003 0.0061 ± 0.0015

2.01 0.0038± 0.0010

2.00 0.0070 ± 0.0011

2.00 0.0046 ± 0.0014

1.91 0.0045 ± 0.0031

Cu1-N2 2.01 2.01 0.003 0.0061 ± 0.0015

2.01 0.0038± 0.0010

1.98 0.0070 ± 0.0011

2.01 0.0046 ± 0.0014

2.00 0.0045 ± 0.0031

Cu1-N3 1.98 1,98 0.003 0.0061 ± 0.0015

2.01 0.0038± 0.0010

2.01 0.0070 ± 0.0011

2.09 0.0046 ± 0.0014

2.02 0.0045 ± 0.0031

Cu1-O3 2.24 2.19 -0.048 0.0116 ± 0.0085

2.48 0.0267 ± 0.0238

2.65 0.0103± 0.0091

2.24 0.0095 ± 0.0049

2.08 0.0198 ± 0.0055

The EXAFS fitting results for complex 1 using the five theoretical models. XRD results for complex 1 from Antolini et al., 1985 are also given.

42

The fitting results for the other four complexes are similar and not shown here.

O(1WA)

Coordination geometries about the Cu(II) ions in complexes 1, 2, 3, 4 and 5 are shown in (a), (b), (c), (d) and (e), respectively. The figures have been drawn following Antolini et al. (1985), Yamauchi et al. (1992) and Sugimori et al. (1997). The distances shown are those obtained from the present EXAFS analysis.

(b)(a) (c)

(d)(e) 43

4. X-ray absorption fine structure study of multinuclear copper (I) thiourea mixed ligand complexes

XAFS studies of the following five copper (I) thiourea complexes have been done.

Hexakis(thiourea)tetracopper(I) Tetranitrate Tetrahydrate [Cu4(thu)6 (NO3)4 (H2O)4]Nonakis(thiourea)tetracopper(I) Tetranitrate Tetrahydrate [Cu4(thu)9 (NO3)4 (H2O)4]Hexakis(thiourea)dicopper(I) Sulfate Hydrate [Cu2(thu)6 (SO4) H2O]Pentakis(thiourea)dicopper(I) Sulfate Trihydrate [Cu2(thu)5 (SO4) (H2O)3]Chloro(thiourea)copper(I) hemihydrate [Cu(thu)Cl 0.5H2O]

44 Published in Journal of Chemical Physics 139 (2013) 034303

Complex 1 is supposed to have one type of copper center in trigonal planar environment. Complexes 2 and 4 are supposed to have two types of copper centers, one center having trigonal planar structure and another center having tetrahedral structure. Complex 3 is supposed to have one type of copper center in tetrahedral environment.

The aim of the present work is to show how EXAFS spectra of these complexes, having different types of coordination environment, can be analyzed to yield the geometry around the central metal ion.

The coordination geometry about the one type of copper center present in complexes 1 and 3 and about the two types of copper centers present in complexes 2 and 4 have been investigated

Another aim of the present study is to determine the coordination geometry of complex 5 from EXAFS spectra for which the crystal structure is unavailable due to inability of growing its single crystals. Hence, the present EXAFS study for this complex becomes important.

45

Normalized EXAFS spectra at the K-edge of copper in complexes 1, 2,3, 4 and 5. Derivative XANES spectra for

complexes 1, 2,3, 4 and 5.

(k) vs. k spectra for complexes 1, 2,3, 4 and 5.46

•The crystallographic data is available for the complexes 1, 2, 3 and 4. However, the details of the positional parameters for complexes 1 and 2 are not available. Hence, theoretical models could not be generated for these complexes. Theoretical models for 3 and 4 have been generated in Artemis.

47

•Analysis of complexes 3 and 4 has been done using their own theoretical models.

•As complex 4 contain two copper centers, one center having trigonal structure and another center having tetrahedral structure, two theoretical models have been generated for 4, one for trigonal structure and another for tetrahedral structure.

•In case of complex 1, the copper atom is supposed to be trigonal planar. Hence, EXAFS analysis of 1 has been done using the theoretical model for trigonal structure of complex 4.

•As complex 2 also contain two copper centers, one center having trigonal structure and another center having tetrahedral structure, EXAFS analysis of both the centers of 2 has been done using the theoretical models for both centers of complex 4.

•As in case of complex 5, the crystal structure is unavailable due to inability of growing its single crystals, the theoretical model for 5 has been generated using the crystal structure of an analogous complex

Fourier transformed EXAFS data for complex 1 and the theoretical fit is shown by red line.

Fourier transformed EXAFS data for complex 2 and the theoretical fit for tetrahedral structure

Fourier transformed EXAFS data for complex 2 and the theoretical fit for trigonal structure

Fourier transformed EXAFS data for complex 3 and the theoretical fit

48

Fourier transformed EXAFS data for complex 4 and the theoretical fit for tetrahedral structure

Fourier transformed EXAFS data for complex 4 and the theoretical fit for trigonal structure

Fourier transformed EXAFS data for complex 2 and the theoretical fit using both the structures

Fourier transformed EXAFS data for complex 4 and the theoretical fit using both the structures

49

Fourier transformed EXAFS data for complex 5. The curve obtained from experimental data is shown by black line. The theoretical fit by red line.

50

Complex 3Atomic

pairEXAFS results XRD

resultsN R(Å) delr(Å) σ2(Å-2) R

Cu1-S6 1 2.27 -0.021 0.0056 ± 0.0010 2.29Cu1-S4 1 2.27 -0.021 0.0056 ± 0.0010 2.29Cu1-S2 1 2.32 -0.034 0.0091 ± 0.0053 2.35Cu1-S1 1 2.41 -0.034 0.0091 ± 0.0053 2.44

The EXAFS fitting results for tetrahedral (Cu) center in complex 3. XRD results from Piro et al., 2000 are also given.

The EXAFS fitting results for tetrahedral (Cu) center in complex 2 and 4. XRD results for complex 4 from Ferrari and Gasparri, 1976 are also given.

Complex 4 Complex 2Atomic

pairEXAFS results XRD

resultsEXAFS results

N R(Å) delr(Å) σ2(Å-2) R N R(Å) σ2(Å-2)Cu1-S1 1 2.28 -0.033 0.0089 ± 0.0006 2.31 1 2.26 0.0080 ± 0.0007Cu1-S4 1 2.30 -0.033 0.0089 ± 0.0006 2.33 1 2.28 0.0080 ± 0.0007Cu1-S3 1 2.31 -0.033 0.0089 ± 0.0006 2.34 1 2.28 0.0080 ± 0.0007Cu1-S2 1 2.37 -0.033 0.0089 ± 0.0006 2.40 1 2.35 0.0080 ± 0.0007

51

The EXAFS fitting results for trigonal (Cu) center in complexes 1, 2 and 4. XRD results for complex 4 from Ferrari and Gasparri, 1976 are also given.

Complex 4 Complex 1 Complex 2Atomic pair

EXAFS results XRD results

EXAFS results EXAFS results

N R(Å) delr(Å) σ2(Å-2) R N R(Å) σ2(Å-2) N R(Å) σ2(Å-2)Cu1-S5 1 2.28 0.07 0.0093± 0.0009 2.21 1 2.24 0.0085 ± 0.0008 1 2.26 0.0084±

0.0009Cu1-S2 1 2.30 0.07 0.0093± 0.0009 2.24 1 2.27 0.0085 ± 0.0008 1 2.29 0.0084±

0.0009Cu1-S3 1 2.35 0.07 0.0093± 0.0009 2.28 1 2.30 0.0085 ± 0.0008 1 2.32 0.0084±

0.0009The EXAFS fitting results for both tetrahedral and trigonal (Cu) centers in complex 2 and 4 with 50% contribution from each site. XRD results for complex 4 from Ferrari and Gasparri, 1976 are also given.

Complex 4 Complex 2 Atomic

pairEXAFS results XRD

results EXAFS results

N R(Å) delr(Å) σ2(Å-2) R N R(Å) σ2(Å-2)Tetrahedral structure

Cu1-S1 1 2.36 0.051 0.0115 ± 0.0058 2.31 1 2.26 0.0080 ± 0.0007Cu1-S4 1 2.39 0.051 0.0115 ± 0.0058 2.33 1 2.28 0.0080 ± 0.0007Cu1-S3 1 2.39 0.051 0.0115 ± 0.0058 2.34 1 2.28 0.0080 ± 0.0007Cu1-S2 1 2.46 0.051 0.0115 ± 0.0058 2.40 1 2.35 0.0080 ± 0.0007

Trigonal structureCu1-S5 1 2.27 0.054 0.0056±0.0013 2.21 1 2.25 0.0040 ± 0.0008Cu1-S2 1 2.29 0.054 0.0056±0.0013 2.24 1 2.28 0.0040 ± 0.0008Cu1-S3 1 2.33 0.054 0.0056±0.0013 2.28 1 2.31 0.0040 ± 0.0008

52

S1

Cu S4 S2 S3

Tetrahedral geometry

S1

S2 S3

Trigonal planar geometry

Tetrahedral geometry about Cu center in complexes 2, 3 and 4, deduced from the EXAFS data analysis

Trigonal planar geometry about Cu center in complexes 1, 2 and 4, deduced from the EXAFS data analysis

53

The EXAFS fitting results for trigonal (Cu) center in complex 5 using theoretical model of an analogous complex.

Atomic pair

EXAFS results N R(Å) σ2(Å-2)

Cu1-S2 1 2.29 0.0056 ± 0.0010Cu1-S1 1 2.30 0.0056 ± 0.0010Cu1-Cl1 1 2.33 0.0091 ± 0.0053

Cl

2.33 2.30 2.29 S1 S2

The coordination geometry about Cu center in complex 5,deduced from the EXAFS data analysis and following Zhang et al. (2003). The values of bond lengths as determined by EXAFS data analysis are also shown.

54

5. XAFS study of aqua (diethylenetriamine) (isonicotinato) -copper(II) complex – inference of square-pyramidal geometry

X-ray absorption fine structure (XAFS) of aqua (diethylenetriamine) (isonicotinato) copper(II) complex has been investigated. The crystal structure of this complex is unavailable.

The X-ray absorption near edge structure (XANES) spectrum of the complex (C) has been compared with those of the standard compounds to estimate the coordination geometry and oxidation state of copper. The XAFS data of these compounds has been recorded at the same setting

Published in X-ray Spectrometry 43 (2014) 238 55

This study indicates that the copper center has +2 oxidation state and that it may be penta or hexa-coordinated.

56

The spectrum C of the studied complex has been further compared with those of the complexes (R1-R8) having square-pyramidal geometry and studied by me in earlier studies.Similarity has been observed between them indicating that the complex should have penta-coordinated square-pyramidal geometry.

R1-R8 are the eight copper (II) complexes studied by me earlier and are as follows: [Cu(L-phen)(bipy)(H2O)] (ClO4) (R1), [Cu(L-glu)(bipy)] (R2), [Cu(L-glu)(phen) (H2O)]. 3H2O (R3), [Cu(Ltyro)(bipy)(ClO4)].2H2O (R4), , [Cu(salen)] (R5), [Cu(salen) CuCl2].H2O (R6), [Cu(salophen)] (R7), and [Cu(salophen) CuCl2].H2O (R8). (where L-glu = L-glutamate, L-tyro = L-tyrosinate, bipy = 2,2’-bipyridine and phen = 1,10-phenanthroline), salen =N, N’-ethylenebis (salicylidenaminato) ; salophen = o-phenylenediaminebis (salicylidenaminato). 57

The same inference has been obtained from the study of the characteristic pre-edge and XANES features in XANES as well as in derivative XANES spectra. 58

This inference has been further examined by analysis of the extended X-ray absorption fine structure (EXAFS) spectrum.

The experimental EXAFS data has been fitted with three different theoretical models for tetra-coordination, penta-coordination, and hexa-coordination.

The tetra model is unable to provide a satisfactory fit so it has been ignored.

Although the penta and hexa models give comparable results, the parameters obtained indicate that the penta-coordinated model fits better to the experimental data than the hexa-coordinated model.

59

Extended X-ray absorption fine structure fitting of the theoretical curve generated using penta-coordination model in (a) R-space and (b) k-space.The experimental curve is shown by black line and the theoretical fit is shown by red line.

60

Extended X-ray absorption fine structure fitting of the theoretical curve generated using hexa-coordination model in (a) R-space and (b) k-space.The experimental curve is shown by black line and the theoretical fit is shown by red line.

61

The EXAFS fitting results for the complex using the two theoretical models generated by employing crystallographic data of penta-coordination and hexa-coordination complex

62

EXAFS fitting of the theoretical curve generated using penta-coordination model and by varying coordination number in (a) R-space and (b) k-space. The experimental curve is shown by black line and the theoretical fit is shown by red line.

63

The EXAFS fitting results for the complex employing the penta-coordination model by varying the coordination number

64

Coordination geometry about the Cu center in the complex asarrived from the present EXAFS study.

65

Four research papers on the study of the different methods of speciation using XAFS.

1. Copper K-edge XANES of Cu(I) and Cu(II) oxide mixtures Journal of Physics: Conference Series 190 (2009) /012084.

The paper has been downloaded for more than 3500 times and has been cited 20 times.

2. A comparative study of the methods of speciation using X-ray absorption fine structure

Acta Physica Polonica A 121 (2012) 647-652

3. Study of XAFS spectroscopic methods of speciation using mixtures of Cu(I) and Cu(II) chlorides Journal of Physics: Conference Series 430 (2013) 012045

4. Speciation of mixtures of Cu(I) and Cu(II) mixed ligand complexes using XAFS spectroscopic methods Spectroscopy Letters 46 (2013) 375-383 66

67

Definitions

•Chemical species are defined as specific forms of an element having different oxidation state or molecular structure etc.

•Determination of the relative quantity of the different species in a given sample is termed as speciation.

•X-ray absorption spectroscopy (XAS) is one of the best known structural techniques for speciation.

•In this technique, the X-ray absorption fine structure (XAFS) spectra of the sample is modelled by the spectra of well-defined chemical species as standards. This can be done both in the X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) regions.

1 & 2. ANALYSIS OF A MIXTURE OF CuO AND Cu2O

Published in Journal of Physics: Conference series 190 (2009) 012084 and in Acta Physica Polonica A 121 (2012) 647-652

Normalized copper K-edge XANES spectraThis work was done at EXAFS wiggler beamline 4–1 at the Stanford Synchrotron Radiation Laboratory (SSRL), Stanford, California, USA.

68

Methods of Speciation

To check the number of components and to confirm the existence of real components in a sample, the following two methods are used Principal Component Analysis (PCA) Target Transformation (TT)

To determine the percentages of species in a sample following methods are used : Linear Combination Fitting (LCF). Normalized difference absorption edge analysis (NDAES). Methods based on derivative spectra Residual Phase Analysis (RPA) A method based on the relative position of the edge.

69

0 2 4 6 8 10 12-2.0

-1.5

-1.0

-0.5

0.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

3

2

1

Wei

gh

ted

co

mp

on

ents

K (in Å-1)

First three components from PCA calculation performed in the EXAFS region and weighted by eigenvalues.

70

Predicted targets obtained through target transformation of the Cu Kedge EXAFS spectra for (a) Cu2O and (b) CuO.

First derivatives of XANES region for Cu2O, CuO and their mixture. Feature γ corresponds to the Cu (I) component. The height of this feature has been used to determine the percentage of Cu (I) in the mixture.

Normalized difference absorption edge spectra for

copper K-edge

71

Reduced statistical chi square obtained by varying the percentage of CuO using RPA performed in EXAFS region.

Results of the LCF for copper K-edge XANES spectra of mixture of Cu2O and CuO

72

S.No. Method of speciation

Percentages of componentsin the mixture

Cu2O CuO Max. % error

1.2.3.4.5.

LCFNDAESRPADer. Cu(I)*

Edge**

7371707479

2729302621

2 % 5 % 5 % 2 % 5 %

As prepared 75 25 -

Results of speciation of the mixture

LCF has been found to be better method as compared to other methods for finding the percentages of the components in the sample, but it can be applied only when the components have been identified.

73

3. ANALYSIS OF MIXTURES OF CuCl AND CuCl2

XANES spectra at the copper K-edge in metal, cuprous chloride, cupric chloride and their five mixtures M1 to M5. Also shown sharp feature P due to the Cu(I) 1s → 4p transition at 8986 eV, very weak peak W at 8978 eV (shown in inset) due to Cu(II) 1s → 3d transition, absorption-edge shoulder S and an intense white line C at 8995 eV attributed to the Cu(II) 1s→4p transition as well as to transitions to continuum states. The work was done EXAFS beamline X-19 A at BNL (USA).

74 Published in Journal of Physics: Conference Series 430 (2013) 012045

First derivatives of XANES region for CuCl, CuCl2 and their

mixtures M1 to M5. Feature A corresponds to the Cu (I) component and B corresponds to the Cu(II) component. These two features have been used to determine the percentages of species in the mixtures.

75

First three components from PCA calculation weighted by eigen values for mixture M3 (taken as representative example). For clarity, components have been displaced vertically.

76

Components Eigenvalues Var Cum var INDC1 10.875 0.487 0.487 0.29223C2 6.010 0.269 0.757 0.23626C3 3.291 0.147 0.904 0.22029C4 1.550 0.069 0.974 0.57370C5 0.573 0.025 1.0 NA

The parameters of the first five components obtained by PCA

Predicted targets obtained through target transformation of the Cu K-XANES spectra for (a) CuCl2 and (b) CuCl for mixture M3 (taken as representative example).

77

Results of XANES fitting, derivative XANES LC fitting, EXAFS LC fitting k2 chi and EXAFS LC fitting k3 chi for mixture M3 (taken as a representative example). Black and lines denote experimental and LC fit data respectively

78

derivative XANES LC fittingXANES fitting

EXAFS LC fitting k2 chi EXAFS LC fitting k3 chi

Normalized difference absorption edge spectra (NDAES) for XANES at copper K-edge. Curves have been obtained by subtracting spectra of CuCl2

and of the five mixtures (M1 to M5) from the spectra of CuCl. The height of positive peak α is the measure of Cu(I) in the mixture. 79

Mixture M1

M2 M3 M4 M5

Method of speciation

max. % error

I II I II I II I II I II

LCF ± 3 13.5

86.5 34.7 65.3 47.3 52.7 52.9 47.1 76.0 24.0

LCF der ± 5 12.5 87.5 33.6 66.4 44.3 55.7 51.3 48.7 75.2 24.8LCF k2 ± 7 12.7 87.3 41.2 58.8 52.1 47.9 58.3 41.7 75.8 24.2LCF k3 ± 6 11.7

88.3 39.8 60.2 51.8 48.2 58.6 41.4 74.3 25.7

NDAES ± 5 13.8

86.2 34.2 65.8 46.7 53.3 51.3 48.7 75.2 24.8

Der. Cu(I)* ± 3 18.0 82.0 36.5 63.5 47.0 53.0 53.0 47.0 77.0 23.0Der. Cu(II)**

± 5 15.2 84.8 39.4 60.6 54.5 45.5 60.6 39.4 75.6 24.4

Edge*** ± 10 9.0 91.0 42.8 57.2 51.3 48.7 57.0 43.0 84.9 15.1As prepared 15 85 35 65 50 50 55 45 75 25

Results of speciation as obtained from different methods. 'I' is the percentage of CuCl and 'II' is the percentage of CuCl2 in the mixture M1 to M5.

* LCF method for the case sum = 100. ** Method based on derivative spectra of Cu(I) component*** Method based on derivative spectra of Cu(II) component**** Method based on position of the edge

80

Mixture

M1

M2 M3 M4 M5

Method of speciation

max. % error

I II I II I II I II I II

LCF ± 3 13.5

86.5 34.7 65.3 47.5 53.4 52.8 46.5 75.8 23.6

LCF der ± 5 13.7 88.5 33.0 65.9 44.2 55.6 48.8 46.5 73.8 23.5LCF k2 ± 7 7.9 89.3 33.2 59.3 44.3 46.0 45.3

35.0 48.2 35.1

LCF k3 ± 6 6.1

90.3 28.6 61.6 51.8 48.2 58.6

41.4 74.3 25.7

As prepared 15 85 35 65 50 50 55 45 75 25

The percentages of CuCl and CuCl2 in the mixtures, as determined

from LCF method for the case sum ≠ 100.

81

4. ANALYSIS OF MIXTURES OF Cu(I) AND Cu(II) COMPLEXES HAVING TWO COMPONENTS

XANES spectra of copper metal, Cu(I) complex [Cu (thu) Cl 0.5H2O] (1) and

Cu(II) complexes [Cu(L-phen)(bpy) H2O] (2), [Cu(L-tyr)(phn) 2.5H2O] (3)

and [Cu(din)(ina)] (4).

82 Published in Spectroscopy Letters 46 (2013) 375-383

Results of PCA

83First four components for mixtures (a) M1, (b) M2, and (c) M3 from PCA calculation performed in the XANES region and weighted by eigenvalues.

(a) M1(b) M2

(c) M3

Results of TT

(a) Predicted targets for mixture M1 obtained through target transformation of the Cu K-edge EXAFS spectra for (i) [Cu (thu) Cl 0.5H2O] and (ii) [Cu(L-phen)(bpy) H2O].

(b) Predicted targets for mixture M2 obtained through target transformation of the Cu K-edge EXAFS spectra for (i) [Cu (thu) Cl 0.5H2O] and (ii) [Cu(L-tyr)(phn) 2.5H2O].

(c) Predicted targets for mixture M3 obtained through target transformation of the Cu K-edge EXAFS spectra for (i) [Cu (thu) Cl 0.5H2O] and (ii) [Cu(din)( ina)].

(a) (b)(c)

(i)

(ii)

(i) (i)

(ii)(ii)

84

First derivatives of XANES region for mixtures (a) M1, (b) M2 and (c) M3 and their Cu(I) and Cu(II) components. Feature γ corresponds to the Cu (I)

component.

85

(a) M1(b) M2

(c) M3

Normalized difference absorption edge spectra for copper Kedge XANES for (a) M1, (b) M2 and (c) M3 . Black line has been obtained by subtracting Cu(II) component spectra from Cu(I) component spectra. Similarly, red line has been obtained by subtracting Cu(II) component spectra from the spectra of mixture.

(a) M1 (b) M2

(c) M3

86

Results of the LCF for copper K-edge XANES spectra of mixtures. Black and blue lines denote experimental and LC fit data respectively. Fractions of Cu(I) and Cu(II) complexes making up the fitted spectra are shown by red and green lines respectively. The goodness-of-fit between experimental data and the LC fit data can be seen from the little difference between the two data, plotted as blue line. 87

M1Components

[Cu (thu) Cl 0.5H2O] (1)

[Cu(L-phen)(bpy) H2O] (2)

As prepared 50.0 50.0LCF 47.3 52.7Derivative 53.8 46.2NDAES 53.4 46.6

M2Components

[Cu (thu) Cl 0.5H2O] (1)

[Cu(L-tyr)(phn) 2.5H2O] (3)

As prepared 50.0 50.0LCF 50.4 49.6Derivative 54.7 45.3NDAES 51.2 48.8

M3Components

[Cu (thu) Cl 0.5H2O] (1)

[Cu(din)(ina)] (4)

As prepared 50.0 50.0LCF 55.0 45.0Derivative 55.1 44.9NDAES 51.7 48.3

Results of speciation of mixtures of the complexesusing different methods

88

X-ray Absorption Fine Structure (XAFS) Spectroscopy – A ReviewProceedings of the Indian National Science Academy 79 (2013) 921-966

Review article on XAFS

This review describes the basic phenomenon of XAFS, theory of EXAFS and the method of extracting structural parameters by EXAFS which relate to the local environment surrounding the absorbing atom. Also, it has been pointed out that XANES can be used to extract information about the oxidation state, three dimensional geometry, and coordination environment of elements under investigation. There are numerous examples of the applications of the XAFS in various fields in the literature. Some selected examples are cited here and discussed so as to give the reader a glimpse of the usefulness and versatility of the XAFS. The two types of EXAFS beamlines available at the synchrotron facilities have been described. The details of BL-8 dispersive EXAFS beamline at 2 GeV Indus-2 synchrotron source at Raja Ramanna Center for Advanced Technology (RRCAT), Indore, India have been given. Details regarding experiment and analysis of the XAFS data have been given in this review so that any one who wants to do research work in the field of XAFS may get necessary information at one place. This is important because the EXAFS beamlines at the Indus-2 synchrotron have become easily available to Indian workers which were not available until now.

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90