x-ray absorption fine structure (xafs) studies of some

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EXAFS oscillations, it is not a particularly convenient form for visualizing the information ..... Introduction to XAFS: A practical guide to X-ray absorption fine structure ...... R=1.0 Å. Note that a factor of 2 is divided out in the Fourier transform of the ...... Cu1-N5B. 1 2.65 0.025 0.0096 ± 0.0054. 2.62. (c) Complex 3. Atomic pair.
X-RAY ABSORPTION FINE STRUCTURE (XAFS) STUDIES OF SOME COPPER COMPOUNDS AND COMPLEXES OF BIOLOGICAL IMPORTANCE

A THESIS SUBMITTED TO VIKRAM UNIVERSITY, UJJAIN FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN PHYSICS

BY

ABHIJEET GAUR

SUPERVISOR

DR. B.D. SHRIVASTAVA PROFESSOR (RETD.) SCHOOL OF STUDIES IN PHYSICS

VIKRAM UNIVERSITY UJJAIN (INDIA)

2012

Dedicated to my grandfather Late Shri Chandrashekhar Gaur

DECLARATION BY THE CANDIDATE

I declare that the thesis entitled "X-RAY ABSORPTION FINE STRUCTURE (XAFS)

STUDIES

OF

SOME

BIOLOGICAL IMPORTANCE"

COPPER

COMPOUNDS

AND

COMPLEXES

OF

is my own work conducted under the supervision of

Dr. B.D. Shrivastava and approved by Research Degree Committee. I have put in more than 200 days of attendance with the supervisor at the centre. I further declare that to the best of my knowledge the thesis does not contain any part of any work, which has been submitted for the award of any degree either in this University or any other University/Deemed University without proper citation.

(Abhijeet Gaur)

(Dr. B.D. Shrivastava) Signature of the Supervisor

Signature of the Candidate

Forwarded

Professor and Head, School of Studies in Physics, Vikram University, Ujjain

Dr.B.D.Shrivastava

Phone:- 0734-2511472 Residence:- 32 Mahashweta Nagar UJJAIN 456010

M.Sc., Ph.D.,

Professor (Retd.) School of Studies in Physics Vikram University, Ujjain Ex. Member, Executive Council Dean, Faculty of Science Chairman, Board of Studies in Physics

Certificate This is to certify that the work entitled "X-RAY ABSORPTION FINE STRUCTURE (XAFS) STUDIES OF SOME COPPER COMPOUNDS AND COMPLEXES OF BIOLOGICAL IMPORTANCE"

is a piece of research work done by Abhijeet

Gaur under my guidance and supervision for the degree of Doctor of Philosophy of Vikram University, Ujjain and that the candidate has put-in an attendance of more than 200 days with me. To the best of my knowledge and belief the thesis: (i)

embodies the work of the candidate :

(ii)

has duly been completed;

(iii)

fulfills the requirements of the Ordinance relating to the Ph.D. degree of the University; and

(iv)

is up to the standard both in respect of contents and language for being referred to the examiner.

, 2012 (Dr. B.D. Shrivastava) Signature of the Supervisor

Forwarded

Professor and Head, School of Studies in Physics, Vikram University, Ujjain

ACKNOWLEDGEMENT I am deeply grateful to my supervisor Dr. B. D. Shrivastava for giving me the confidence to explore my research interests and the guidance to avoid getting lost in my exploration. Incidentally, he has also been supervisor of my father’s Ph.D. thesis. He is a fabulous advisor: sharp, cheery, perceptive, and mindful of the things that truly matter. His selfless perseverance and attention to my work consistently found pearls among my heaps of data and he has thrown enough research questions my way to keep me busy the rest of my life. His continuous encouragement and guidance kept my enthusiasm alive, without which it would have been difficult to complete my thesis. He always clearly defined the problems and actively participated in their solutions with the help of his extensive knowledge and intuition. His sincerity, punctuality and disciplined work groomed my research aptitude. It is an honor for me to be one of his students. My special thanks are due to Dr. J. Prasad and Dr. K. Srivastava, Chemistry Department, University of Allahabad, Allahabad, for providing me the copper complexes studied in the present investigation. I am also grateful to them for their enthusiastic interest and help in the present work. I wish to express my sincere thanks to Dr. S. K. Ghosh (Head of the Department), Dr. G. K. Upadhyay, Dr. S. B. Shrivastava, Dr. R. K. Chhajlani, Dr. S. Dubey, Dr. N. Yadav, Dr. G. Ahirwar, Dr. N. Nimje and all the members of the School of Studies in Physics, Vikram University, Ujjain, for their valuable help. I am extremely thankful to Dr. S. K. Deb, Raja Ramanna Centre of Advanced Technology (RRCAT), Indore and Dr. S. N. Jha, Dr. D. Bhattacharyya, A. Poswal and Dr. N. K. Sahoo, Bhabha Atomic Research Centre (BARC), Mumbai, for providing me the beamline and other necessary facilities at Indus-2, RRCAT, Indore. I am thankful to Dr S. Khalid, Brookhaven National Laboratory NSLS, Upton, NewYork for his help in recording the spectra at BNL, NewYork. I am thankful to Dr C. R. Natoli, Dr. M. Benfatto and others for taking keen interest in explaining me the theory and practice of XAFS when I attended the Dissemination workshop on SRS-MST held at the Laboratori Nazionali di Frascati, Frascati, Italy. I am thankful to Dr. Bruce Ravel, Dr. Adam Webb and others for teaching me the technique of EXAFS data analysis when I attended the 1st ASEAN Workshop on X-ray Absorption Spectroscopy held at Synchrotron Light Research Institute (SLRI), Nakhon Ratchasima, Thailand.

Thanks are due to ICTP-ELETTRA authorities for providing me support by sanctioning an ICTP grant for doing experiments at ELETTRA, Italy. I am thankful to Dr. Olivi Luca for his help while recording the spectra. Thanks are due to Madhya Pradesh Council of Science & Technology (MPCST), Bhopal (India) for a research grant and also for the travel support in attending and presenting the papers at the 14th International EXAFS conference held at Camerino, Italy. I have the pleasure to thank my fellow research workers Dr. Vijay Kumar Hinge, Dr. Ajita Johari, Dr. Renuka Kendurkar, Shri Aman Deep Aacharya for their cheerful cooperation and support that created friendly and productive atmosphere during the course of research work. Special gratitude goes to Dr. (Mrs.) Rashmi Shrivastava for her constant encouragement and hospitality during the course of this research work. She has made available her support in a number of ways during this research work. I am highly thankful my friend Mr. Vikram Singh Raghuwanshi, Helmholtz Centre Berlin for Materials and Energy, Berlin, Germany for making available most of the research papers during the course of this research work. I wish to thank my best friend Mr. Sudarshan Singh for helping me get through the difficult times, and for all the emotional support, entertainment, and caring he provided. I acknowledge gratefully the help of my friends, well wishers and relatives, whose names have not appeared here, but who helped me directly or indirectly towards the successful completion of this thesis. I express my deep sense of gratitude to my dearest sisters and all my family for their constant encouragement, which gave me courage and confidence to materialize my dreams. Last but not least, I would like to thank my parents Mrs. Kusum Gaur and Dr. Dinesh Chandra Gaur for their unconditional support, both financially and emotionally throughout my research work. In particular, the patience and understanding shown by my mother during the work is greatly appreciated. I know, at times, my temper is particularly trying.

(Abhijeet Gaur)

PREFACE X-ray absorption spectroscopy (XAS) has been extensively used in the past to obtain information about molecular structure viz., the valency, bond type, ionic charges, coordination stoichiometry etc. Many research centers in Indian universities and institutes have been doing extensive research work in this field since 1950 or so. Some of the important centers for X-ray absorption and emission spectroscopic research with principal investigators can be recollected as follows: Lucknow (Dr. B. G. Gokhale), Pune and Nagpur (Dr. C. Mande), Mumbai ( Dr. B. D. Padalia), Jodhpur (Dr. A. N. Nigam, Dr. S. N. Soni), Jaipur (Dr. K. B. Garg), Kanpur (Dr. Amarnath Nigam), Allahabad (Dr. G. B. Deodhar, Dr. B. K. Agarwal, Dr. H. L. Nigam), New Delhi ( Dr. V. G. Bhide), Indore (Dr. A. Mishra) and Ujjain (Dr. B. D. Shrivastava). At all of these centers, the laboratory X-ray spectroscopic set-ups were in use which employ photographic method of registration of spectra. These types of set-up comprise of low power (0.5kW - 3kW) X-ray tubes and Cauchois-type curved mica crystal spectrographs employing X-ray films as detectors. After obtaining a number of spectrograms, the analog and digital spectral records are obtained with the help of microphotometers. These analog and digital spectral records were used to be analyzed manually. The results about X-ray absorption edge energies, edge structures, near edge structures and extended fine structures were being reported. The data was used to be generally analyzed qualitatively and empirically to yield useful information about molecular structure. The data was also analyzed through some established relations to yield information about valency, effective nuclear charge, coordination type, average bond length etc. Unfortunately, nearly all of these centers ceased to work in 1980s because research workers around the world had started using X-rays from synchrotron instead of Xray tubes for recording the X-ray absorption spectra. Unfortunately, the synchrotron was not available in India at that time. Indian synchrotron could become operational only a few years back. Even the last two theses from our laboratory (Hinge, 2010, Johari, 2011) were mainly based on the work done on laboratory set-ups. X-ray absorption spectroscopy (XAS) refers to the details of how X-rays are absorbed by an atom at energies near and above the core-level binding energies of that particular atom. The absorption of X-rays on the high energy side of absorption edges does not vary monotonically in condensed matter but has a complicated behavior which extends past the edge by an amount typically of the order of 1 keV. This non-monotonic variation has received the name of X-ray absorption fine structure (XAFS). The X-ray absorption fine structure is typically divided into two regimes: X-ray absorption near-edge (XANES) structure and extended X-ray absorption fine-structure (EXAFS) structure. The EXAFS has been known for over 80 years. There was a lot of confusion about the theory of EXAFS. The situation changed when Sayers, Stern and Lytle (1971) pointed out, based on a theoretical expression of the EXAFS (Sayers et al., 1971) that a Fourier transform of the EXAFS function with respect to the photoelectron wave number should peak at distances corresponding to nearest neighbor coordination shells of atoms. The

introduction of the Fourier transform changed EXAFS from a confusing scientific curiosity to a quantitative tool for structure determination. The experimental X-ray absorption spectroscopic data obtained from X-ray tube sources is plagued by noise and systematic errors. It wasn't until the 1970s that high brilliance synchrotron radiation began to be used to obtain absorption spectra. Experimental techniques have continued to develop over the years, and due to the exponential increase in brilliance over time, high quality EXAFS data is now routinely collected at a variety of second and third generation synchrotron sources. Over the past three decades, the technique of EXAFS has made great strides toward the goal of providing such information. The existence of intense new synchrotron X-ray sources alone was not enough to achieve this goal, even though such facilities spurred considerable progress. In addition, the full success of the EXAFS technique must be attributed in large part to advances in theory, which have led ultimately to a highly quantitative understanding of the phenomena. When in October 2008, I got myself enrolled as a Ph.D. research scholar to work in the field of XAFS, my supervisor decided that I shall not be doing experimental research work on laboratory X-ray absorption spectroscopic set-ups, using X-ray tubes, available in our laboratory, but instead I shall try to work on synchrotron XAFS set-ups. The EXAFS beamline was going to become operational at Indus-2 at Raja Ramanna Center for Advanced Technology (RRCAT), Indore. Before working there, fortunately I got hold of the XAFS data recorded by my supervisor, when he worked with Prof. E. A. Stern at the University of Washington, Seattle, USA. The data was recorded at XAFS beamline at Stanford Synchrotron Radiation Laboratory (SSRL), Stanford, USA. This data could not be analyzed earlier because the software for its analysis was unavailable. I analyzed the data using the XAFS data analysis programs Athena and Artemis, which had become freely available in 2008. As a result of this analysis, we wrote two papers which were presented at 14th International EXAFS conference held at Camerino, Italy. In April 2010 and October 2011, we got beamtimes at EXAFS beamline BL-8 at Indus-2, RRCAT, where we recorded data of several copper compounds and complexes. This work has been included in this thesis. The BL-8 beamline is a dispersive EXAFS beamline and has been recently commissioned. While working on it we felt the necessity of devising the correct method for the calibration of the beamline. Hence, myself with other workers have proposed a method for such calibration (Gaur et al., 2011). During my tenure as research scholar, I was fortunate to get opportunities to visit foreign countries where synchrotrons are situated and where EXAFS beamlines are available. The details of my foreign visits which have helped me in the present research work is given below in brief.

In 2009, I had the opportunity of attending the 14th International EXAFS conference held at Camerino, Italy from 26th July to 1st August, 2009 and presenting my two research papers (Gaur et al., 2009, Joshi et al., 2009) which were later published in Journal of Physics: Conference Series, vol. 190. In 2010, I attended the Dissemination workshop on SRS-MST held at the Laboratori Nazionali di Frascati, Frascati, Italy from 29 March to 2nd April, 2010. In this workshop the theory and practice of XAFS was taught by Dr C . R. Natoli, Dr. M. Benfatto and others. Again in 2010, I got opportunity to attend the 1st ASEAN Workshop on Xray Absorption Spectroscopy held at Synchrotron Light Research Institute (SLRI), Nakhon Ratchasima, Thailand from 29-31 July, 2010. There, I got a chance to visit the XAS beamline at SLRI. In this workshop I learnt from Dr. Bruce Ravel and Dr. Adam Webb the technique of EXAFS data analysis and specially the fitting of theoretical model to the experimental EXAFS data. Though, EXAFS data analysis programs Athena and Artemis are available, the fitting is still a tricky job and has to be done in the correct manner otherwise the results obtained are not good. Since, Dr Bruce Ravel is one of the persons mainly responsible for writing these programs, I was lucky to learn from him how to correctly use these programs. It was because of attending these two workshops that I got confidence for doing analysis of the EXAFS data. In 2011, I again got an opportunity to do research work in a foreign country. Myself along with my supervisor were allotted beamtime of 48 hours on XAFS beamline 11.1 at ELETTRA Synchrotron Light Source, Trieste, Italy from 15-21 June, 2011. There we recorded the XAFS spectra of several copper compounds and complexes. The results of these studies have been included in the present thesis. During the course of my work, specially while analyzing the EXAFS data, generating the theoretical models and fitting them to the experimental EXAFS data, I faced difficulties on a number of occasions. I discussed these difficulties on the online facility of [email protected]. The experts of this mailing list helped me a lot in solving the difficulties. In the present thesis, the X-ray absorption fine structure (XAFS) spectroscopy has been used to study copper compounds and complexes. Studies have been done using both EXAFS and XANES spectroscopies. Basically, following two types of studies have been made. Firstly, EXAFS study at the K-edge of copper in mixed ligand copper complexes of biological significance have been done to yield useful and important information about the molecular structure of the complexes which are mononuclear, binuclear as well as trinuclear.

Secondly, an evaluative and comparative study of the different methods of speciation using XANES at the K-edge of copper have been done by taking several mixtures of copper compounds and complexes.

The thesis is divided in ten chapters. Chapter I is introductory in nature and describes the basic phenomenon of absorption of X-rays. The terms used in the X-ray absorption spectroscopy have been explained. Theory of EXAFS has been given in brief and the method of extracting structural parameters has been outlined. 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 and that the parameters determined by XANES and EXAFS relate to the local environment surrounding the absorbing atom. The reasons for choosing the five series of mixed ligand complexes of copper studied in this thesis using EXAFS (in chapters IV to IX) have been outlined. The use of XANES has been discussed, specially in speciation. It has been shown that by taking standards of well-defined chemical species, analysis of XANES can be used to determine metal speciation, i.e., determination of the chemical forms along with the relative quantity of the different species in a given sample. The need for making a comparative study of the different methods of speciation (in chapter X) has been outlined. Chapter II gives the experimental details. The copper complexes studied in this thesis have been prepared by Dr. Jagdish Prasad and Dr. Krishna Srivastava at the Department of Chemistry, Allahabad University, Allahabad. The absorption screens have been prepared by the author following standard methods at RRCAT, Indore. The details of the four EXAFS beamline at four different synchrotron facilities, where the X-ray absorption spectra have been recorded, are described in this chapter. The copper K-edge EXAFS spectra of the complexes studied in chapters IV, VII and IX have been recorded at the BL-8 dispersive EXAFS beamline at 2 GeV Indus-2 synchrotron source at Raja Ramanna Center for Advanced Technology (RRCAT), Indore, India. The copper K-edge XAFS spectra of the copper complexes studied in chapter V, VI and VIII were recorded at EXAFS beamline 11.1 at ELETTRA Synchrotron Light Laboratory, Basovizza, Italy. The copper K-edge XAFS spectra of the copper compounds and their mixtures studied in chapter X were recorded at three EXAFS beamlines, namely, (1) EXAFS beamline X-19A at National Synchrotron Light Source (NSLS), Brookhaven National Laboratory, Upton, New York, USA, (2) EXAFS beamline 11.1 at ELETTRA Synchrotron Light Laboratory, Basovizza, Italy and (3) EXAFS wiggler beamline 4–1 at the Stanford Synchrotron Radiation Laboratory (SSRL), Stanford, California, USA. In chapter III, the method of calibration of BL-8 dispersive EXAFS beamline at 2 GeV Indus-2 synchrotron source at Raja Ramanna Center for

Advanced Technology (RRCAT), Indore, India has been outlined (Gaur et al., 2011, Johari, 2011). A comparative study of the EXAFS spectra recorded at this beamline with those recorded at three other well known synchrotron EXAFS beamlines has been done in order to evaluate the quality and reliability of the recorded data and the usefulness of this beamline. It has been demonstrated that the results obtained from the EXAFS spectra recorded at this beamline are comparable to those obtained from other synchrotron EXAFS beamlines. This attempt appears to be the first in this direction. Chapters IV-VIII describe the results of XAFS study at the K-edge of copper in five different series of copper complexes. The studied copper complexes are interesting from the point of view of analysis of the EXAFS spectral data. First series has binuclear monohydroxo-bridged and dihydroxo-bridged copper(II) complexes. Second series has copper(II) mixed ligand complexes, having analogous structures. Third series has Schiff-base mononuclear and binuclear copper(II) salen/salophen complexes. Fourth series has mixed ligand copper(II) complexes having different coordination environments and geometries. Fifth series has copper (I) thiourea complexes having different types of coordination environment. In chapter IX, a trinuclear Schiff-base copper complex in which three metal sites are present, has been studied. Chapter X gives the details of work done on speciation. The different methods of speciation have been described in detail. The objective of the present work is to make a comparison of the different methods of speciation by taking several examples of mixtures of Cu(I) and Cu(II) compounds. Four different types of studies have been done for this purpose. The present work represents a transition from laboratory based experiments to highly technological synchrotron based experiments, from X-rays from X-ray tubes to X-rays from synchrotrons and from semi-empirical and qualitative analysis of the X-ray absorption data to its quantitative analysis. The work has been done at four different beamlines at four synchrotron facilities. In India, the work has been done on recently developed Indus-2 synchrotron facility which was not earlier available to Indian workers. For the last forty years research workers in our laboratory were doing experiments on laboratory set-ups. Now, it is hoped that future research workers not only from our laboratory but also from other Indian laboratories will do experiments on synchrotrons. Hence, details regarding experiment and analysis of the XAFS data have been given at the appropriate places in the thesis so that any body who wants to start research work in the field of XAFS may get necessary information at one place. I consider this as important because the beamtime at EXAFS beamline at Indus-2 synchrotron facility may easily become available to Indian workers which was not available uptil now. The references for all the chapters are given at the end of the thesis.

The author has published six research papers. They are given in the appendix. In the appendix are also reproduced the features of the four computer software programs Athena, Artemis, Hephaestus and SixPack which have been used in the present thesis for XAFS data analysis, in order to make readers well acquainted with these software programs.

(Abhijeet Gaur)

CONTENTS

CHAPTER

PAGE

1.

Introduction

1

2.

Experimental

55

3.

BL-8 dispersive EXAFS beamline at Indus-2 synchrotron – its calibration and a comparative study of the spectra recorded at this beamline with other beamlines.

99

4.

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

122

5.

EXAFS analysis of mixed ligand copper (II) complexes by fitting different theoretical models.

140

6.

XAFS investigations of copper (II) complexes with tetradentate Schiff base ligands.

167

7.

EXAFS analysis of mixed ligand copper complexes having ligands 4,4' dimethyl-2,2'-bipyridine and nicotinic acid.

191

8.

EXAFS study of multinuclear copper (I) thiourea mixed ligand complexes.

210

9.

EXAFS analysis of Schiff-base trinuclear copper complex

239

10.

A comparative study of the methods of speciation using X-ray absorption fine structure (XAFS) at Cu K-edge in copper compounds and their mixtures.

256

References

324

Appendix

335

List of published research papers and their copies

345

CHAPTER I INTRODUCTION 1.1 X-rays X-rays are electromagnetic waves in the wavelength range from ~25Ǻ to 0.025 Ǻ, i.e., having wavelengths much shorter than visible light, but longer than high energy gamma rays. The conventional source of X-rays is X-ray tube, which can be sealed fixed target tube, rotating anode tube or demountable tube. In an X-ray tube the electrons emitted from the cathode are accelerated towards the metal target anode by an accelerating voltage of typically 50-100 kV. The high energy electrons interact with the atoms in the metal target. Sometimes the electron comes very close to a nucleus in the target and is deviated by the electromagnetic interaction. In this process, which is called bremsstrahlung (braking radiation), the electron looses much energy and a photon (X-ray) is emitted. The energy of the emitted photon can take any value up to a maximum corresponding to the energy of the incident electron. The process can be thought as if the electron is emitting a series of photons with varying energies. These emitted photons are ‘continuous X-rays’. The high energy electron can also cause an electron close to the nucleus in a metal atom to be knocked out from its place. This vacancy is filled by an electron further out from the nucleus. The well defined difference in binding energy, characteristic of the material, is emitted as a mono-energetic photon. When detected this X-ray photon gives rise to a characteristic X-ray line in the energy spectrum. Thus, the spectrum of the radiation emitted from an X-ray tube consists of characteristic spectrum of the target superimposed over the continuous spectrum. Their wavelength is well suited to study crystal structures and details of the human body. Because of the many varied properties of X-rays, they have been used in various applications in science and industry. X-rays are used a lot in medicine to the great benefit of mankind. In the present thesis, investigations have been carried out on X-ray absorption spectra using X-rays from synchrotrons instead of X-rays from X-ray tubes.

1

1.2 Synchrotron as X-ray source The modern and most intense source of X-rays is a synchrotron. In a synchrotron, the electrons are accelerated and are directed into storage ring which has auxiliary components such as bending magnets and insertion devices (undulators or wigglers). These supply the strong magnetic fields perpendicular to the beam which are needed to convert the high-energy electron energy into light or some other form of electromagnetic radiation. The electrons can be maintained for many hours in the storage ring. In a synchrotron storage ring, in which the electrons have more than 1 GeV energies, radiations are obtained in the X-ray region. The most important property of synchrotron radiation is its brightness. Apart from this, the broad spectral range, pulse time structure, natural collimation, high vacuum environment, high polarization, small source-spot size and stability make synchrotron radiation a unique and rather extraordinary source for a wide variety of science and technological experiments (Winick and Doniac, 1980). An important point which should be noted is that the synchrotron radiation consists of only continuous X-rays and no characteristic X-rays. With these characteristics, the synchrotron radiation has become extremely useful for X-ray absorption spectroscopic work in the past three decades. 1.3 X-rays absorption A monochromatic beam of X-rays of the energy E, which passes through a homogeneous sample of the thickness x, is attenuated (fig. 1.1). In analogy to the Lambert-Beer law (Agarwal 1991), this attenuation can be described by: -µ(E).x

I(E) = I0(E) e

(1.1)

where I0(E) and I(E) are the incident and transmitted X-ray intensities, and µ(E) is the linear absorption coefficient, which describes how strongly X-rays are absorbed as a function of X-ray energy E. Generally, µ(E) smoothly decreases as the energy increases (approximately as 1/E3), i.e., the X-rays become more penetrating. At certain energies, the absorption increases drastically and gives rise to an absorption edge. Each such edge occurs when the energy of the incident photons is just sufficient to cause excitation of a core electron of the absorbing atom to a continuum state, i.e. to produce a photoelectron. Thus, the energies of the absorbed radiation at these edges correspond to the binding 2

energies of electrons in the K, LI, LII and LIII etc, shells (1s1/2, 2s1/2, 2p1/2 and 2p3/2 orbitals (states)) of the absorbing elements. Accordingly, the K absorption edge arises from the electronic transitions from innermost 1s states (K level) to unoccupied states above the Fermi energy (EF) level. Beyond the absorption edge the absorption coefficient decreases monotonically with increasing energy, until the next absorption edge is reached. In the present work, investigations have been carried out at the K absorption edge of copper in its compounds and complexes. 1.4 X-ray absorption spectroscopy – XANES and EXAFS Although most of the absorption spectrum is quite smooth, oscillatory features called fine structure is found directly above an edge. This fine structure is intrinsically quantum mechanical phenomenon that is based on the X-ray photoelectric effect, in which an X-ray photon incident on an atom within a sample is absorbed and liberates an electron from an inner atomic orbital (e.g., 1s). The “photoelectron” wave scatters from the atoms around the X-ray absorbing atom, creating interferences between the outgoing and scattered parts of the photoelectron wave function. These quantum interference effects cause an energy-dependent variation in the X-ray absorption probability, which is proportional to the X-ray absorption coefficient, a measurable quantity. This fine structure contains a wealth of local structural information. When properly decoded these modulations provide information about the structure, atomic number, structural disorder, and thermal motions of neighboring atoms. Traditionally, this fine structure is split into two energy regions. The first termed as X-ray absorption near edge structure (XANES), occurs in the region from the edge to approximately 40eV above the edge, while the second termed as the extended X-ray absorption fine structure (EXAFS) which extends from 40 eV to 1000 eV above the edge. The reason for this division into the XANES and EXAFS regions is that the XANES region is theoretically difficult to describe, while the EXAFS region is relatively simple to interpret. XANES is sensitive to the treatment of interactions between the photoelectron and the core hole, while the effects of the core hole on the EXAFS are relatively weak. Quantitative analysis of EXAFS has been available since the 1970s and standard techniques 3

have been developed to extract the parameters of interest. Quantitative XANES analysis has only been available for a few years and is not a widely used technique. (Kas, 2009) X-ray absorption spectroscopy (XAS) refers to the details of how X-rays are absorbed by an atom at energies near and above the core-level binding energies of that particular atom. XAS is the modulation of an atom’s X-ray absorption probability due to the chemical and physical state of the atom. Following the division of fine structure into the two energy regions, i.e., XANES and EXAFS, the X-ray absorption spectroscopy is also divided into two regimes: X-ray absorption near-edge spectroscopy (XANES) and extended X-ray absorption fine-structure spectroscopy (EXAFS). The term “XAFS” is a broad one that comprises several different techniques: EXAFS (extended X-ray absorption fine structure); XANES (X-ray absorption near edge structure); NEXAFS (near edge XAFS); and SEXAFS (surface EXAFS). (Bunker, 2010) X-ray absorption fine structure (XAFS) spectroscopy is a unique tool for studying, at the atomic and molecular scale, the local structure around selected elements that are contained within a material. XAFS can be applied not only to crystals, but also to materials that possess little or no long-range translational order: amorphous systems, glasses, quasicrystals, disordered films, membranes, solutions, liquids, metalloproteins and even molecular gases. This versatility allows it to be used in a wide variety of disciplines: physics, chemistry, biology, biophysics, medicine, engineering, environmental science, materials science, and geology. 1.5 Absorption edge and its position X-ray absorption edge is an arctangent curve (Richtmyer et al., 1934). The inflection point on this curve gives the position of the absorption edge. The energy of this point corresponds to the binding energy of the inner shell from which the electron has been ejected during the absorption process. When the absorption edge is found to split in two or more components, the inflection point of the first rise in the absorption edge corresponds to the binding energy corresponding to that edge. In case of copper compounds and complexes studied in the present thesis, the absorption edge is found to split in 4

two components K1 and K2. In such cases the energy (EK1) of the inflection point on the K1 edge corresponds to the binding energy E0 or EK of the K level. The best method to determine the exact position of the inflection point is to compute the first derivative of the µ(E) versus E curve. The first maximum on the first derivative curve gives the position of the inflection point and hence the position of the absorption edge. An alternative method is to compute the second derivative of the µ(E) versus E curve. The first zero crossing point on this second derivative curve also gives the position of the absorption edge correctly. The second derivative spectrum is generally used whenever there is any difficulty in measuring the position of the edge from the first derivative spectra. The above procedure holds good even in those cases where the absorption edge is found to split in two or more components. For the K absorption edge, the position of the edge is written as EK in eV. The determination of the position of the absorption edge can be illustrated by taking an example, say, of K-absorption edge of copper metal. Fig.1.2(a) shows the Cu metal K absorption spectra (µ(E) vs. E spectra). This figure also shows the pre-edge, XANES and EXAFS regions. Fig.1.2(b) shows the small portion (i.e., the XANES region) of fig.1.2(a). The first derivative spectra of fig.1.2(b) is shown in fig.1.2(c), while the second derivative spectra is shown in fig.1.2(d). Some of the different terms defined above have been depicted in these figures and the reasons for their existence are discussed below. (Kau et al., 1987) The K absorption edge of Cu metal, LMA, is found to split in two components K1 and K2. The initial rise LM in the Cu metal K-edge (often called the K1 edge) arises from the transitions from 1s states to unoccupied states having admixed 4s-4p-3d symmetry. The energy EK1 of the inflection point of this initial rise, as determined from the first peak in the derivative spectra, corresponds to the Fermi energy EF (8980.5 eV). The second absorption rise MA (often called the K2 edge) arises from the transitions to the Laporte-allowed states of nearly pure 4p symmetry. As the inflection point on K1 locates the Fermi level EF, above EF the s-p-d admixed states first acquire pure s symmetry just around M and finally pure 4p symmetry around the inflection point on K2. The kink at M arises because the transition probability suddenly decreases for 5

the pure s character of states at M and this causes a decrease of the absorption. The structure K2 that ends peak A is assigned 1s→4p transitions, and the region beyond A shows maxima of absorption, corresponding to the transitions 1s→np, n = 5, 6, 7, etc. The energy EA of this peak A can be called the principal absorption maximum, as determined from the second zero crossing in the derivative spectra. Because the curve between M and A is called the K2 edge, the energy of the inflection point of this second rise, as determined from the second peak in the derivative spectra, is written as EK2. The difference between the energies EA and EK1, i.e., EA - EK1 is called the edge-width. There is no pre-absorption features in the Cu metal K absorption spectra. Such a feature is a characteristic of K absorption spectra of Cu(II) compounds and is attributed to the dipole forbidden, quadrupole allowed, 1s→3d transition. The value of EK1 for Cu metal is 8980.5 eV (Deslattes et al. 2003). However, for EXAFS data analysisthis value is generally taken as ita theoretical value, i.e., 8979 eV. 1.6 Chemical shift (Shift in the position of the absorption edge) It is an established fact that absorption edge shifts towards higher or lower energy side relative to metal edge, depending upon whether the absorbing atom bears positive or negative charge. In the X-ray absorption measurement, the energy of the position of an edge is equal to the difference of the energies of the initial and final states involved in the transition. If a valence electron is removed from the absorbing atom, the effective potential seen by the initial and final states changes. The change in the transition energy, which is displayed as the shift of the absorption edge due to the removal of an electron, is approximately equal to the difference in the energy variation of the two states, on account of the screening change. The shift of the X-ray absorption edge i (i = K, L, M …) of an element in a compound with respect to that of the pure element is written as: ∆Ei = Ei (compound) – Ei (element)

6

(1.2)

In general, the shift ∆E is positive (towards high energy) and ranges usually from ~1 eV to ~15 eV. In this thesis the chemical shift of the Cu K- absorption edge in any copper complex has been written as ∆Ek = Ek(complex) – Ek(Cu metal)

(1.3)

On compound formation usually charge flows from metal atom (cation) to the other atom of the ligand (anion) due to redistribution of valence electrons. This results in the increase of binding energy of K electrons on account of increase in the effective nuclear charge. Consequently, the K absorption edge is shifted towards high energy side with respect to that in the metal atom. The shifts in the edge of the metal ion in the complex are primarily influenced by the oxidation state of the metal ion and are known to undergo a systematic shift towards higher energy with an increase in the oxidation state. As the electro-negativity of the ligand increases, the edge position moves to higher energy. Furthermore, for a given set of ligands, the edge moves to higher energy as the metal oxidation state increases. The totality of the edge-shift data indicates a prominent role of many other factors besides the metal oxidation state. The residual charge on the metal ion, ionic/covalent character of the metalligand bond, the electro-negativity and polarizability of the ligand plays a decisive role in the final analysis of the K absorption spectra. Agarwal and Verma (1970) suggested an empirical rule for the chemical shift: in general, the chemical shift is towards the high-energy side of the metal edge; it increases progressively with increase of the valence of the cation, unless the shift is either suppressed by the covalent character of the bond or enhanced by the formation of a metal-metal bonding. The first part of the rule, namely the valence dependence of the shift, is well known and several workers have used this dependence to determine the valences of the absorbing ions in the compounds. Sapre et al. (1972) tested this rule and found that the covalence suppresses the shift, not only for the cations but also for the anions. Moreover, anions show a negative (low energy) shift. Unless other factors intervene, the metal-metal bond results in large shift. A quantitative correlation of chemical shift of the absorption edges is difficult because many parameters enter the argument. Assuming that the main factors are valence and effective charge of the absorbing atom empirical 7

correlations have been attempted. Ghatikar et al. (1977 and 1978) have surveyed considerable data on chemical shifts of different elements in a large number of compounds and proposed the following relations between the chemical shift ∆E and the effective ionic charge q: ∆E = c1 + c2q. For the Cu K-edge, the position of the absorption edge shifts to higher energy as the number of valence electrons removed increases the oxidation number of the Cu atom. By comparing the observed chemical shift in the sample under consideration with the earlier data on the edge-shift measurements in different oxidation states of a metal, the metal oxidation state in a sample can be assigned. (Sinha et al., 1963, a,b, Mande et al., 1964 a,b, 1966, 1982, Bhide et al., 1968, Adhyapak et al., 1976, 1978, Agarwal et al., 1970, 1976, 1977 a,b, Dey et al., 1971, 1973, Gupta et al., 1972 a,b, Kumar et al., 1974, Nigam et al., 1971, 1973, Nigam et al., 1973, 1974, Padalia et al., 1971, Prasad et al., 1976, a,b,

1977 a, b, Sarode et al., 1978, 1979, Shrivastava et al., 1979, a, b,

Shrivastava et al., 1971, 1978, Ballal et al., 1977, a,b) 1.7 Extended X-ray absorption fine structure (EXAFS): The EXAFS process can be thought of as an in situ electron diffraction, in which the X-ray absorbing atom is the photoelectron source. When the kinetic energy of the ejected photoelectron is great enough to enable it to escape the bound state, it interacts with electrons in the bound states of other atoms within the local chemical environment surrounding the absorber. Energetically, the ‘continuum’ is up to several hundred electron volts (eV) above the absorption edge. Interactions between the ejected photoelectron and other electrons produce secondary sources of scattering and interference on return of the backscattering waves to the absorber. Interferences between outgoing scattering and incoming backscattering waves result in low frequency oscillations between ~50 and ~1000 eV above the absorption edge. These oscillations constitute EXAFS and are of interest as they contain structural and chemical information specific to the scattering atomic shells. An atomic shell is a group of atoms of the same species at the same distance from the absorbing atom. Qualitatively, the EXAFS oscillations are of higher frequency for long interatomic distances between the backscattering elements and the absorber, and of lower frequency for shorter 8

interatomic distances. Quantitatively, the amplitudes of EXAFS oscillations can identify the type and number of backscattering atoms as well as the distribution of these atoms about a mean distance from the absorbing atom. Because a XAFS spectrum is taken over a range of increasing X-ray energies, single- and multiple-scattering events dominate in different portions of the spectrum. The higher energy portions of EXAFS spectra are dominated by single-scattering events within only some tenths of nm (5-6 Ǻ) from the absorber, and contain information specific to the local structure surrounding the absorber. On the other hand, XANES spectra, being centered close to the absorption jump, are dominated by multiple-scattering events extending a few nm from the absorber. (Newville, 2004, Gates, 2006, Kelly et al., 2008) XAFS can be measured either in transmission or fluorescence geometries The geometry for Auger measurements is typically the same as for fluorescence. The absorption coefficient µ(E) in transmission is µ(E)x = log(I0/It)

(1.4)

and in X-ray fluorescence (or Auger emission) is µ(E)x ∝ If /I0

(1.5)

where It and I0 are the intensities of the transmitted and incident radiations respectively, x is the thickness of the absorber and If is the monitored intensity of a fluorescence line (or, again, electron emission) associated with the absorption process. For the EXAFS, we are interested in the oscillations well above the absorption edge, and define the EXAFS fine-structure function χ (E), as

χ(E) =

µ(E) − µ0(E) ∆µ0(E)

(1.6)

where µ(E) is the measured absorption coefficient, µ0(E) is a smooth background function representing the absorption of an isolated atom, and ∆µ0(E) is the measured jump in the absorption µ(E) at the threshold energy E0. It is common to convert the X-ray energy to k, the wave number of the photo-electron, which has dimensions of 1/distance and is defined as

k=

2m(E − E0) h

2

= 0.263 (E − E 0) (in eV) (in Ǻ-1 )

9

(1.7)

where E0 is the absorption edge energy and m is the electron mass. The primary quantity for EXAFS is then χ(k), the oscillations as a function of photo-electron wave number, and χ(k) is often referred to simply as “the EXAFS”. 1.8. EXAFS equation The observed EXAFS, χ(k), oscillations can be described by an equation popularly called the EXAFS equation. Though, several derivations of the EXAFS equation are available in literature, the derivation given by Matthew Newville (2004) is reproduced here and is similar to that given by Johari (2011). Fig. 1.3 shows the photoelectric effect in which an X-ray is absorbed by a core-level electron with binding energy E0, and a photo-electron with wave number k is created and propagates away from the atom. The photo-electron can scatter from the electrons of this neighboring atom and the scattered photoelectron can return to the absorbing atom (fig. 1.4). Since the absorption coefficient depends on whether there is an available electronic state (that is whether there is an electron at the location of the atom and at the appropriate energy and momentum), the presence of the photo-electron scattered back from the neighboring atom alters the absorption coefficient: This is the origin of XAFS. Since X-ray absorption is a transition between two quantum states (from an initial state with an X-ray, a core electron, and no photo-electron to a final state with no X-ray, a core hole, and a photo-electron), the µ(E) can be described with Fermi’s golden rule:

µ(E) ∝ i H f

2

(1.8)

where i represents the initial state (an X-ray, a core electron, and no photoelectron), f is the final state (no X-ray, a core-hole, and a photo-electron), and H is the interaction term. The initial state is not altered by the presence of the neighboring atom, but the final state is affected by the neighboring atom because the photo-electron is able to see it. If we expand f into two pieces, one that is

10

the “bare atom” portion ( f 0

) , and one that is the effect of the neighboring atom

( ∆f ) as f = f0 + ∆f

(1.9)

we can expand eqn. 1.8 to

µ(E) ∝ i H f0

2

[1 + i H ∆f

f0 H i i H f0

* 2

+ C.C]

(1.10)

where C.C means complex conjugate. This expression resembles the relationship between µ(E) and χ(E), µ(E) = µ0 (E)[1 + χ(E)]

Thus, µ0 = i H f0

2

(1.11)

can be assigned as the “bare atom absorption”, which

depends only on the absorbing atom - as if the neighboring atom wasn’t even there. Also the fine-structure χ can be written as χ(E) ∝ i H ∆f

(1.12)

This can be worked out (at least roughly) as an integral equation fairly easily. The interaction term H represents the process of changing between two energy and momentum states. Hence, interaction term needed is the p·A term, where A is the quantized vector potential. Here, this reduces to a term that is proportional to eikr. The initial state is a tightly bound core-level, which can be approximated by delta function δ(r) (a 1s level for atomic number Z extends to around a0/Z, where a0 is the Bohr radius of ~ 0.529 Ǻ). The change in final state is just the wave-function of the scattered photo-electron, ψscatt (r) . Putting all these terms together, a simple expression for the EXAFS is obtained:

χ(E) ∝ ∫ dr δ(r) eikr ψscatt (r) = ψscatt (0)

(1.13)

In words, this simply states the physical picture shown in fig. 1.4: the EXAFS χ(E) is proportional to the amplitude of the scattered photo-electron at the absorbing atom. The amplitude of the scattered photo-electron at the absorbing atom can be further evaluated, to get the EXAFS equation. Again, using the simple

11

physical picture from fig. 1.4, one can describe the outgoing photo-electron wave-function ψ (k, r) traveling as a spherical wave: ψ (k, r) =

e ikr kr

(1.14)

traveling a distance R to the neighboring atom, then scattering from a neighbor atom, and traveling as a spherical wave a distance R back to the absorbing atom. All these factors are simply multiplied together to get: ikR eikR iδ(k) e χ(k) ∝ ψscatt (k, r = 0) = + C.C [2kf (k)e ] kR kR

= 2f (k)

=

ei[2kR+δ (k)] kR 2

+ CC

2f (k) i[2kR+δ(k)] -i[2kR+δ(k)] +e [e ] kR 2

(1.15) (1.16) (1.17)

where f(k) is called backscattering amplitude and δ(k) is the phase factor, both of which depend on the Z of the neighboring atom, as shown in fig. 1.5. These scattering factors make EXAFS sensitive to the atomic species of the neighboring atom. The real part of this complex function is

χ(k) =

f (k) kR 2

sin[2kR + δ(k)]

(1.18)

Number of atomic pairs, thermal and static disorder The treatment here was for one pair of absorbing atom and scattering atom, but for a real measurement we’ll average over millions of atom pairs. Even for neighboring atoms of the same type, the thermal and static disorder in the bond distances will give a range of distances that will affect the EXAFS. As a first approximation, this disorder will change the EXAFS equation to

χ(k) =

N kR 2

2 2 f (k) e−2k σ sin[2kR + δ(k)]

(1.19)

where N is the coordination number and σ2 is the mean-square-displacement in the bond distance R. Number of neighbouring atoms Real systems usually have more than one type of neighboring atom around a particular absorbing atom. This is easily accommodated in the EXAFS 12

equation by summing the contributions from each scattering atom type (or coordination shell, as it is often called - the terms coordination sphere and scattering path are also used), χ (k) = ∑

Nj

2 j kR j

f j (k) e

−2k 2 σ 2j

sin[2kR j + δ j (k)]

(1.20)

where j represents the individual coordination shell of identical atoms at approximately the same distance from the central atom. Core-hole lifetime One of the most important approximations made above has to be corrected. When it was asserted that the outgoing photo-electron went out as a spherical wave in eqn. 1.14, the fact was neglected that the photo-electron can also scatter inelastically from other sources – other conduction electrons, phonons, and so on. In order to participate in the EXAFS, the photo-electron has to scatter from the neighboring atom and return to the absorbing atom elastically (i.e., at the same energy) as the outgoing photo-electron. In addition, the photoelectron has to make it back to the absorbing atom before the excited state decays (i.e., before the core-hole is filled). To account for both the inelastic scattering and the core-hole lifetime, a damped spherical wave: ψ (k, r) =

eikr e −2r λ (k) kr

(1.21)

can be used as the photo-electron wave-function where λ is the mean-free-path of the photo-electron (that is, how far it typically travels before scattering inelastically and before the core hole is filled). The mean-free-path is typically 5 to 30 Ǻ and has a significant but fairly universal dependence on k, shown in fig. 1.6. Including the λ(k), the EXAFS equation becomes: χ (k) = ∑

Nj

2 j kR j

f j (k) e

−2k 2 σ 2j −2R j λ (k)

e

sin [2kR j + δ j (k)]

(1.22)

Amplitude reduction factor A constant reduction factor S02 has to be added after the derivation is done. S02 is an overlap factor which includes the intrinsic losses due to inelastic effects in the equation, while, λ(k) includes the extrinsic losses due to inelastic effects. S02 is typically ~0.9. Hence, the final EXAFS equation becomes 13

χ (k) = ∑

Nj

2 j kR j

S0 2 f j (k) e

−2k 2 σ 2j −2R j λ (k)

e

sin [2kR j + δ j (k)]

(1.23)

Two parts of the equation This EXAFS equation consists of two main parts. (1) The first part is the amplitude Aj(k) given by: A j (k ) =

Nj kR 2j

S02 f j ( k ) e

− 2k 2 σ 2j − 2R j / λ (k )

e

(1.24)

and contains the coordination number (N) and disorder (σ), which is the fluctuation in Rj due to thermal motion or structural disorder. (2) The second part is the sine function which accounts for the oscillations seen in the EXAFS, i.e., sin [2kR j + δ j (k)] where δj(k) is the phase shift. Phase shift The argument inside the sine function can be thought of as being related to the time for the electron to travel to the neighboring atom and return. In fig. 1.7, 2kR would represent this time if the kinetic electron were constant across the entire R-range. However, it is altered by an amount, δscatterer (i.e., 2δs) resulting in part from the increase in velocity of the photoelectron as it approaches the neighbouring atom and then slows again as it returns. A similar phase shift,

2δabsorber (i.e., 2δa) results from the absorber atom itself. The velocity increases as it approaches an atom because as shown in fig. 1.7, the potential that an electron experiences decreases to more negative values as the electron is attracted more by the nucleus, and hence its kinetic energy increases. For convenience, this atomic potential is “squared off” in fig. 1.7. Thus, the phase factor is

δ j ( k ) = 2δabsorber ( k ) + δscatterer ( k )

(1.25)

From the EXAFS equation, we can draw a few physical conclusions about EXAFS. First, because of the λ(k) term and the R−2 term, EXAFS is seen to be an inherently local probe, not able to see much further than 5 or so Angstroms from the absorbing atom. Second, the EXAFS oscillations will consist of different frequencies that correspond to the different distances for each coordination shell. This will lead us to use Fourier transforms in the analysis. 14

Fourier transformation of χ(k) Although EXAFS equation provides a complete description of the EXAFS oscillations, it is not a particularly convenient form for visualizing the information content of an EXAFS spectrum. As with NMR spectroscopy, Fourier transformation can be used to decompose a frequency-space signal into its different constituent frequencies. The Fourier transformation of χ(k) is defined by FT ( R ) =

1 2π

k max



k n χ (k) ei2kR dk

(1.26)

k min

The Fourier transformation of the EXAFS spectrum for Cu metal is given in fig. 1.2(e). For EXAFS, the canonical variables are k (in Ǻ-1) and R (in Ǻ), and the Fourier transform (FT) of an EXAFS spectrum gives a pseudo-radial distribution function. It is pseudo in that the FT amplitude cannot be related directly to electron density around the absorber due to the f(k) factor and the damping factors in eqn. (1.24), and because the distance found from the Fourier transform is about 0.2-0.5Ǻ shorter than the actual distance due to the energy dependence of the phase factors in the sine function (eqn. (1.24)). The FT is a useful way of judging qualitatively what shells may be present in a system and for comparing a fit to the data. However, it is important to remember that Fourier transforms are subject to several potential artefacts. In many cases, multiple shells of scatterers do not give rise to multiple peaks in the FT (Riggs et al., 1995). Similarly, interference between two different peaks in the FT may give rise to a spurious third peak. The latter results from the fact that the FT of an EXAFS spectrum is actually a complex number, with both real and imaginary components. Typically, however, only the modulus of the FT is plotted. This is useful for visualizing the major contributions to the EXAFS spectrum, but should never be used for quantitative data analysis. 1.8.1 Theoretical model In order to extract the distances and coordination numbers from the experimental EXAFS data, we need to have accurate values for the scattering amplitude and phase-shifts f(k) and δ(k). The need for accurate scattering 15

amplitude and phase-shifts has been a crucial issue in the field of EXAFS. In the earliest EXAFS analyses, these factors could only be determined accurately from experimental spectra in which the near-neighbor distances and species were known (generally from measurements of crystals with well known structures). Such experimental standards can be quite accurate, but are generally restricted to first neighbor shell. Until the early 1990’s, their use was quite common. In the past decade or so, calculations of f(k) and δ(k) have become more accurate and readily available, and use of experimental standards in EXAFS analysis is now some what rare. Calculated scattering factors such as those from the programs FEFF, GNXAS, and EXCURVE have been shown numerous times to be accurate enough to be used in real analysis, and in some cases are more accurate than experimentally derived scattering factors. In addition, the calculated factors are not restricted to the first shell and can account for multiple-scattering of the photo-electron. The general approach for determining the average coordination structure around the absorber atom from EXAFS data is to generate a theoretical model for the sample and calculate the theoretical EXAFS spectrum for that model using the FEFF computer program. Currently, the software program Artemis comes with the freely available program FEFF6L (Zabinsky et al., 1995) for computing theoretical EXAFS models. Artemis can adjust the structural parameters in the EXAFS equation until a least-squares fit is obtained between the theoretical (modeled) and experimental EXAFS spectra. The model is adjusted as needed (e.g., with different atom types) until the best possible fit is obtained between theoretical and experimental spectra. The parameters that are often determined from a fit to the EXAFS spectrum affect either the amplitude of the EXAFS oscillations (N, S02, σ2) or the phase of the oscillations (∆E0 and ∆R). (Kelly et al., 2008) 1.8.2 EXAFS data analysis and determination of structural parameters In practice, some of the parameters in the EXAFS equation are calculated ab initio, while others are found by fitting the model to experiment. For example, the effective scattering phases and amplitudes are generally calculated using a multiple scattering code such as FEFF (which stands for feff, the effective 16

scattering amplitude), while a variety of other parameters are used as fitting variables. Of particular interest are the half path lengths R, and the path degeneracy N since for single scattering paths these parameters are directly related to structural properties (i.e. bond length and coordination number). The standard procedures used for preprocessing of data, and the extraction of structural parameters by fitting to the EXAFS equation can be described in brief as follows. First the oscillatory fine structure χ(k) is extracted from the data by subtracting a smooth background function µ0. The most prevalent method for obtaining µ0 is to fit the curve to a cubic or other spline function which is constrained to have low curvature (Newville et al., 1993). The oscillatory EXAFS signal χ(k) is then Fourier transformed to real (R) space which gives an amplitude that is akin to a radial distribution function, with contributions from longer scattering paths peaking at higher R value. Phase correction gives a \χ(R)\ which is akin to the radial distribution function. The peaks in the Fourier transform, appear at approximately the different shell distances. In order to obtain more accurate values for the parameters, or to obtain additional parameters, a model consisting of a few important terms from the EXAFS equation is fit to the data. Fitting of the model (EXAFS equation) to the data is performed in R space using a limited range of the Fourier transformed data, in order to isolate the contribution from a relatively small number of short scattering paths. Most EXAFS analysis programs use the least squares algorithm for fitting the model to the data. In practice, fj(k), δj and λ are calculated while a number of the other parameters (i.e. Rj, Nj, etc.) may be allowed to vary during fitting (Kas, 2009). Thus, the parameters that are determined from the fitting of the theoretical model to the experimental EXAFS data are N, S02, σ2, ∆E0 and ∆R. 1.9 Multiple scattering In the physical model presented above, the X-ray excited photoelectron travels from the absorbing atom to the scattering atom and back. However, far more complex scattering pathways are also possible. For example (see fig. 1.8), the photoelectron may travel from the first scattering atom (S1) to a second (S2) and even a third (S3) before returning to the absorbing atom. Each scattering 17

interaction defines an angle, e.g., θ1 that determines the intensity, and hence the significance, of that multiple-scattering pathway. The scattering of an electron by an atom is strongly focused in the forward direction (θ ≈ 180°) and falls off very rapidly for θ ≤150°. Multiple scattering depends on the simultaneous positions of three or more atoms, i.e., on the distances and angles between the atoms. This means that multiple scattering can, at least in principle, provide information about the three-dimensional structure around the absorbing site. For this reason, there has been a great deal of interest in developing methods to use multiple scattering in XAS analyses, and thus to avoid the limitation that EXAFS provides only radial structure information. Two obstacles confront attempts to use multiple-scattering to determine molecular geometry. The first is computational: since hundreds, and even thousands of multiple scattering pathways can contribute to the observed XAS, the theoretical description of multiple scattering can be computationally formidable. This makes it difficult to perform effective refinements of complete multiple scattering. A more fundamental problem is the limited information content of XAS spectra. ( Penner Hahn, 1999) 1.10 X-ray absorption near edge structure (XANES) The physical principles that govern EXAFS apply equally in the XANES region. However, at low kinetic energy the photoelectron mean-free-path increases dramatically. Similarly, the exp(-k2) dependence of the Debye–Waller factor means that this damping factor is negligible in the XANES region. These effects combine to render the XANES region sensitive to a wide range of absorber–scatterer distances, as compared to the (relatively) simple short-range treatment that can be used for most EXAFS. This is, in principle, an advantage since it provides the possibility of extracting three-dimensional structure information from XANES spectra. However, this also makes theoretical simulations of XANES spectra extremely difficult. Although much progress has recently been made in the theoretical modeling of XANES, most of the applications of this energy region remain qualitative. On the low energy side of the absorption edge one frequently observes several weak transitions. In contrast with the electron-scattering model that is used to describe the EXAFS and the 18

other XANES features, these low energy transitions arise from bound state transitions. For the first transition series metals, bound state transitions include both 1s-3d and 1s-4p transitions. XANES is a much larger signal than EXAFS and can be obtained at lower concentrations, and at less than perfect sample conditions. The processes responsible for near-edge absorption structure are related to ejection of core electrons into ‘continuum states’, and involve single- and multiple-scattering events off the first atomic shell surrounding the absorber, as well as multiplescattering events from more distant atomic shells. XANES is considerably harder to fully interpret than EXAFS. The interpretation of XANES is complicated by the fact that there is not a simple analytic (or even physical) description of XANES. The main difficulty is that the EXAFS equation breaks down at low-k, due to the 1/k term and the increase in the mean-free-path at very low-k. Precise and accurate calculations of all spectral features are still difficult, timeconsuming, and not always reliable. This situation is improving, but at this point, quantitative analyses of XANES using ab initio calculations are very rare. Recent advances in multiple scattering formalisms have, however, shown that XANES spectra can be treated like EXAFS spectra to gain element-specific information on bonding environment, such as coordination number and interatomic distances. Though the lack of a simple analytic expression complicates XANES interpretation, XANES can be described qualitatively (and nearly quantitatively) in terms of coordination chemistry, molecular orbitals, band-structure and multiple-scattering. These chemical and physical interpretations are all related, of course. There is much chemical information obtainable from the XANES region, notably formal valence (very difficult to experimentally determine in a nondestructive way) and coordination environment. Clearly, the edge position and shape is sensitive to formal valence state, ligand type, and coordination environment. Hence, edge features (position and shape) reflect oxidation states and coordination environments in the vicinity of the absorber. An important and common application of XANES is to use the shift of the edge position to determine the valence state. This technique is now routinely applied to discern 19

coordination and oxidation states of metals in compounds and complexes. Decomposition of the spectral components can differentiate between different site symmetries and assist in quantifying oxidation states. The heights and positions of pre-edge peaks can also be reliably used to empirically determine oxidation states and coordination chemistry. These approaches of assigning formal valence state based on edge features and as a fingerprinting technique make XANES somewhat easier to crudely interpret than EXAFS, even if a complete physical understanding of all spectral features is not available. X-ray absorption near edge structure (XANES) is an elemental specific technique that uses the measurement of the X-ray absorbance in the vicinity of an absorption edge of the element of interest. XANES spectrum reflects the local structure around the absorbing atom and provides information about oxidation state of an excited atom and the coordination symmetry (Berry et al., 2006). By taking standards of well-defined chemical species, analysis of XANES can be used to determine metal speciation, i.e., determination of the chemical forms along with the relative quantity of the different species in a given sample. 1.11 Speciation using XANES The species, speciation and speciation analysis are defined as followss (a) Chemical species - Specific form of an element defined as to isotopic composition, electronic or oxidation state, and/or complex or molecular structure. (b) Speciation - Distribution of an element amongst defined chemical species in a system. (c) Speciation analysis - Analytical activities of identifying and/or measuring the quantities of one or more individual chemical species in a sample. Though, the commonly used methods for speciation are principal component analysis (PCA) with target transformation method (TT) (Malinowski 1991, Beauchimen et al., 2002, Bazin et al., 2003, Strawn et al., 2008, 2009, Seiter et al., 2008, Wang et al., 2008 & Lau et al., 2008) and linear combination fitting (LCF) (Manceau et al., 2000, Hsiao et al., 2001, Roberts et al., 2002, 20

Scheinost et al. 2002, 2006, Farquar et al. 2003, Huang et al. 2003, Kretschmer et al. 2004, Liu et al. 2004 (a,b), Takaoka et al. 2005, Voegelin et al. 2005, Ajiboye et al. 2007, Huggins et al. 2009, Legros et al. 2010 & Van Damme et al. 2010), several other approaches for the analysis of XANES data have also been developed, which can be listed as follows: residual phase analysis (RPA) (Frenkel et al. 2002), multiple dataset (MDS) fit method (Frenkel et al. 2002), derivative spectra methods (Lamberti et al. 2003) and normalized difference absorption edge analysis (NDAES) (Penner Hahn et al. 1983, 1984, Kau et al. 1986, 1987, Liang et al. 1995, Tranquada et al. 1989). In the present work, we have studied the different methods of speciation to make a comparative study of these methods of speciation and to discuss their relative merits. 1.12 XAS vs. Crystallography Structural characterization of metal complexes has played a crucial role in the development of coordination chemistry. Despite the tremendous advances that have taken place in spectroscopic methods for structure elucidation, X-ray crystallography remains the method of choice for definitive determination of the structure of a new coordination complex. Unfortunately, X-ray crystallography cannot always be used. Some samples simply cannot be crystallized in diffraction quality crystals, despite the best efforts of skilled experimenters. In other cases, crystals may be available but the structural questions of interest involve solution structure. For example, it may be necessary to determine whether a molecule remains structurally intact in solution. Finally, there are a variety of situations, involving for example crystallographic disorder, in which X-ray crystallography is unable to provide a complete structural description. In all of these cases, X-ray absorption spectroscopy (XAS) can provide unique structural information. XAS has been known for most of this century, and has been available as a useful structural probe for over 25 years. Much of the interest in XAS, however, has focused on its applications to biological systems and to amorphous materials. These were natural areas for early developments of XAS, since in both areas, almost all of the samples of interest are non-crystalline. In this context, any structural information is valuable. In contrast, XAS has found 21

fewer applications in coordination chemistry, perhaps because X-ray crystallography is such a powerful tool for the structural characterization of coordination complexes. Penner Hahn (1999) has reviewed the physical principles of XAS and illustrated through selected examples why XAS should be thought of as a key tool in the toolkit of the coordination chemist. 1.13 Advantages and limitations of XAS The principal advantage of XAS as a structural probe is that it is a local structure probe. None of the discussion above requires the presence of longrange order. This means that XAS can be used to study non-crystalline samples. In ideal circumstances, EXAFS data can be analyzed to determine the absorber– scatterer distance with an accuracy of ca. 0.02 A and perhaps even better. Coordination numbers can be determined with an accuracy of ca. 25% and scatterer identity can typically be defined to the nearest row of the periodic table. In comparison with small molecule crystallography, the information available from XAS is relatively limited. However, for non-crystalline systems, XAS may provide the only available structural information. Even for crystalline systems, there are cases in which EXAFS can provide a different, and perhaps better, structural description than is available from crystallography. XANES analysis have the ability to provide oxidation state and spin-state information that can be difficult or impossible to extract from crystallographic measurements. In comparison with other spectroscopic methods, XAS has the decided advantage that it is always detectable, without the need for specific spin states or isotopic substitution, and that it is element specific. Every element has at least one unique absorption edge. The universal detectability of XAS is, of course, a mixed blessing since it means that XAS is a bulk technique sensitive to all of the forms of an element that are present in a sample. If the element of interest occurs in multiple environments, only the average structure can be determined. Any discussion of the advantages of XAS would be incomplete without a summary of the limitations of the technique (Penner Hahn, 1999). Ultimately, all of these involve different limitations in experimental resolution. Several of these are widely recognized. EXAFS provides only limited chemical resolution 22

scattering atoms that differ by two or three in atomic number (e.g. C, O, N, and F) typically cannot be resolved. EXAFS, at least as described thus far, provides no angular resolution. It is thus not possible to learn anything directly about geometry. There are some possibilities for introducing angular resolution but this remains a limitation in most XAS studies. Finally, the finite k range of the EXAFS spectrum limits the bond-length resolution of the method. Two scattering shells can only be resolved if they differ sufficiently in frequency to cause a detectable change in the EXAFS amplitude, due to the interference between the two different EXAFS components. For small differences in distance, the interference simply introduces an exponential damping factor. This is indistinguishable from an increase in the Debye-Waller term in EXAFS eqn (1.24). For perfect data, two shells of the same scatterer should become resolvable when the difference in their distances, dR, is large enough to cause a ‘beat’ in the EXAFS amplitude. This occurs for ∂R ≥ π / 2 k max , where kmax is the maximum value of k for which a signal can be measured. Notwithstanding the dire warnings (above) regarding the limitations of XAS, the fact remains that XAS has the ability to provide unique information about coordination compounds. 1.14

Books and review articles on XAFS Several books and various review articles have been published which

give comprehensive, detailed and exhaustive description of the different aspects of XAFS since 1975, when the modern practice in XAFS spectroscopy was started by Prof. E. A. Stern and his group (Sayers et al., 1970, 1971, Stern, 1974, 1978, Stern et al., 1975). The important ones are listed below to help those readers who wish to start work on this branch of X-ray absorption spectroscopy. 1. Extended X-ray absorption fine structure - its strengths and limitations as a structural tool by P A Lee, P H Citrin, P Eisenberger, and B M Kincaid (1981). In this research article, the authors have reviewed the development of extended X-ray absorption fine structure (EXAFS) upto 1980. Advances in experimental techniques using synchrotron radiation and the theory of EXAFS have been described. The authors have reviewed the details of the analysis of EXAFS data, starting from the treatment of raw data to the extraction of 23

distances and amplitude information. They have also discussed selected examples of applications of EXAFS chosen to illustrate both the strength and limitations of EXAFS as a structural tool. 2. Basic principles and applications of EXAFS, (Chapter 10 of Handbook of synchrotron radiation) by E A Stern and S M Heald (1983). This article appears to be the first exhaustive and detailed review on EXAFS spectroscopy. Apart from the historical development, theoretical discussion about EXAFS is given considering the independent particle model as well as many body effects. Different experimental techniques have been described for EXAFS measurements. The interpretation of EXAFS has been discussed in detail. Finally, the applications on Br2-graphite, biological systems, liquids, glasses, amorphous materials, disordered subsystems and catalysts have been described. Application of EXAFS under high pressure is also pointed out. 3. X-ray absorption: principles, applications, techniques of EXAFS, SEXAFS and XANES, edited by D C Koningsberger and R.Prins (1988). This book describes several specific spectrometric techniques that are very useful in elucidating the fundamental nature of matter: EXAFS - Extended X-ray absorption fine structure; SEXAFS - which is EXAFS applied to surface phenomena; and XANES - X-Ray absorption near edge structure. The articles in the book explain the phenomena and describe examples of X-ray absorption applications in several fields, including chemistry, biochemistry, catalysis, amorphous and liquid systems, synchrotron radiation, and surface phenomena. Contributors explain the underlying theory, how to set up X-ray absorption experiments, and how to analyze the details of the resulting spectra. 4. Theoretical approaches to X-ray absorption fine structure by J J Rehr and R. C. Albers (2000). In this review article, the authors focus on extended X-ray absorption fine structure (EXAFS) well above an X-ray edge, and, to a lesser extent, on Xray absorption near-edge structure (XANES) closer to an edge. The discussion includes both formal considerations, derived from a many-electron formulation, 24

and practical computational methods based on independent-electron models, with many-body effects lumped into various inelastic losses and energy shifts. The main conceptual issues in XAFS theory are identified and their relative importance is assessed; these include the convergence of the multiple-scattering expansion, curved-wave effects, the scattering potential, inelastic losses, selfenergy shifts, and vibrations and structural disorder. The advantages and limitations of current computational approaches are addressed, with particular regard to quantitative experimental comparisons. 5. Progress in the theory and interpretation of XANES by J J Rehr and A.L. Ankudinov (2005) . In this research article, the authors have reviewed the progress in both the theory and in ab initio codes for calculations of X-ray absorption spectra (XAS), and in particular, the near edge structure (XANES) leading up to the current state. Authors have focused on the real-space multiple scattering (RSMS) approach which gives a unified treatment of both EXAFS and XANES, as well as many other spectroscopies. They have also discussed the close connection between RSMS theory and excited state electronic structure, and in particular, corrections to the independent particle approximation which are essential in a quantitative theory. These developments have led to a number of ab initio codes for the calculation and interpretation of XAS in terms of the electronic structure and coordination chemistry of materials. 6. Analysis of soils and minerals using X-ray absorption spectroscopy (Chapter 14 in Methods of soil analysis, Part 5 - Mineralogical methods) by S D Kelly, D Hesterberg, and B Ravel (2008). This chapter focuses mainly on the basic principles and methods of XANES and EXAFS spectroscopy of soils, minerals, and mineral-associated (e.g., adsorbed or coprecipitated) chemical species. Emphasis is placed on sample preparation, data collection, and data analysis. The procedures for XAFS data analysis using the softwares Athena and Artemis are best described in this review article and have been followed by several authors. In the present work also these methods have been used for data analysis. 25

7. Introduction to XAFS: A practical guide to X-ray absorption fine structure spectroscopy by Grant Bunker (2010). This is the latest book on X-ray absorption fine structure spectroscopy (XAFS). This textbook is a comprehensive, practical guide to carrying out and interpreting XAFS experiments. Assuming only undergraduate-level physics and mathematics, the textbook is ideally suited for graduate students in physics and chemistry starting XAFS-based research. It contains concise executable example programs in Mathematica 7. The book addresses experiment, theory, and data analysis and is a useful guide for researchers entering the subject. 8. Proceedings of the fourteen International Conferences on XAFS Apart from the important books and review articles mentioned above, excellent source of information on the work done in the field of XAFS spectroscopy are the proceedings of the fourteen International Conferences on XAFS which are all published in the form of books or in the form of special issues of research journals. These fourteen conferences are listed below along with the references. Conference no. XAFS 1 XAFS 2 XAFS 3 XAFS 4

Year 1981 1982 1984 1986

Place Daresbury (UK) Frascatti (Italy) Stanford (USA) Fontevraud (France)

Reference

Bianconi et al. (1983) Hodgson et al. (1984) Proc. XAFS-4 conf. (1986) J. de Phys. Coll. Vol. 47 C8 XAFS 5* 1988 Seattle (USA) De Leon et al. (eds.) (1989) Physica B 158 (1989) XAFS 6 1990 York (UK) Hasnain (1991) XAFS 7 1992 Kobe (Japan) Kuroda et al. (eds.) (1992) Jpn. J.Appl. Phys., 32 (1992) XAFS 8 1994 Berlin (Germany) Baberschke and Arvanitis (eds.) (1994) Physica B 208 and 209 (1994) XAFS 9 1996 Grenoble (France) Coulon-Ginet and Brookes (eds.) (1996) J. de Phys. IV, 7 (1996) XAFS 10 1998 Chicago (USA) Proc. XAFS-10 conf. (1999) J. Synchrotron Rad., 6 XAFS 11 2000 Akoh (Japan) Proc. XAFS-11 conf. (2001) J. Synchrotron Rad. 8 XAFS 12 2003 Malmo (Sweden) Proc. XAFS-12 conf. (2005) Physica Scripta, 17 XAFS 13 2006 Stanford (USA) Hedmann and Pianetta (eds.) (2007) XAFS 14 2009 Camerino (Italy) Proc. XAFS-14 conf. (2009) J. Phys. Conf. Series, 190 * Dr. B. D. Shrivastava was a member of the International Organizing Committee of this conference.

26

9. Other important books Apart from the books mentioned above, the following books are also good source of information on the work done in the field of X-ray absorption spectroscopy. (i) B. K. Agarwal, 1989, X-Ray Spectroscopy, (Springer-Verlag, Berlin). (ii) S K Joshi, B D Shrivastava and A P Deshpande (eds.), 1998, X-Ray Spectroscopy and Allied Areas, (Narosa Publishing House, New Delhi). (iii) A Meisel, 1989, X-Ray Spectra and Chemical Binding, (Springer-Verlag Berlin). (iv) C Bonnelle and C Mande (eds.), 1982, Advancec in X-Ray Spectroscopy, (Pergamon Press, New York) (v) J Stoher, 1992, NEXAFS Spectroscopy, (Springer-Verlag, Berlin). (vi) B K Teo and D C Joy (eds.), 1981, EXAFS Spectroscopy Techniques and Applications, (Plenum Press, New York) (vii) B K Teo, 1986, EXAFS: Basic Principles and Data Analysis, (SpringerVerlag, New York), Inorganic Chemistry Concepts 9. (viii) E A Stern, 1980, Laboratory EXAFS Facilities, (American Institute of Physics, New York). 1.15 Earlier work done on K absorption spectra of copper 1.15.1 Work done in our laboratory Several research workers have studied copper complexes in our laboratory at School of Studies in Physics, Vikram University, Ujjain from time to time and the results have been published in the form of about 100 research papers in international journals. Some of the research papers are mentioned in the references of this thesis (Awasthi et al., 1989, a,b, Gupta et al., 1992, Kumar et al., 1980, 1981, Prasad et al., 1982, Shah et al., 1983, Rajput et al., 1984, Shrivastava et al., 1988, 1989, 1992, 2001, Katare et al., 2002, Gupta et al., 2005, Joshi et al., 2004, 2006, 2007, Vyas et al., 2009, Johari et al., 2011). Several theses have been submitted by the research scholars and a summary of their studies, as given in their theses, is given below.

27

Mool Krishna Gupta (1979) has studied simple compounds of copper, viz., Cu2SO3H2O, Cu2Br, CuS, Cu2Cl2, CuCl2, CuCrO4, Cu(NO3)23H2O, CuC2O4. His main contribution has been the determination of effective nuclear charge (ENC) from the chemical shifts. He has also summarized in his Ph.D. thesis the earlier investigations on copper compounds and complexes, available in literature, up to 1970. Ashutosh Mishra (1987) has studied copper K absorption spectra of six copper mixed ligand complexes in solid form as well as in aqueous solution form. The mixed ligand complexes are: Cu(Gly)(Val), Cu(Gly)(GG), Cu(Gly)(αAba), Cu(Gly)(Thre), Cu(Gly)(Ser), Cu(Gly)(Alan), where glycine (Gly) has been used as primary ligand and valine (Val), glycylglycine (GG), alfa amino butric acid (α-Aba), threonine (Thre), serine (Ser), and alanine (Alan) as the secondary ligands. He has also described similar studies of six more copper mixed ligand complexes of the type [Cu(A)(B)], [where A = alanine (Alan), and B = valine (Val), glycylglycine (GG), alfa amino butric acid (α-Aba), threonine (Thre), serine (Ser) and glycine (Gly)]. He has further studied the copper complexes Cu(α-Aba)(Val),

Cu(α-Aba)(Gly), Cu(α-Aba)(Ser), and Cu(α-

Aba)(Alan) in which alfa amino butric acid (α-Aba) has been used as primary ligand and valine (Val), glycylglycine (GG), serine (Ser), and alanine (Alan) as the secondary ligands. These studies have been done in solid form as well as in aqueous solution form. Such complexes are known to be important in the transport of copper through biological membranes. Arvind Chandra Gharia (1987) has done X-ray absorption spectroscopic investigations of five Cu(II) mixed ligand amino acid complexes, viz.,: Cu(Threo)(Hist),

Cu(Threo)(GG),

Cu(Threo)(α-Aba),

Cu(Threo)(Val)

Cu(GG)(Val). In four of this complexes threonine (Threo) has been used as primary ligand and histeridene (Hist), glycylglycine (GG), alfa amino butric acid (α-Aba), valine (Val) are the secondary ligands. In the fifth complex Cu(GG)(Val), glycylglycine (GG) is the primary ligand and valine (Val) acts as the secondary ligand. He has studied these complexes in both the solid form and in aqueous solution form. This has enabled him to make a unique study where comparison could be made of the structure of the complexes when they go from solid to aqueous solution form. 28

Ramesh Chandra Kumawat (1990) have studied copper K absorption spectra of a large number of copper complexs. which can be grouped as follows: (1) (chtsc)2Cu.CuI, (pptsc)2Cu.CuI, (aptsc)2Cu.CuI, (bmtsc)2Cu.CuI and (detsc)2Cu.CuI. (2) (1,10-phenanthroline)[malonato(2-)]copper(II)dihydrate and (1,10-phenanthroline)[serinato(2-)]copper(II)dihydrate. (3) Cu(dmg)2, Cu(sal)2, Cu(dmg)2Cl2 and Cu(sal)2Cl2, where dmg = dimethylglyoximato and sal = salicylaldoximato. (4) Cu-tryptophan-tyrosine, Cu-phenylalanine-tyrosine, Cu-phenylalanine-tryptophan and Cu-phenylalanine-histidine. (5) One mononuclear and two binuclear copper (II) complexes of Schiff base. He has made exhaustive study of this complexes and has studied edge structure, chemical shifts, bond lengths etc. and has derived important information regarding the molecular structure of these complexes. Bhakt Darshan Shrivastava (1996) has studied copper K absorption spectra of the three sets of the following copper complexes. (1) (X2.dtc)2Cu, where dtc = dithiocarbamate and X= ethyl, isopropyl, normal propyl, methyl and cyclohexyl groups (2) (X2.dtc)2Cu.CuCl2, where X= methyl, n-propyl, ethyl and cyclohexyl groups (3) Cu.C6H5CONHNH2,

Cu.C6H5(OH)CONHNH2(ortho),

Cu.C6H5(OH)CONHNH2(meta),

Cu.C6H5(OH)CONHNH2(para),

Cu.C6H5(NO2)CONHNH2(ortho), Cu.C6H5(NO2)CONHNH2(meta), Cu.C6H5(NO2)CONHNH2(para),

Cu.C6H5(Cl)CONHNH2(ortho),

Cu.C6H5(Cl)CONHNH2 (para) The X-ray absorption spectroscopic studies of above complexes were done using laboratory X-ray spectroscopic set-up emplyoing photographic method of registration of spectra in the departmental laboratory. He also recorded EXAFS spectra of three copper complexes namely, [Cu(et2.dtc)2], [Cu(ipr2.dtc)2] and [Cu(npr2.dtc)2], where et = ethyl, ipr = isopropyl and npr = normal propyl, using laboratory EXAFS set-up, available at UGC-DAE Consortium for Scientific Research, Indore, India, the details of which are given by Deshpande et al., (1991). This set-up has a 12 kW rotating anode X-ray generator (Rigaku RU200, 60kV, 200mA) with a focus size of 0.5mm×10mm. Although different 29

anode materials can be used, we have used a cobalt anode. The curved crystal spectrometer of Johansson type, having radius of Rowland circle 400 mm, based on the design of Tohji et. al. (1983), has silicon crystal of 15mm×50mm size. Reflections from (311) planes (d = 1.663 Å) provided energy range from Emax= 21862 eV at θ =10 deg. to Emin= 4040 eV at θ=70 deg. A scintillation detector (Canberra model 1702) supported by fast electronic circuits to minimize counting loss was used. Convenient menu-driven computer software was used for control and data acquisition. The incident intensity (I0), the transmitted intensity It or the ratio of the two I0/It, could be plotted on screen, to view the spectrum while it was being recorded. The characteristic emission lines Kα1 and Kα2 of cobalt source have been used for calibration. The resolution of this spectrometer was about 7 eV at Cu K-edge. The EXAFS data was Fourier transformed and first shell fitting was done using the Aldea and Indrea computer programs. (Indrea and Aldea, 1980, Aldea and Indrea, 1988, 1990). Though this work has been presented in his thesis, but it has never been published. Rajkumar Katare (2000) has studied copper K absorption spectra of the three sets of the following copper complexes: (1) copper(II) mixed ligand complexes, viz.,Cu(et2dtc), Na[Cu(asp)(et2dtc)], Na2[Cu(asp)(et2dtc)2], Na[Cu(glut)(et2dtc)], Na2[Cu(glut)(et2dtc)2], where et2dtc = diethyldithiocarbomate, asp = aspartic acid and glut = glutamic acid. (2) copper(II) mononuclear, binuclear and trinuclea complexes, viz., [Cu(bipy)(Cl2)], [Cu(imH)(Cl)2], [(Cl)2(imH)2Cu(imH)2Cu(bipy)(Cl)2], and [(Cl)2(bipy)Cu(imH)2Cu(imH)2Cu(bipy)(Cl)2], (3) copper(II) mixed ligand complexes, with glutamic acid and aspartic acid as primary ligands, viz., [Cu(glut)(H2O)2], [Cu(glut)(imH)].2H2O, [Cu(glut)(py)], [Cu(glut)(bz-imH)].2H2O, [Cu(asp)(H2O)2], [Cu(asp)(imH)].2H2O, [Cu(glut)(py)] and [Cu(asp)(bz-imH)].2H2O, where asp = aspatric acid, glut = glutamic acid, imH = imidazole, py = pyridine and bz-imH = benz- imidazole The study of these complexes has provided fruitful information regarding electronic structure and chemical bonding. It has also provided useful information on the effect of secondary ligands on the position, shapes and structure of copper(II) K-discontinuity in these complexes. 30

Ravindra Kumar Vyas (2006) has studied copper K absorption spectra of the three sets of the following copper complexes: (1) [(dien)Cu(H2O)2] (ClO4)2, [(dien)Cu(imH)](ClO4)2, [(dien)Cu-im-Cu(dien)](ClO4)3, [(dien)Cu-im-Ni(dien)](ClO4)3, [(dien)Cu-im-Zn(dien)] (ClO4)3, where dien = diethylenetriamine and imH = imidazole (2) [(PMDT)Cu(H2O)] (ClO4)2, [(PMDT)Cu(imH)] (ClO4)2, [(PMDT)Cu-im-Ni(PMDT)](ClO4)3, [(PMDT)Cu-im-Cu(PMDT)](ClO4)3, [(PMDT)Cu-im-Zn(PMDT)](ClO4)3, where PMDT = pantamethyldiethylenetriamine (3) [(PMDT)Cu-Ox-Ni(PMDT)](BPh4)2, [(PMDT)Cu-Ox-Cu(PMDT)](BPh4)2, [(PMDT)Cu-Ox-Zn(PMDT)](BPh4)2, [(dien)Cu-Ox-Cu(dien)](BPh4)2, [(dien)Cu-Ox-Ni(dien)](BPh4)2, [(dien)Cu-Ox-Zn(dien)](BPh4)2, where Ox = oxalate and BPh4 = tetraphenylborate He has determined nuclear charge and percentage covalency from chemical shifts and has correlated edge width with coordination stoichiometry nearest neighbour distances have also been found out. He has also correlated Wiener index, Zagrab index and Randic index with chemical shifts. Ram Dayal Gupta (2006) has studied copper K absorption spectra of the three sets of the following copper complexes. They were: (1) [(salgly)Cu(H2O)], [(salgly)Cu(ImH)], [(salgly)Cu-Im-Cu(salgly)]Na, [(salgly)Cu-Im-Zn(salgly)]Na, [(salgly)Cu-Im-Ni(salgly)]Na, where salgly = salicylideneglycinate and ImH = imidazole. (2) [(glygly)Cu(H2O)], [(glygly)Cu(ImH)], [(glygly)Cu-Im-Cu(glygly)]Na, [(glygly)Cu-Im-Zn(glygly)]Na, [(glygly)Cu-Im-Ni(glygly)]Na, where glygly = glycylglycine. (3) [(glyval)Cu(H2O)], [(glyval)Cu-Im-Cu(glyval)]Na, [(glyval)Cu-Im-Zn(glyval)]Na, where glyval = glycylvaline These studies are similar to those of Vyas (2006). In all of these investigations (except the one mentioned above by Bhakt Darshan Shrivastava), the laboratory X-ray spectroscopic set-up has been used 31

which employs photographic method of registration of spectra. This type of setup, which has been used in our laboratory for the last 40 years, comprises of low power (0.5kW - 3kW) X-ray tubes and Cauchois-type curved mica crystal spectrographs employing X-ray films as detectors. After obtaining a number of spectrograms, the analog and digital spectral records are obtained with the help of a Carl-Zeiss GII microphotometer. These analog and digital spectral records have been analyzed manually. The results about X-ray absorption edge energies, edge structures, near edge structures and extended fine structures have been reported. The data has generally been analyzed qualitatively and empirically to yield useful information about molecular structure. The data has also been analyzed through some established relations to yield information about valency, effective nuclear charge, coordination type, average bond length etc. To our knowledge, the data has not been analyzed using Fourier transform and fitting procedures which have now become standard methods of EXAFS data analysis. Only in the last two theses (Hinge 2010 and Johari 2011), the digital spectral data have been processed using the computer programs Athena and Artemis. The details are given below: Vijay Hinge (2010) has studied the structure of the following 22 copper complexes using laboratory X-ray spectroscopic set-up, having 0.5kW X-ray generator, fixed tungsten target X-ray tube, Cauchois type curved mica crystal spectrograph, photographic method of registration of spectra, microphotometer etc. The digital X-ray spectroscopic data were processed using Athena. Chemical shift, edge-width, and shift of principal absorption maximum for these complexes have been reported and the effective nuclear charge and percentage covalence in these complexes have been estimated. From the positions of EXAFS maxima and minima bond lengths have been estimated using various methods viz., Levy (1965, 1966), Lytle (1964, 1966) and Lytle, Sayers and Stern (LSS) (1975). The extended absorption fine structure (EXAFS) has not been analyzed using theoretical models, as is generally done currently when the spectra are recorded using an X-ray spectroscopic set-up on a synchrotron. Only one copper complex, i.e., Cu(en)2(ONO2)2 has been studied using beamline BL-8 at Indus-2 synchrotron at RRCAT, Indore. The data has been analyzed using

32

Fourier transform and fitting procedures and structural parameters have been obtained. Following complexes have been studied. (1) X-ray K-absorption studies of Cu(II) mixed ligand complexes with benzimidazole as one of the ligands: Cu(BzIm)2, Cu(BzImH)4(NO3)2, Cu(BzImH)4 (ClO4)2 , Cu(BzImH)4SO4, Cu(BzImH)4Cl2, Cu(BzImH)4 Br2, (2) X-ray K-absorption studies of Cu(II) mixed ligand complexes with ethylenediamine (en) as one of the ligands: Cu(en)2(ClO4)2, Cu(en)2(ONO2)2, Cu(en)2(SCN)2, Cu(en)2Cl2.H2O, Cu(en)2Br2.H2O, Cu(en)2SO4, Cu(asp).2H2O, Cu(glu).2H2O. (3) X-ray K-absorption studies of Cu(II) mixed ligand complexes with tetramethylethylenediamine (tmen) as one of the ligands : Cu(tmen)Cl2, Cu(tmen)Br2, Cu(tmen)(ox).4H2O, Cu(tmen)(acac) (ClO4), Cu(tmen)(en)SO4. 4H2O, Cu(tmen)(gly)ClO4, Cu(tmen)(bipy)(ClO4)2 and Cu(tmen)(phen)(ClO4)2. Ajita Johari (2011) has recorded X-ray absorption spectra at the K-edge of copper in the copper complexes using two experimental set-ups. The first type of the set-up is laboratory X-ray spectroscopic set-up and the photographic method of registration of spectra. The second type of set-up is the EXAFS beamline BL-8 at the Indus-2 synchrotron source at RRCAT, Indore. K absorption spectral studies have been carried out on the following nine mixed ligand copper complexes with imidazole (ImH) as primary ligand and five mixed ligand copper complexes with 2,9-dimethyl-1,10-phenanthroline (dmp) as primary ligand (1) Cu(ImH)4(ClO4)2, Cu(ImH)4(NO3)2, Cu(ImH)4Cl2, Cu(ImH)4Br2, Cu(ImH)2Cl2, Cu(ImH)4SO4, [Cu(ImH)6](NO3)2, [Cu(ImH)2](Im-)Cl] and [Cu2(dien)2(Im-)](CIO4)3, where ImH = Imidazole, Im- = Imidzolate anion and dien = diethylenetriamine (2) [CuI(dmp)2]ClO4, [CuII(dmp)2](ClO4)2, Cu(dmp)2Cl2, [CuI(dmp)2]1/2SO4 and [Cu(dmp)2]SO4, where dmp = 2,9-dimethyl-1,10-phenanthroline. The various parameters determined from her study of the copper K absorption spectra of the copper complexes are - position of inflection point of the absorption edge and principal absorption maximum, edge-width, position of maxima and minima of the EXAFS etc. The data for chemical shift of the 33

absorption edge and the shift of the principal absorption maximum have been interpreted to yield useful structural information about the complexes and the effective nuclear charge have been reported. The estimated edge-widths have been correlated with the stoichiometry of the complexes. From the positions of the EXAFS maxima and minima, bond lengths have been estimated from three different methods - (i) Levy’s method (1965, 1966), (ii) Lytle’s method (1964, 1966) and (iii) Lytle, Sayers and Stern (LSS) method (1975). The absorption spectra, i.e., the absorption coefficient µ(E) versus energy E curves have been normalized and converted to χ(k) versus k curves. They have been then Fourier transformed. The Fourier transformed spectra peaked at the bond lengths. The distances of the absorbing atom from the neighbours (bond lengths) are shorter than the actual distances due to the scattering phase-shifts being not taken into account. However, the relative order of the bond lengths have been compared with the results obtained from different methods. Finally, the effects of variation of the secondary ligands on the various parameters have been discussed. It has been observed that the results obtained from the laboratory X-ray spectroscopic set-up employing the photographic method of registration of spectra are comparable with those obtained from the Indus-2 synchrotron EXAFS beamline (Johari et al., 2011). She has, however, made no attempt to fit theoretical models to the experimental EXAFS data. In the present work, the author has carried out X-ray absorption spectroscopic investigations using only synchrotron radiation. The EXAFS data for copper complexes has been analyzed using Fourier transform and fitting procedures and structural parameters have been obtained. XANES has been used for speciation of several mixtures of copper compounds in different ratios. 1.15.2 Review of the work done on speciation Speciation has already been defined and described in section 1.11. Some important recent reports on the work done on speciation have been reviewed below: Work done by Beauchemin et al. (2002) The objective of their research was to evaluate principal component analysis (PCA) coupled with target transformation to model S K-XANES spectra 34

of humic acid samples, and to compare the results with least-squares LCF. The selected standard and the scaling coefficients obtained by the PCA approach deviated by ≤ 6 mol% from results obtained by performing LCF using a large number of binary, ternary, and quaternary combinations of seven standards, i.e., benzyl disulfide, cysteic acid (sulfonate), benzyl sulfoxide, methionine (organic sulfide), Na2SO4 (inorganic sulfate), and chitin sulfate (ester sulfate) and elemental S. They have concluded that statistical ranking of the most likely standard spectra contributing to the unknown spectra enhanced LCF by reducing the analysis to a smaller set of standard spectra. They have also found that the PCA approach is a valuable complement to other spectral fitting techniques as it provides statistical criteria that improve insight to the data, and lead to a more objective approach. Work done by Frenkel et al. (2002) As a quantitative structural technique EXAFS spectroscopy has largely been limited by its application to the microscopically homogeneous systems, in which the local environment around each absorbing atom in the sample is the same. The growing interest in time-resolved EXAFS studies of systems in physics, chemistry, biology, and materials science, however, requires an analytical tool to probe heterogeneous mixtures in situ. EXAFS studies of mixtures have been particularly difficult due to the strong model dependence and correlations between parameters in the fit. To circumvent these drawbacks, they have introduced two new techniques in EXAFS analysis: the principal component analysis and the residual phase analysis. Using a test case of a heterogeneous mixture of two organometallic cobalt compounds, i.e, cobalt acetylacetonate and cobalt tetraphenyl-prophine, they have demonstrated that these new EXAFS modeling techniques, together with the existing one, the multiple datasets fit method are the most suitable and adequate methods for phase speciation. In addition, they have discussed the application of these data analysis approaches to biological systems. Work done by Lamberti et al. (2003)

35

They have illustrated the use of XANES spectroscopy, both in classical and in dispersive geometries, for the study of copper-based catalysts under in situ or in operando conditions. As case studies, copper-exchanged MFI zeolites and CuCl2/γ-Al2O3 systems are considered. In the former case, in situ XANES spectroscopy was used to characterise well defined complexes (Cu+N2, Cu+(CO)3, Cu+(NH3)(CO) and Cu+(NO)2) formed on copper ions inside the zeolite cavities under controlled conditions. From these results, useful information concerning the symmetry of the formed complexes has been gained. The latter case showed the use of dispersive XANES spectroscopy allows in real time, the evolution of a system in working conditions. The simultaneous determination of the catalyst activity and of the average oxidation state of copper in the catalyst allows the evolution of a system in working conditions to be followed in real time. The criteria used for the quantification of the Cu(I) and Cu(II) fraction from XANES spectra have been discussed in detail. Work done by Strawn et al. (2008) Bioavailability of Cu in the soil is a function of its speciation. In their research paper they have investigated Cu speciation in six soils using X-ray absorption near edge structure (XANES), extended X-ray absorption fine structure (EXAFS), and synchrotron-based micro X-ray fluorescence (µ-XRF). The XANES and EXAFS spectra in all of the soils were the same. µ-XRF results indicated that the majority of the Cu particles in the soils were not associated with calcium carbonates, Fe oxides, or Cu sulfates. Principal component analysis and target transform of the XANES and EXAFS spectra suggested that Cu adsorbed on humic acid (HA) was an acceptable match. Thus it has been shown that Cu in all of the soils is primarily associated with soil organic matter (SOM). Theoretical fitting of the molecular structure in the soil EXAFS spectra revealed that the Cu in the soils existed as Cu atoms bound in a bidentate complex to O or N functional groups. Work done by Huggins et al. (2009) They have made a detailed comparison of determinations by

57Fe

Mössbauer spectroscopy and four different XAFS spectroscopic methods of %Fe 36

as hematite and ferrihydrite in 11 iron-based SBA-15 catalyst formulations. The four XAFS methods consisted of least-squares fitting of iron XANES, d(XANES)/dE, and EXAFS (k3chi and k2chi) spectra to the corresponding standard spectra of hematite and ferrihydrite. The comparison showed that, for this particular application, the EXAFS methods were superior to the XANES methods in reproducing the results of the benchmark Mössbauer method in large part because the EXAFS spectra of the two iron-oxide standards were much less correlated than the corresponding XANES spectra. Furthermore, the EXAFS and Mössbauer results could be made completely consistent by inclusion of a factor of 1.3±0.05 for the ratio of the Mössbauer recoilless fraction of hematite relative to that of ferrihydrite at room temperature (293 K). This difference in recoilless fraction is attributed to the nanoparticle nature of the ferrihydrite compared to the bulk nature of the hematite. Also they have discussed the possible alternative non-least-squares XAFS methods for determining the iron speciation in this application as well as criteria for deciding whether or not least-squares XANES methods should be applied for the determination of element speciation in unknown materials. Work done by Legros et al. (2010) The aim of their study was to present a multitechnique approach to investigate Cu speciation in pig slurry. Firstly, size fractionation and chemical characterization of each size fraction were performed to complement results obtained in raw samples. Micro X-ray fluorescence spectroscopy (µXRF) highlighted the colocalization of Cu and sulfur (S). Finally, X-ray absorption near-edge structure spectroscopy (XANES) showed that Cu speciation in raw pig slurry and size fractions could be described by Cu2S and that its oxidation state is Cu(I). In addition, geochemical calculation demonstrated that chalcocite (Cu2S) was the major Cu species present under pig slurry lagoon physical-chemical conditions. This Cu speciation in pig slurry may be the main reason for the observed Cu accumulation at the soil surface. 1.15. 3 Review of the work done on copper complexes

37

Some important recent reports on the work done on speciation have been reviewed below: Work done by Kau et al. (1987) Kau et al., (1987) have done pioneering work on K absorption spectra of copper compounds and complexes, which is widely referred by research workers. They have focused their studies on XANES part only. Hence, anybody, who wants to study XANES of copper compounds or complexes, should first study this research work. In their research paper, Kau et al., have systematically studied K absorption XANES spectra of 19 Cu(I) and 40 Cu(II) model compounds and complexes. The Cu K-edge features have been correlated with oxidation state and geometry. According to Kau et al., all Cu(I) compounds exhibit a low energy peak maximum in the region between 8983 and 8986 eV. Alternatively, the Cu(II) compounds exhibits only a broad low energy tail in the region below 8985.0 eV. The appearance of a pre-edge peak below 8985.0 eV in the Cu absorption edge spectrum indicates the presence of Cu(I) in the sample. Some Cu(I) complexes have their pre-edge intensity maxima at energy somewhat higher than 8985.0 eV. Therefore, the lack of a pre-edge feature below 8985.0 eV does not necessarily mean that Cu(I) is not present in the sample. This requires the assignment of this 8983-8984 eV peak as the 1s→4px,y electric dipole-allowed transition. For the linear 2-coordinate Cu(I) complexes, this would involve repulsive interaction along the z axis which raises the energy of the antibonding copper 4pz molecular orbital relative to the 4px,y levels. In addition, covalent ligand overlap along the z axis will reduce the intensity of the 1s→4pz transition, as this mixing lowers the Cu 4pz character in this antibonding orbital. Thus, the transition from 1s to the doubly degenerate 4px,y final state would result in an intense pre-edge peak at lower energy than the 1s→4pz transition. All of the Cu(II) complexes studied have a very weak 8979 eV peak which corresponds to the 1s→3d transition. In addition, many Cu(II) complexes exhibits a rather intense peak (normalized absorption amplitude of 0.62-0.68) on the absorption edge at energies between 8986 and 8988 eV. Cu(II) peak is always observed at energies greater than 8985.0 eV and thus will not complicate the Cu(I) 1s→4p region between 8983.0 and 8985.0 eV. 38

Work done by Riggs et al. (1995) They have extensively used the X-ray absorption fine structure (XAFS) spectroscopy for investigating the local structural environment of metal ions in metalloproteins. Although it is widely accepted that XAFS provides accurate structural information for the nearest neighbors to the metal (i.e., the ligands), the use of XAFS for determining metal-metal distances in multi-nuclear proteins is more problematic. They have reviewed the origin of the information in XAFS spectra and discussed some of the limitations that apply in extracting structural data from XAFS spectra. Recent advances in the theory and application of XAFS for determining metal-metal distances are also reviewed, with particular emphasis on dinuclear iron and manganese proteins and models. They have concluded that for distances less than 3 Å, it is straightforward to determine accurate metal-metal separations using XAFS. For distances > 3 Å, the unique assignment of an XAFS feature to a metal-metal interaction continues to be difficult, despite recent advances in XAFS theory and analysis. However, when additional information is available to constrain the possible metal site structures, XAFS can provide very accurate metal-metal distances. Work done by Westre et al. (1997) Though this research paper concerns Fe K absorption spectra, it is worthwhile to mention this work here because the findings are similar to those expected in case of Cu K absorption spectra. In this paper, the authors have studied X-ray absorption Fe K-edge data on ferrous and ferric model complexes to establish a detailed understanding of the 1s-3d pre-edge feature and its sensitivity to the electronic structure of the iron site. The energy position and splitting, and intensity distribution, of the pre-edge feature were found to vary systematically with spin state, oxidation state, geometry, and bridging ligation (for binuclear complexes). A methodology for interpreting the energy splitting and intensity distribution of the 1s-3d pre-edge features was developed for high spin ferrous and ferric complexes in octahedral, tetrahedral, and square pyramidal environments and low-spin ferrous and ferric complexes in octahedral environments. In each case, the allowable many-electron excited states were 39

determined using ligand field theory. The energies of the excited states were calculated and compared to the energy splitting in the 1s-3d pre-edge features. The relative intensities of electric quadrupole transitions into the many electron excited states were obtained and compared to the intensity pattern of the preedge feature. The effects of distorting the octahedral iron site to tetrahedral and square pyramidal geometries were analyzed. The contributions to the pre-edge intensity from both electric quadrupole and electric dipole (from 3d-4p mixing) intensity mechanisms were established for these distorted cases; the amount of 4p character and its distribution over the many-electron final states were experimentally estimated and compared to theoretical predictions from density functional calculations. Work done by Penner-Hahn (1999) In this review, the physical basis of XAS is reviewed, the advantages and limitations of the technique are discussed, and several examples of the applications of XAS to coordination chemistry are presented. The prospects for future applications of XAS are summarized. Work done by Manceau and Matynia (2010) Using XANES and EXAFS spectroscopy, along with supporting thermodynamic equilibrium calculations and structural and steric considerations, the authors have shown evidence at pH 4.5 and 5.5 for a five-membered Cu(malate)2-like ring chelate at 100-300 ppm Cu concentration, and a sixmembered Cu(malonate))1–2-like ring chelate at higher concentration. A “structure fingerprint” is defined for the 5.0–7.0 Å-1 EXAFS region which is indicative of the ring size and number (i.e., mono- vs. bischelate), and the distance and bonding of axial oxygens (Oax) perpendicular to the chelate plane formed by the four equatorial oxygens (Oeq) at 1.94Å. Work done by Aquilanti et al. (2011) They have investigated, both in the solid state and in aqueous solution, the coordination environment and stability behavior of four macrocyclic ligands (three N2S2 and one N3S2) and of the corresponding Cu(II) complexes. The 40

structural characterization in the solid state of the copper derivatives was performed by X-ray absorption spectroscopy. Copper is found to be 4-fold coordinated with a CuN2S2 environment with different Cu–S distances depending on the size of the macrocyclic ring. The EXAFS technique has indicated that nitrogen and sulfur atoms are more preferable to oxygen atoms as donor systems, without the evidence of coordination of the carboxylic moieties to copper in the first shell. The joint EXAFS and XANES study of the copper(II) complex with the N3S2 ligand confirms the 4-fold coordination with an additional long Cu–N interaction. 1.16 Present work The object of the present study is to carry out systematic investigations in the K absorption spectra of copper compounds and complexes. The X-ray absorption spectra are best recorded when a highly intense beam of X-rays from a synchrotron is used along with a good resolution double crystal or curved crystal spectrometer and

detectors like ionization chambers, scintillation

counters, solid state detectors etc. Several synchrotrons around the world have X-ray beamlines dedicated specifically to XAFS spectroscopy. In the present work, four beamlines at four different synchrotrons have been used for recording Cu metal K absorption spectra. The present thesis describes the results of the Xray K-absorption fine structure studies carried out on some copper compounds and complexes. The work has been divided into ten chapters. The present chapter is introductory in nature and describes the basic phenomenon of the absorption of X-rays. The terms used in the X-ray absorption spectroscopy have been explained. The various parameters that can be determined from the X-ray spectroscopic measurements and the information that can be obtained from them have been discussed. In the recent years XAFS has proved to be an important tool in structure determination. Detailed review articles are now available in literature on XAFS. In the present chapter, theory of EXAFS has been given in brief and the method of extracting parameters has been outlined. 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 and that the 41

parameters determined by XANES and EXAFS (combined called as XAFS) relate to the local environment surrounding the absorbing atom. Transition metals are important as many of the metals e.g., copper, cobalt etc. are used in bonding of metals for many models of proteins, as trace elements in the modern pharmaceuticals etc. The mixed ligand complexes are important in bioinorganic chemistry and in biological processes. Complexation with copper enhances the biological activity of a wide variety of organic ligands. The study of binuclear complexes of Cu (II) is very active and highly interesting field due to their significance in bioinorganic chemistry, magnetochemistry, multimetal centre catalysis, materials science, superconductivity and multielectron redox chemistry (Melnic et al., 1998, Spiro, 1991, Soloman et al., 1983). These complexes are also of theoretical interest, because they provide examples of the simplest case of magnetic interactions with only two unpaired electrons. Also, these

complexes

exhibit

ferromagnetic

or

antiferromagnetic

exchange

interactions (Elerman et al., 2003)]. Binuclear hydroxo-bridged copper (II) complexes have been found (Meinders et al., 1979) to be catalytically active for oxidative coupling reactions, a fact that adds to the practical importance of studying the electronic structure of such complexes. Hence, for the present study we have chosen five series of mixed ligand complexes of copper. The results of these studies are described in chapters IV to IX. Chapter II gives the experimental details. The copper complexes studied in this thesis have been prepared by Dr. Jagdish Prasad and Dr. Krishna Shrivastava at the Department of Chemistry, Allahabad University, Allahabad. The absorption screens have been prepared by the author by standard methods at RRCAT, Indore. The details of the four EXAFS beamline at four different synchrotron facilities, where the X-ray absorption spectra have been recorded, are described in this chapter. The copper K-edge EXAFS spectra of the complexes studied in chapters IV, VII and IX have been recorded at the BL-8 dispersive EXAFS beamline at 2 GeV Indus-2 synchrotron source at Raja Ramanna Center for Advanced Technology (RRCAT), Indore, India (Bhattacharyya et al. 2009 a,b and Das et al. 2004).

42

The copper K-edge XAFS spectra of the copper complexes studied in chapter V, VI and VIII were recorded at EXAFS beamline 11.1 at ELETTRA Synchrotron Light Laboratory, Basovizza, Italy. The copper K-edge XAFS spectra of the copper compounds and their mixtures studied in chapter X were recorded at three EXAFS beamlines, namely, (1) EXAFS beamline X-19A at National Synchrotron Light Source (NSLS), Brookhaven National Laboratory, Upton, New York, USA, (2) EXAFS beamline 11.1 at ELETTRA Synchrotron Light Laboratory, Basovizza, Italy and (3) EXAFS wiggler beamline 4–1 at the Stanford Synchrotron Radiation Laboratory (SSRL), Stanford, California, USA. The method of calibration of BL-8 dispersive EXAFS beamline at 2 GeV Indus-2 synchrotron source at Raja Ramanna Center for Advanced Technology (RRCAT), Indore, India has been outlined by the author and others (Gaur et al., 2011, Johari, 2011). The same is reproduced in brief in chapter III of this thesis. The author has also made a comparative study of the XAFS spectra recorded at this beamline with those recorded at three other well known synchrotron EXAFS beamlines, in order to evaluate the quality and reliability of the recorded data and the usefulness of this beamline. This has also been described in chapter III, where it has been demonstrated that the results obtained from the EXAFS spectra recorded at this beamline are comparable to those obtained from other synchrotron EXAFS beamlines. This attempt appears to be the first in this direction. In chapter IV, EXAFS have been recorded at the K-edge of copper in binuclear

monohydroxo-bridged

copper(II)

complex

[(bpy)2Cu-OH-

Cu(bpy)2](ClO4)3 , its analogous complex [(phen)2Cu-OH-Cu(phen)2](C1O4)3 and dihydroxo-bridged copper(II) complex [Cu2(µ-OH)2(bipy)2]SO4.5H2O, its analogous complex [Cu2(µ-OH)2(phen)2]SO4.5H2O (where bpy and phen are 2,2'-bipyridine and 1,10-phenanthroline, respectively), using the dispersive EXAFS beamline at 2 GeV Indus-2 synchrotron source at RRCAT, Indore, India.

Theoretical

models

have

been

generated

using

the

available

crystallographic data and then fitted to the experimental EXAFS data to obtain the structural parameters, which include bond-lengths, coordination numbers and thermal disorders. The structural parameters, thus determined have been 43

reported. Further, the oxidation states of copper have been determined in all of these complexes. In the chapter V, Extended X-ray absorption fine structure (EXAFS) spectra have been studied at the Cu K-edge in copper(II) complexes, having analogous structures, viz., [Cu(L-glu)(bpy)], [Cu(L-glu)(o-phen)(H2O)].3H2O, [Cu(bipy)(L-tyro)]Cl, Cu(L-phen)(bpy)H2O(ClO4) and Cu(L-tyr)(phn).2.5H2O (ClO4). The aim of the present work is to show that if the crystal structure is not available for a complex, then the crystal structure of a similar or analogous complex can be used satisfactorily for generating the theoretical model for the EXAFS data analysis of that complex. By using the crystallographic data of the five complexes, five theoretical models have been generated. Firstly, EXAFS data of each complex has been fitted to its own theoretical model and then with theoretical models of the four remaining complexes. The structural parameters determined from the analysis of the EXAFS spectra have been reported and the coordination geometry about the copper (II) ion has been depicted. To our knowledge, the EXAFS study of these mixed ligand complexes have not been made earlier. In chapter VI, XAFS have been investigated at the K-edge of copper in mononuclear and binuclear copper(II) salen/salophen complexes: [Cu(salen)], [Cu(salen)CuCl2].H2O , [Cu(salophen)] and [Cu(salophen) CuCl2].H2O (where salen = N,N’-ethylenebis (salicylideneiminato) dianion and salophen = N,N’-ophenylenediaminebis (salicylideneiminato) dianion), using EXAFS beamline 11.1 at ELETTRA Synchrotron Light Laboratory, Basovizza, Italy. From EXAFS analysis the different geometries around the copper centers have been determined. The different XANES features for the four complexes have been identified and discussed. The intensity of ls→3d pre-edge feature has been used to investigate the geometry and binuclear nature of the complexes. Further, the oxidation states of copper have been determined in all of these complexes. In chapter VII, EXAFS spectra have been recorded at the Cu K-edge in four copper(II) complexes [Cu(5,5’Me2bipy)(salicylate¯)]NO3, [Cu3(NA)4(dca)2 (H2O)8].2H2O,

[Cu2(2,2’-bipy)(NA)2](ClO4)2.H2O

and

[Cu(5,5’Me2bipy)

(malonate¯)(H2O)](ClO4) (where Me2bipy = 4,4’-dimethyl- 2,2’-bipyridine; NA = Nicotinic acid; dca = dicyanamide anion), using the dispersive EXAFS 44

beamline at 2.5 GeV Indus-2 synchrotron source at RRCAT, Indore, India. The aim of the present work is to investigate the copper K-edge EXAFS spectra of the copper (II) complexes having different coordination environments and geometries. First complex is supposed to have four coordinated geometry, second complex six coordinated geometry and third and fourth complexes five coordinated geometry. These complexes have been chosen to show how theoretical models can be generated for complexes having different coordination environments and geometries and how the EXAFS data can be analyzed to obtain the structural parameters. To our knowledge, the EXAFS studies of these mixed ligand complexes have not been made earlier. In chapter VIII, EXAFS spectra of the complexes, Cu4(thu)6(NO3)4 (H2O)4, Cu4(thu)9 (NO3)4 (H2O)4 , Cu2(thu)5](SO4).3H2O, Cu2(thu)6](SO4).H2O and Cu(thu)Cl.0.5H2O (where thu = thiourea) having different types of coordination environment, have been analyzed to yield the geometry around the central metal ion. First four complexes have more than one copper center. The coordination geometries of Cu centers in the first four complexes are either tetrahedral or trigonal planar or both, which have also been verified from the EXAFS data analysis. The crystal structure of the fifth complex is unavailable due to inability of growing its single crystals. This study is important because not only it has been possible to predict the geometry of the Cu center but also to find the bond lengths from the EXAFS analysis, specially when it has not been possible to study the structure by crystallography due to inability of growing of single crystals of the complex. Further, the oxidation states of copper have been found in all of these complexes. In chapter IX, a trinuclear Schiff-base copper complex tetraaqua-di-µ3(N-salicylidene-DL-glutamato)-tricopper(lI)heptahydrate,

[Cu3(C12H10NO5)2

(H2O)4].7H2O, in which three metal sites are present, has been studied using EXAFS spectroscopy. One metal site is square-pyramidal (4+1) and other two similar metal sites are tetragonally distorted octahedral (4 + 2). EXAFS has been recorded at the K-edge of copper in the complex, using the dispersive EXAFS beamline at 2 GeV Indus-2 synchrotron source at RRCAT, Indore, India. Using the available crystal structure of the complex, theoretical models have been generated for the different copper sites separately, which are then fitted to the 45

experimental EXAFS data. The contributions of the different copper sites to the experimental spectrum have been estimated and the structural parameters, which include bond-lengths, coordination numbers and thermal disorders, for the different copper sites have been reported. Further, the oxidation states of copper have been found at these metal sites. Chapter X gives the details of work done on speciation. The objective of the present work is to make a comparison of the different methods of speciation by taking several examples of mixtures of Cu(I) and Cu(II) compounds. The following four studies have been done for this purpose 1. XAFS at the copper K-edge has been recorded for cuprous oxide and cupric oxide separately and also for a mixture of the two in a specific ratio. The LCF method and the normalized difference absorption edge analysis have been used for extracting the information about the proportions of the Cu2O and CuO. This work was done at EXAFS wiggler beamline 4-1 at the Stanford Synchrotron Radiation Laboratory (SSRL), Stanford, California, USA. 2. Mixtures have been prepared by mixing cuprous chloride and cupric chloride in five different proportions. The X-ray absorption spectra have been recorded at the copper K-edge in the mixtures. The spectra of the two chlorides have also been recorded separately and their different characteristic features have been identified. XANES have been analyzed for extracting the information about the proportions of the CuCl2 and CuCl in the mixtures, using the different methods. This work was done at EXAFS beamline X-19A at National Synchrotron Light Source (NSLS), Brookhaven National Laboratory, Upton, New York, USA. 3. Further, we have chosen Cu(I) compounds (Cu2O, CuCl and CuBr)and Cu(II) compounds ( CuO, CuCl2 and CuS ) as the different species in powder form (solid state). They have been mixed in definite proportions to make a number of mixtures. The X-ray absorption spectra at the K-edge of copper in the mixtures as well as in the standard compounds, separately, will be taken under similar conditions at room temperature. The data has been analyzed to yield the proportions of the species in the sample by LCF method. The experiments have been performed at EXAFS beamline 11.1 at ELETTRA Synchrotron Light Laboratory, Basovizza, Italy. 46

4. Lastly, studies on speciation have been done in mixtures of copper complexes. Three heterogeneous mixtures of four copper complexes, i.e., [Cu (thu) Cl 0.5H2O], [Cu(L-phen)(bpy) H2O], [Cu(L-tyr)(phn) 2.5H2O] and [Cu(din)(ina)] have been studied. The different methods of speciation have been used to yield the proportions of the complexes in the mixtures. The experiments have been performed at EXAFS beamline 11.1 at ELETTRA Synchrotron Light Laboratory, Basovizza, Italy. The references for all the chapters are given at the end of the thesis. The author has published six research papers. They are given in the appendix. In the appendix are also reproduced the features of the four computer software programs Athena, Artemis, Hephaestus and SixPack which have been used in the present thesis for XAFS data analysis, in order to make readers well acquainted with these software programs.

*****

47

Fig. 1.1 Schematic of an x-ray absorption measurement in transmission mode. After the x ray has traversed a distance x into the slab, the intensity has been reduced to I=I0e-µx, where µ is the definition of the absorption coefficient (Rehr and Albers 2000).

EXAFS

XANES

Pre-edge

Fig. 1.2(a) The normalized K absorption spectrum of copper metal recorded at EXAFS beamline 11.1 at Elettra, Italy, showing the pre-absorption, XANES and EXAFS regions

48

K1

S

K2

A

P

Fig. 1.2(b) Portion of the normalized spectrum given in Fig.1.2(a). The edge position is determined from the inflection point

K1

S

K2

A

Fig. 1.2(c) First derivative of the spectrum given in Fig.1.2(b). The edge position is determined from the yellow dot.

49

Fig. 1.2(d) Second derivative of the spectrum given in Fig.1.2(b). The zero crossing (yellow dot) shows the position of the edge.

Fig. 1.2(e) Fourier transform of the spectrum given in fig 1.2(a).

50

Fig. 1.3 Cartoon of X-ray absorption through the photoelectric process. When an X-ray has the energy of a tightly bound core electron level, E0, the probability of absorption has a sharp rise. In the absorption process, the tightly bound core-level is destroyed, and a photoelectron is created.The photoelectron travels as a wave with wave number proportional to (E−E0). (Newville, 2004)

Fig. 1.4 XAFS occurs because the photo-electron can scatter from a neighboring atom. The scattered photo-electron can return to the absorbing atom, modulating the amplitude of the photo-electron wave-function at the absorbing atom. This in turn modulates the absorption coefficient µ(E), causing the EXAFS. (Newville, 2004) 51

Fig. 1.5 Functional forms for f(k) (top) and δ(k) (bottom) for O, Fe, and Pb showing the dependence of these terms on atomic number Z. The variations in functional form allow Z to be determined (±5 or so) from analysis of the EXAFS. (Newville, 2004)

Fig.1.6 The photo-electron mean-free-path for XAFS λ(k), representing how far the photo-electron can travel and still participate in the XAFS. This term includes both the inelastic scattering of the photo-electron, and the effect of the finite lifetime of the core-hole. (Newville, 2004)

52

Phase (i) KE

2kR

(ii) 2kR- δs

(iii) 2kR- δs- 2δa KE Absorber

Scatterer

Fig. 1.7 Schematic illustration of the contributions to the total phase in the EXAFS sine function. The thickness of the arrows is suggestive of the relative speeds of the photoelectron. (i) The phase delay is equal to 2kR, reflecting the time required for the photoelectron to travel out to the scatterer atom and return, (ii) This his phase is decreased by an amount δs because near the scatterer the kinetic energy of the electron is increased thereby decreasing the time required to transverse the 2R distance (represented by thick arrow at the scatterer) and (iii) The he phase is decreased by the additional term 2δa because near the absorber core the photoelectron kinetic energy rgy is also larger (represented by thick arrows at the absorber).(figure taken from Koningsberger Koningsberg et al., 2000).

53

Fig. 1.8 Selected single and multiple scattering pathways for a tetraatomic system. (Top) Geometry of the absorber (A) relative to the three scattering atoms. The positions can be specified by three distances and two angles (for a planar system). (Bottom) Scattering pathways for outgoing and backscattered photoelectron (indicated by arrows). Left column is for the nearest neighbor, S1; Middle for S2; and Right for S3. For S1, only the single scattering pathway is shown. For S2, both double and triple scattering pathways are also indicated. For S3, only two of the possible double scattering pathways are shown. Note that, for a nonplanar system, several additional distances and angles are required to completely specify the scattering pathways. In general, all possible multiple scattering pathways (of which only a small fraction are shown) will contribute to the observed EXAFS, each with oscillations of slightly different frequency. (Penner Hahn, 1999)

54

CHAPTER II EXPERIMENTAL 2.1 Introduction In the School of Studies in Physics, Vikram University, Ujjain, regular experimental and theoretical work on X-ray absorption spectroscopy has been done, which has been submitted as Ph.D. theses of research scholars and published in the form of about 100 research papers in international journals. A book based on proceedings of a conference on X-ray spectra (held in Ratlam, M.P.) has also been published (Joshi et al. 1998). Many of these theses are devoted to the study of copper and cobalt complexes (M K Gupta 1970, N K Mahajan 1981, M C Shah 1981, P K Awasthi 1982, S K Joshi 1986, A Mishra 1987, A C Gharia 1987, R C Kumawat, 1990, G D Gupta 1990, P K Sharma 1992, Bhakt D Shrivastava 1996, R Katare 2000, R K Vyas 2006, R D Gupta 2006, V K Hinge 2010 and A Johari 2011). In all of these investigations, the laboratory X-ray spectroscopic set-up has been used which employs photographic method of registration of spectra. (Shrivastava, 1972). This type of set-up, which has been used in our laboratory for the last 40 years, comprises of Cauchois type 400 mm curved mica crystal spectrograph of transmission type, X-ray generator supplied by M/S Radon House, Calcutta and tungsten target X-ray tube. The spectra are recorded on Xray films. After obtaining a number of spectrograms, the analog and digital spectral records are obtained with the help of a Carl-Zeiss GII microphotometer. These analog and digital spectral records are analyzed manually. Only in the last two theses (Hinge 2010 and Johari 2011), the digital spectral data have been processed using the computer programs Athena and Artemis. Such laboratory set-ups having low power (0.5kW - 3kW) X-ray tubes and Cauchois-type curved mica crystal spectrographs employing X-ray films as detectors have also been in use, since long, specially in many Indian laboratories. Several workers (Agarwal, 1989, Bonnelle and Mande, 1982) have been using such photographic technique and reporting the results about X-ray absorption edge energies, edge structures, near edge structures and extended fine structures. The data has generally been analyzed qualitatively and empirically to yield useful information about 55

molecular structure. The data has also been analyzed through some established relations to yield information about valency, effective nuclear charge, coordination type, average bond length etc. To our knowledge, the data has not been analyzed using Fourier transform and fitting procedures which have now become standard methods of analysis of EXAFS data recorded on synchrotron X-ray absorption spectroscopic set-ups. Only recently from our group, Johari (2011) has shown that the EXAFS data obtained from photographic method of registration of spectra can be analyzed by employing Fourier transformation and fitting procedures using Athena and Artemis. She has also shown that the structural information obtained for the first two shells is comparable with that obtained from synchrotron X-ray absorption spectroscopic set-ups. The author has also been a collaborator in this work. (Joshi et al., 2009 and Johari et al., 2011). It is well known that the X-ray absorption spectra are best recorded when a highly intense beam of X-ray from a synchrotron is used along with a good resolution double crystal or curved crystal spectrometer and detectors like ionization

chambers,

scintillation

counters,

solid

state

detectors

etc.

(Koningsberger et al., 1988). Several synchrotrons around the world have X-ray beamlines dedicated specifically to XAFS spectroscopy. The availability of synchrotron is difficult, specially because the Indian synchrotron has become operational only recently. Hence, the earlier workers employed only laboratory X-ray spectroscopic set-ups. In the present investigation, however, the author has carried out the X-ray absorption spectroscopic investigations using only synchrotron radiation. The production and characteristics of synchrotron radiation and its comparison with the X-radiation obtained from X-ray tubes is described below in brief. 2.2 Synchrotron radiation XAFS spectroscopy has developed hand in hand with the growth of synchrotron radiation research. The first useful synchrotron X-ray facilities were developed around 1970, about the time of Stern, Sayers, and Lytle’s modern synthesis of EXAFS spectra. XAFS requires an X-ray beam of finely tunable 56

energy; although it is possible to do limited experiments with a laboratory X-ray source, most experiments benefit enormously from the availability of synchrotron radiation. Consequently, nearly all modern XAFS experiments are performed at synchrotron radiation sources (SRSs). SRSs are shared regional research facilities that, with few exceptions, are operated under government support. SRSs are based on technology originally developed for high-energy physics experiments, but subsequently they have been adapted to reliably produce high-energy electromagnetic radiation such as X-rays with desirable spectral characteristics. Electrons moving close to the speed of light within an evacuated pipe are guided around a closed path of 100-1000 meter circumference by vertical magnetic fields. Wherever the trajectory bends, the electrons accelerate (change velocity vector). Accelerating charged particles emit electromagnetic radiation, and the fact that the electrons are moving at nearly the speed of light implies that relativistic effects are important. In this case, they profoundly affect the properties of the emitted radiation: the average energy of the X-rays and the total radiated power are greatly increased, and the radiation pattern becomes more directional, making it much easier to employ X-ray optics such as monochromators. Often “insertion devices” such as “wigglers” and “undulators” also are used to further enhance the characteristics of the emitted radiation. The flux of X-radiation obtained from synchrotron sources are up to 1010 larger than that obtained from X-ray tubes. The X-ray tubes emits characteristic radiation along with the continuous background. These characteristic radiations interfere with the X-ray absorption spectra to be recorded and hence limit the energy region in which only specific X-ray absorption spectra can be recorded. On the other hand synchrotron radiation is only continuous radiation and does not contain any characteristics radiation. The X-rays emitted by synchrotron have tunable energy and hence X-ray absorption spectra of almost all the elements can be recorded. Another advantage of synchrotron radiation is that the radiation is polarized. Further, the flux of X-radiation can be increased by insertion devices in straight sections. The result is that the XAFS spectra obtained using synchrotron radiation are much more cleaner (very little noise) than those obtained from X-ray tubes (large noise). 57

In the laboratory set-ups one uses X-ray spectrometers for recording the X-ray absorption spectra. In synchrotron set-ups one uses beamlines. The description of the various beamlines used in the present work is given in brief in the following section. 2.3 Synchrotron radiation beamline Synchrotron beamline refer to the instrumentation that carries beams of synchrotron radiation to an experimental end station, which uses the radiation produced by the bending magnets and insertion devices in the storage ring of a synchrotron. At a large synchrotron facility there are many beamlines, each optimized for a particular field of research. The differences will depend on the type of insertion device, the beam conditioning equipment and the experimental end station. A typical beamline is 25 to 100 m long from the storage ring to the end station. The beamline elements are located in radiation shielding enclosures, called hutches, which are of the size of a small room (cabin). A typical beamline consists of two hutches, an optical hutch for the beam conditioning elements and an experimental hutch, which houses the experiment. Between hutches, the beam travels in a transport tube. Entrance to the hutches is forbidden when the beam shutter is open and radiation can enter the hutch. This is enforced by the use of elaborate safety systems with redundant interlocking functions, which make sure that no one is inside the hutch when the radiation is turned on. The safety system will also shut down the radiation beam if the door to the hutch is accidentally opened when the beam is on. Elements that are used in beamlines by experimenters for conditioning the radiation beam between the storage ring and the end station include the following: (i)

Windows – They are made of beryllium and transmit almost the entire beam, but protect the vacuum within the storage ring.

(ii)

Slits - They control the physical width of the beam and its angular spread

(iii)

Focusing mirrors – There are one or more mirrors, which may be flat, bent-flat, or toroidal, which help to collimate (focus) the beam

58

(iv)

Monochromators – They are devices based on diffraction by crystals which select particular wavelengths.

(v)

Spacing tubes – They provide proper space between optical elements and shield any scattered radiation, maintaining vacuum.

(vi)

Sample stages – The sample under study is mounted and manipulated on the sample stages. The temperature and pressure etc. can be varied.

(vii)

Radiation detectors – They are used for measuring the radiation before and after the sample. Devices along the beamline which absorb significant power from the

beam are actively cooled by water, or liquid nitrogen. The entire length of a beamline is normally kept under ultra high vacuum conditions. The line sketch of a typical beamline, employing a double crystal monochromator (DCM), is given in fig. 2.1. The list of synchrotron facilities having XAFS beamlines across the world are listed below in table 2.1 for ready reference to any user.

Synchrotron radiation source

ionization chamber

Fig. 2.1. The line sketch of a typical EXAFS beamline using DCM.

59

Table 2.1 List of synchrotron facilities having XAFS beamlines in different countries. S.

Asia & Oceania

No 1

S. No

Australian Synchrotron

1

Victoria, Australia 2

BSRF INDUS-2

2

3

NSRF Hefei, China

5

NSRRC PAL

5

Photon Factory KEK

6

SAGA

7

SLRI, Siam

8

SPring-8

9

SSLS

10

SSRC

2

HASYLAB ISI-800 KIPT KSRS

11

MAXLAB Lund, Sweden

12

Novosibirsk, Russia

SLS Villingen, Switzerland

13

SOLEIL Saint-Aubin, France

14

TNK Moscow, Zelenograd, Russia

60

APS Argonne, IL, USA

3

CLS Saskatoon, Canada

4

LNLS Campinas, Brazil

5

NSLS Brookhaven, NY, USA

6

Moscow, Russia

Singapore 12

ESRF

Kharkov, Ukraine

Hyogo pref, Japan 11

ELETTRA

Kiev, Ukraine

Nakhon, Thailand 10

Diamond

Hamburg, Germany

Tosu, Japan 9

DELSY

Grenoble, France

Tsukuba, Japan 8

BESSY II

ALS Berkeley, CA, USA

Trieste, Italy

Pohang, Korea 7

1

United Kingdom

Hsinshu, Taiwan, ROC 6

ANKA

Dubna, Russia 4

America

No

Berlin, Germany

Indore, India 4

S.

Karlsruhe, Germany

Beijing, China 3

Europe

SSRL Stanford, CA, USA

2.4 Details of the EXAFS beamlines at different synchrotron facilities used in the present work The following four EXAFS beamlines at different synchrotron facilities have been used for recording the X-ray absorption spectra at the K-edge of copper in copper metal, copper compounds and the copper complexes, studied in the present investigation. (1) EXAFS beamline X-19A at National Synchrotron Light Source (NSLS), Brookhaven National Laboratory, Upton, New York, USA. (2) EXAFS beamline 11.1 at ELETTRA Synchrotron Light Laboratory, Basovizza, Italy. (3) EXAFS wiggler beamline 4–1 at the Stanford Synchrotron Radiation Laboratory (SSRL), Stanford, California, USA. (4) BL-8 dispersive EXAFS beamline at 2 GeV Indus-2 synchrotron source at Raja Ramanna Center for Advanced Technology (RRCAT), Indore, India. The necessity of using the different beamlines in this thesis is mainly the availability of these beamlines during the course of the present investigations. It may be remarked here that beamlines are not easily available to a user and hence whenever a beamline is available, one wants to utilize it to the maximum. We were allotted only 48 hours at Elettra, 12 hours at BNL and a few hours at SSRL which we fully utilized. The rest of the work was done at RRCAT. The details of these EXAFS beamlines are given below in brief. 2.4.1 Beamline BL-8 at RRCAT, India The X-ray absorption measurements of the copper complexes have been performed at the recently developed BL-8 Dispersive EXAFS (DEXAFS) beamline at 2·5 GeV Indus-2 synchrotron source at Raja Ramanna Centre for Advanced Technology (RRCAT), Indore. This EXAFS beam-line can be used for the X-ray absorption measurements in energy dispersive mode involving no time-consuming scanning mechanism and thus can be applied to study in-situ fast and time-resolved processes (Iwasawa, 2003). Das et al. (2004) and Bhattacharyya et al. (2009 a, b) have described this beamline in detail. The same is being described here in brief. A schematic diagram describing the principle of action of the beam-line is shown in fig. 2.2. 61

The basic idea is to use a single crystal (CC) bent in the shape of an ellipse in a particular fashion such that the source (S0) and the sample positions (S3) are situated at the two foci of the ellipse (Lee et al., 1994). White synchrotron radiation from the source (S0) is made incident on the crystal and depending on the angle of incidence of the beam and its radius of curvature, the crystal reflects a particular central energy (E0) with a certain bandwidth (∆E) and this spatially dispersed polychromatic radiation is then focused at the sample position (S3). The transmitted radiation from the sample is then detected by a positionsensitive detector (D). Thus, the energy dispersed absorption spectra of the sample over the whole band width (∆E) around the central energy (E0) is recorded on the detector simultaneously. The proposed beam-line covers the photon energy range of 5 keV to 20 keV by a bent Si (111) crystal having 2d value equal to 6.2709Å. The beam-line provides band widths of the order of 0.3 keV, 1 keV and 2 keV at photon energies of 5 keV, 10 keV and 20 keV respectively. The average resolution at the detector has been estimated to be ~1 eV per channel (Das et al., 1999). The detailed optical layout of the beam-line is shown in fig. 2.3. This figure gives a line drawing of the top-view and also the side-view of the beamline. The positions of the slit systems, pre-mirror, beryllium window, bent crystal monochromator, sample and detector are shown in this figure. The beam coming from the synchrotron source is first collimated by two copper blocks (K, K) kept at an angle of 15° with the beam path. The collimated beam with horizontal divergence of 1.5 mrad then falls on a Be window (B) of suitable thickness which help to cut-off the unwanted low-energy part from the continuum. The transmitted beam through the Be window falls on the slit (S1) which defines the final divergence of the synchrotron beam. The beam emerging from slit with required vertical and horizontal divergences falls on the crystal (CC). After reflection from the crystal the dispersed beam passes through the second slit (S2). The slit (S2) helps in shielding the scattered radiation so that the beam gets sharply focused on the sample (S3). From the sample, the beam diverges further and finally gets detected at the CCD-type position sensitive detector (D). A plane mirror (M) is then used before the detector to cut-off the

62

higher harmonics from the radiation diffracted by the Si crystal. W is the shielding wall that isolates the front-end of the beam-line from the rest portion. Fig. 2.4 shows the position of the BL-8 beamline of the Indus-2 synchrotron. Fig. 2.5 shows the photograph of the control consol and shielding hutch of the dispersive EXAFS beamline. Fig. 2.6 shows a photographic view of the beamline. Fig. 2.7 shows mechanical lay-out of the dispersive EXAFS beamline. At this beamline, the incident intensity obtained at 2.0 GeV beam energy and 50-60 mA beam current is such that the CCD detectors gets saturated even in a few microseconds when I0 is measured. Hence, the typical time to record a spectrum can be kept only a few micro-seconds. If the time is increased, the detectors get saturated. Hence, we have taken a large number of spectra keeping the time as few microseconds and then summed them up. This increases the signal to noise ratio and good spectrum is obtained. Hence, 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 method of calibration of this beamline has been outlined by the author and others (Gaur et al., 2011, Johari, 2011). The same is reproduced in brief in chapter III of this thesis. The author has also made a comparative study of the XAFS spectra recorded at the BL-8 beamline with those recorded at three other well known synchrotron EXAFS beamlines, in order to evaluate the quality and reliability of the recorded data and the usefulness of the BL-8 beamline. This has also been described in chapter III. 2.4.2 Beamline X-19A at BNL, USA The EXAFS beamline X-19A at National Synchrotron Light Source (NSLS), Brookhaven National Laboratory, Upton, New York, USA have beam energy 2.8 GeV and current 280 mA (energy range: 2.1-17 keV and energy resolution: 2x10-4). A double silicon crystal Si(111) was used as monochromator (fixed-exit double-crystal monochromator). Harmonics were suppressed by detuning the crystal spectrometer (collimating and focusing mirrors (Rh-coating) (Yang et al., 1989). The EXAFS data at the K-absorption edge of copper were obtained in the transmission mode at room temperature. Cu metal foil (8 63

mg/cm2) spectra were recorded simultaneously, for calibration, in each case. Three ionization chambers were employed as detectors. For each spectrum, the integration time was 0.5 s, the delay time was 0.3 s and the total numbers of points recorded were 510. Atleast three runs were taken for each sample. Energy was calibrated by setting the first inflection point of the copper metal K absorption edge to 8979 eV. Fig. 2.8 gives a photographic view of the beamline at BNL, USA. 2.4.3 Beamline 11.1 at ELETTRA, Italy The EXAFS beamline 11.1 at the ELETTRA Synchrotron Light Laboratory, Basovizza, Italy (Di Cicco et al., 2009, Aquilanti et al., 2011) has the storage ring operated at 2.37 GeV with a typical current of 130 mA. An internal reference of copper foil was used for energy calibration at each scan. This allows for a continuous monitoring of the energy during consecutive scans. Three ionization chambers (Oxford Instruments) were used for measurements in transmission mode. These are filled with optimal He, Ne2, Ar, Kr gas mixture at a total pressure of 2 bars and are operated at a field of 2 kV per 30 cm of length. The ionization chambers signals are amplified by Keithley amplifiers, digitalized by a voltage to frequency converters and finally read by the counters of the data collection PC. A multi-sample holder with movement on vertical axis has been provided. A removable motorized table (1.5 x 1 m) with horizontal and vertical movements is placed between the first two ion chambers. Data were acquired in transmission mode. The white beam was monochromatized using a fixed exit monochromator equipped with a pair of Si(111) crystals. Harmonics were rejected by using the cutoff of the reflectivity of the platinum mirror placed at 3 mrad with respect to the beam upstream the monochromator and by detuning the second crystal of the monochromator by 30% of the maximum. XAS spectra were collected from 8830 eV to 10000 eV in the constant k mode. Integration time from 8940-9010 was 0.5 sec and maximum integration time was 5 sec. One spectrum could be recorded in 31 minutes. The energy was defined by assigning the first inflection point of the Cu foil spectrum to 8979.0 eV. Fig. 2.9 gives a photographic view of this beamline. Fig. 2.10 gives a photograph of the control consol. Fig. 2.11 shows a photograph of the sample 64

holder. Fig. 2.12 gives a photograph of the ionistaion chambers. Fig. 2.13 shows a photograph of window of the operating program used to control the beamline, as seen on the computer screen. Fig. 2.14 shows the photograph of the double crystal monochromator (DCM) used in the beamline. 2.4.4 Beamline 4–1 at SSRL, USA The EXAFS wiggler beamline 4–1 at the Stanford Synchrotron Radiation Laboratory (SSRL), Stanford, California, USA has a double silicon crystal Si(111) which is used as monochromator. It has energy range of 5,500-38,000 eV with energy resolution 10-4. The spot size of beam obtained is 4x18 mm. Harmonics were suppressed by detuning the crystal spectrometer. The XAFS data at the K-absorption edge of copper were obtained in the transmission mode. Three ionization chambers were employed as detectors. The energy of the first inflection point of the copper metal K absorption edge was taken as 8979 eV for this purpose. In the following sections, the XAFS data recorded at these four beamlines have been abbreviated as RRCAT data, BNL data, ELETTRA data and SSRL data, respectively. 2.5 Preparation and characterization of the copper compounds and complexes The object of the present study is to carry out a systematic investigation in the K-absorption spectra of copper as follows: 1. Copper compounds: Commercially available 99.99% pure Cu(I) and Cu(II) compounds (in powder form) were mixed in the specific ratios by weight to prepare mixtures. Absorption screens were prepared of the finely powdered pure compounds and their mixtures. The copper K-edge XAFS spectra of the copper compounds and their mixtures studied in chapter X were recorded at three EXAFS beamlines, namely, (1) EXAFS beamline X-19A at National Synchrotron Light Source (NSLS), Brookhaven National Laboratory, Upton, New York, USA, (2) EXAFS beamline 11.1 at ELETTRA Synchrotron Light Laboratory, Basovizza, Italy and (3) EXAFS wiggler beamline 4–1 at the Stanford Synchrotron Radiation Laboratory (SSRL), Stanford, California, USA. 65

2. Copper complexes: The complexes were prepared by Dr. Jagdish Prasad and Dr. Krishna Shrivastava at the Department of Chemistry, Allahabad Univesity, Allahabad. The absorption screens were prepared by the author by standard methods at RRCAT, Indore. The copper K-edge EXAFS spectra of the complexes studied in chapters IV, VII and IX have been recorded at the BL-8 dispersive EXAFS beamline at 2 GeV Indus-2 synchrotron source at Raja Ramanna Center for Advanced Technology (RRCAT), Indore, India. The copper K-edge XAFS spectra of the copper complexes studied in chapter V, VI and VIII were recorded at EXAFS beamline 11.1 at ELETTRA Synchrotron Light Laboratory, Basovizza, Italy. 2.6 Preparation of samples for XAFS measurements 2.6.1 Sample preparation for XAS In transmission mode, to produce a high-quality absorption signal, the sample should be uniform and the thickness should be optimized such that the partial absorption due to the absorber atoms is approximately one absorption length (∆µx = 1) and the total absorption from all atoms in the sample is less than 2.5 absorption lengths (µx = 2.5) (Heald, 1988 a,b). The partial absorption is easily measured as it corresponds to the step height of the absorption edge in transmission mode. An incident X-ray intensity of 107 is needed to measure a sample with a total absorption length of 2.5 and this X-ray intensity is mostly available in second-generation synchrotrons. An example of the calculation of the amount of the sample required to be spread uniformly in 1cm2 area and to be used in transmission mode is given below. 2.6.2

X-ray absorption calculation The mass absorption coefficient (µρ) by a sample is the sum of

absorptions by each constituent element:

µρ = ∑ fi µρi i

(2.1)

where fi is the mass fraction of element i having mass absorption coefficient µρi. Energy dependent mass absorption coefficients for the elements are tabulated in handbooks (Elam et al., 2002) and in XAS utility programs such as Hephaestus. 66

The mass absorption coefficient µρ can be either the total mass absorption coefficient (µρ)t or the step mass absorption coefficient ∆µρ, across an absorption edge. As an example, a calculation for partial absorption and total absorption of copper complex [Cu2(2,2’-bipy)(NA)2](ClO4)2.H2O which has molecular formula C16H13ClCuN3O6.5 is given in table 2.2. This calculation is for making a tablet of this complex by mixing it with cellulose acetate. The tablet can be made in a palletizer using a die of diameter 12 mm with a cross-sectional area of 1.16 cm2 and a sample capacity of approximately 100 mg of cellulose acetate. The calculations are for yielding an edge step of 1.0 across the Cu K-edge (8979 eV) for the sample and having a total absorption length less than 2.5. The mass fraction of each element in the complex is calculated from their mole fractions and atomic weights. Because the tabulated mass absorption coefficients do not include EXAFS structure, it is reasonable to choose energies several electron volts above and below the absorption edge of the absorber element (Cu in this example). It can be seen from table 2.2 that Cu shows a sharp increase in the mass absorption coefficient across the edge energy at 8979 eV, whereas the cross sections of C, H, Cl, N and O remain essentially unchanged. The Cu concentration (ρx, g cm−2) yielding a given edge step (S) (unitless absorption) is calculated as follows: ρx = S/∆µρ

(2.2)

Multiplying S/∆µρ by the cross-sectional area of the sample holder (1.16 cm2 in this example) gives the mass of Cu in the diluted sample (converted to milligrams), which is then converted to the mass of the complex through its mass fraction of Cu. For the final Cu concentration in this example, the total sample mass includes the masses of the complex and cellulose acetate.

2.6.3

Preparation of absorption screens The particles of the sample in the absorption screen should be

considerably smaller than one absorption length of material at the energy of interest. To prepare fine particles, samples have been grounded by hand in a porcelain or agate (aluminium oxide) mortar and pestle in the present work.

67

While preparing the absorption screens care should be taken that the areal density of material presented to the beam is uniform and specially the thin regions (gaps, pin holes) are minimized. Two methods have been used to prepare absorption screens in the present study. In the first method used for preparing absorption screens, the fine particles of the sample have been uniformly coated on a commercial adhesive tape like Scotch Magic transparent tape. Multiple layers have been used to obtain the desired absorption and also to cover gaps between particles. In the second method, the sample has been uniformly mixed with a filler/binder material like cellulose acetate or boron nitride (BN). The well mixed sample has then been made into a pellet using a press (pelletizer). The effect of pin holes and size of the particles on the X-ray absorption spectra recorded using synchrotron beamlines are discussed below in brief. 2.6.4

Thickness effects or pin hole effects The absorption screens that contain regions that are nearly X-ray opaque

(large particles or dense areas) interspersed with gaps between particles of high X-ray transparency produce distortions in the spectra. The resulting spectral distortions are termed thickness effects or pin-hole effects (Heald, 1988 a,b). These distortions introduce systematic noise in the measured spectrum. Pin-hole and thickness effects are more pronounced in transmission mode than in fluorescence mode. Reducing the particle size of the sample is a remedy for thickness effects because it makes the sample more uniform and diminishes the size of interstices between particles. 2.6.5

Particle size effects In transmission mode, substantial distortions in the X-ray absorption

spectra result from inhomogeneous samples. It is generally beneficial, although not always essential, to reduce the particle size of a sample to