The effect of long-range order on intermolecular interactions in organic semiconductors: zinc octaethyl porphyrin molecular thin film model systems.

In order to optimize the performance of devices based on porphyrin thin films it is of great importance to gain a physical understanding of the various factors which affect their charge transport and light-harvesting properties. In this work, we have employed a multi-technique approach to study vacuum deposited zinc octaethyl porphyrin (ZnOEP) thin films with different degrees of long-range order as model systems. An asymmetrical stretching of the skeletal carbon atoms of the porphyrin conformer has been observed and attributed to ordered molecular stacking and intermolecular interactions. For ordered films, a detailed fitting analysis of the X-ray absorption near edge structure (XANES) using the MXAN code establishes a symmetry reduction in the molecular conformer involving the skeletal carbon atoms of the porphyrin ring; this highlights the consequences of increased π-π stacking of ZnOEP molecules adopting the triclinic structure. The observed asymmetrical stretching of the π conjugation network of the porphyrin structure can have significant implications for charge transport and light harvesting, significantly influencing the performance of porphyrin based devices.

Direct deconvolution of two-state pump-probe X-ray absorption spectra and the structural changes in a 100 ps transient of Ni(II)-tetramesitylporphyrin.

Full multiple scattering (FMS) Minuit XANES (MXAN) has been combined with laser pump-probe K-edge X-ray absorption spectroscopy (XAS) to determine the structure of photoexcited Ni(II)tetramesitylporphyrin, Ni(II)TMP, in dilute toluene solution. It is shown that an excellent simulation of the XANES spectrum is obtained, excluding the lowest-energy bound-state transitions. In ground-state Ni(II)TMP, the first-shell and second-shell distances are, respectively, d(Ni-N) = (1.93 +/- 0.02) A and d(Ni-C) = (2.94 +/- 0.03) A, in agreement with a previous EXAFS result. The time-resolved XANES difference spectrum was obtained (1) from the spectra of Ni(II)TMP in its photoexcited T(1) state and its ground state, S(0). The XANES difference spectrum has been analyzed to obtain both the structure and the fraction of the T(1) state. If the T(1) fraction is kept fixed at the value (0.37 +/- 0.10) determined by optical transient spectroscopy, a 0.07 A elongation of the Ni-N and Ni-C distances [d(Ni-N) and d(Ni-C)] is found, in agreement with the EXAFS result. However, an evaluation of both the distance elongation and the T(1) fraction can also be obtained using XANES data only. According to experimental evidence, and MXAN simulations, the T(1) fraction is (0.60 +/- 0.15) with d(Ni-N) = (1.98 +/- 0.03) A (0.05 A elongation). The overall uncertainty of these results depends on the statistical correlation between the distances and T(1) fraction, and the chemical shift of the ionization energy because of subtle changes of metal charge between the T(1) and S(0) states. The T(1) excited-state structure results, independently obtained without the excited-state fraction from optical transient spectroscopy, are still in agreement with previous EXAFS investigations. Thus, full multiple scattering theory applied through the MXAN formalism can be used to provide structural information, not only on the ground-state molecules but also on very short-lived excited states through differential analysis applied to transient photoexcited species from time-resolved experiments.

Light-induced relaxation of photolyzed carbonmonoxy myoglobin: a temperature-dependent x-ray absorption near-edge structure (XANES) study.

X-ray absorption near-edge structure (XANES) spectra at the Fe K-edge have been measured and compared on solution samples of horse carbonmonoxy-myoglobin and its photoproducts, prepared by two different photolysis protocols: 1), extended illumination at low temperature (15 K) by white light; and 2), slow-cool from 140 to 10 K at a rate of 0.5 K/min while illuminating the sample with a 532-nm continuous-wave laser source. CO recombination has been followed while increasing the temperature at a rate of 1.2 K/min. After extended illumination at 15 K, a single process is observed, corresponding to CO recombination from a completely photolyzed species with CO bound to the primary docking site (formally B-state, in agreement with previous x-ray diffraction studies). The temperature peak for this single process is approximately 50 K. Using slow-cool illumination, data show a two-state recombination curve, the two temperature peaks being roughly assigned to 50 K and 110 K. These results are in good agreement with previous FTIR studies using temperature-derivative spectroscopy. The XANES spectroscopic markers probe structural differences between the photoproduct induced by extended illumination at 15 K and the photoproduct induced by slow-cool illumination. These differences in the XANES data have been interpreted as due to light-induced Fe-heme relaxation that does not involve CO migration from the B-state. A quantitative description of the unrelaxed and relaxed B-states, including the measurements of the Fe-N(p), Fe-N(His), and Fe-CO distances, and the out-of-plane Fe displacement, has been obtained via a procedure (MXAN) recently developed by us. This work shows that XANES, being able to extract both kinetic and structural parameters in a single experiment, is a powerful tool for structural dynamic studies of proteins.

XANES quantitative structural determination of the sandwich bis(naphthalocyaninato) cerium complex.

The molecular structure of the sandwich double-decker bis(naphthalocyaninato) cerium complex was determined for the first time in a quantitative way using a new method of analysis of the Ce L3-edge X-ray absorption near-edge structure (XANES) in the framework of the full multiple scattering theory. An average Ce-N bond length of 2.47 A was determined. In this complex structure the pyrrole rings play the key role in the determination of the XANES spectral features, and the differences in bond lengths between the Ce atom and the eight pyrrole N atoms are 0.14 A, addressing a significant distortion of these rings around cerium. These results may be used to study double-decker imidazole rings, present as the structure model in the photosynthesis center and in sandwich-structured lanthanide chlorophyll molecules.

The role of Zn in the interplay among Langmuir-Blodgett multilayer and myelin basic protein: a quantitative analysis of XANES spectra.

We have performed a quantitative analysis of the X-ray absorption near-edge structure (XANES) spectra at the Zinc K-edge of systems formed by phospholipid Langmuir-Blodgett multilayers (LBMLs) in the presence and in the absence of myelin basic protein (MBP) and in two hydration conditions. These spectra have been analysed by a new procedure called Minuit XANes (MXAN) which is able to perform a quantitative fit of XANES data in terms of structural parameters. By this method, we have been able to correlate the relevant differences between the spectra observed in the XANES range with the coordination changes due to reduction of the space around the Zinc when the level of hydration is lowered and/or the myelin basic protein is added. These spectral differences are peculiar of the XANES energy range, and are not present in the extended X-ray absorption fine structure (EXAFS) energy range where the analysis was previously performed. With this investigation, we give an unambiguous answer to the question of the role of zinc in such complexes by showing that the metal interacts with both the phospholipid heads of the substrate and the myelin basic protein.

Redox-induced structural dynamics of Fe-heme ligand in myoglobin by X-ray absorption spectroscopy.

The Fe(III) --> Fe(II) reduction of the heme iron in aquomet-myoglobin, induced by x-rays at cryogenics temperatures, produces a thermally trapped nonequilibrium state in which a water molecule is still bound to the iron. Water dissociates at T > 160 K, when the protein can relax toward its new equilibrium, deoxy form. Synchrotron radiation x-ray absorption spectroscopy provides information on both the redox state and the Fe-heme structure. Owing to the development of a novel method to analyze the low-energy region of x-ray absorption spectroscopy, we obtain structural pictures of this photo-inducible, irreversible process, with 0.02-0.06-A accuracy, on the protein in solution as well as in crystal. After photo-reduction, the iron-proximal histidine bond is shortened by 0.15 A, a reinforcement that should destabilize the iron in-plane position favoring water dissociation. Moreover, we are able to get the distance of the water molecule even after dissociation from the iron, with a 0.16-A statistical error.

X-ray absorption spectroscopy: state-of-the-art analysis.

State-of-the-art techniques for analysing X-ray absorption spectra are reviewed, with an eye to biological applications. Recent attempts to perform full spectral fitting of the XANES energy region and beyond for the purpose of structural analysis have met with encouraging success. The present paper analyses the theoretical motivations behind this success and indicates routes for future improvements. The theoretical background is not entirely new, although the point of view is, and some sections and appendices present material that the Authors believe has never been published before. The aim of this paper is to provide a theoretical analysis that is as self-contained as possible.

The MXAN procedure: a new method for analysing the XANES spectra of metalloproteins to obtain structural quantitative information.

The first quantitative analyses are reported of the Fe K-edge polarized X-ray absorption near-edge structure (XANES) of a single crystal of the iron protein carbonmonoxy-myoglobin (MbCO) and of its cryogenic photoproduct Mb*CO. The CO-Fe-heme local structure has been determined using a novel fitting procedure, named MXAN, which is able to fit the XANES part (from the edge to about 200 eV) of experimental X-ray absorption data. This method is based on the comparison between the experimental spectrum and several theoretical spectra that are generated by changing the relevant geometrical parameters of the site around the absorbing atom. The theoretical spectra are derived in the framework of the full multiple-scattering approach. The MXAN procedure is able to recover information about the symmetry and atomic distances, and the solution is found to be independent of the starting conditions. The extracted local structure of Mb*CO includes an Fe-CO distance of 3.08 (7) A, with a tilting angle between the heme normal and the Fe-C vector of 37 (7) degrees and a bending angle between the Fe-C vector and the C-O bond of 31 (5) degrees

Quantitative analysis of x-ray absorption near edge structure data by a full multiple scattering procedure: the Fe-CO geometry in photolyzed carbonmonoxy-myoglobin single crystal.

We report the first quantitative analysis of the Fe K-edge polarized x-ray absorption near edge structure of the iron protein carbonmonoxy-myoglobin (MbCO) single crystal and of its cryogenic photoproduct Mb(*)CO. The CO-Fe-heme local structure has been determined using a novel fitting procedure based on the full multiple scattering approach. The extracted local structure of Mb(*)CO includes a Fe-CO distance of (3.08+/-0.07) A, with a tilting angle between the heme normal and the Fe-C vector of (37+/-7) degrees, and a bending angle between the Fe-C vector and the C-O bond of (31+/-5) degrees.

Double-channel excitation in the XAS spectra of divalent and trivalent iron complexes in water solution.

We present a detailed analysis of XAS spectra of divalent and trivalent iron complexes in water solutions. The interpretation of the spectra has been provided by multi-channel multiple scattering approach. On this basis, good agreement between experimental data and theoretical calculations has been obtained in both cases including two excitation channels in the final state.

MXAN: a new software procedure to perform geometrical fitting of experimental XANES spectra.

A new software procedure, MXAN, to fit experimental XANES spectra is presented here. The method is based on the comparison between the experimental spectrum and several theoretical calculations generated by changing the relevant geometrical parameter of the site around the absorbing atom. The x-ray photoabsorption cross section is calculated using the general multiple-scattering scheme, utilizing a complex Hedin-Lunqvist energy-dependent potential to describe the exchange correlation interaction. Our method has been applied to the study of geometrical environment of the tetrahedral zinc site of the protein superoxide dismutase (SOD). The experimental Zn K-edge XANES spectrum has been fitted in the space of the first shell coordination parameters (ligand distances and angles) following the behavior of the chi-square as a function of the local distortion from the starting crystallographic structure. The recovered structure is found to be independent on the starting conditions, showing the theoretical uniqueness of the structural solution. Strengths and limitations of the application to real systems are also discussed.

Multiple scattering approach to DAFS.

In this article we outline a general approach to the anomalous correction to the atomic scattering factor "ab-initio" calculation based on the multiple scattering theory. This approach can be used for structural determination in any system and in particular in the surfaces where symmetry conditions make usual analysis impossible. We show as an application of the formalism calculations related to experimental data of bulk Ge.

NEXAFS multiple scattering calculations of KO2.

Since many years the oxidation of alkali metals has being attracted much interest due to the catalytic properties of metal promoters and the simple electronic structure of alkali atoms. The alkali-oxides phase diagram indicates that the interaction of oxygen with alkali metals can lead to the formation of different atomic O2- ions and molecular O2(-) and O(2)2- ions. Potassium superoxide has been prepared in situ and high resolution O k-edge absorption NEXAFS spectra have been measured at the VUV beam-line at ELETTRA facility. The experimental data have been analyzed by multiple scattering approach deriving many geometrical and electronic details. In particular, we have found that the growth material structure is of the KO2 type with an O-O distance of about 1.35A and that the transition involving single pi molecular empty state of the superoxide O2(-) anion has a fine structure. Multiple Scattering self consistent calculation indicates that the bond between oxygen anion and K atom is totally ionic and that the fine structure is essentially due to solid state effects.

Geometrical fitting of experimental XANES spectra by a full multiple-scattering procedure.

In this paper a new software procedure is presented, named MXAN, able to fit the XANES part (from the edge to about 200 eV) of experimental X-ray absorption data. The method is based on the fitting between the experimental spectrum and several theoretical calculations generated by changing the relevant geometrical parameters of the site around the absorbing atom. The X-ray photo-absorption cross section is calculated using the full multiple-scattering scheme; different choices of the exchange correlation part of the potential can be utilised. To show the potentialities of the method the analysis of the nickel K-edge of the nickel ion in aqueous solution is presented. The procedure is able to recover the correct information on the symmetry and atomic distances from the experimental Ni K-edge XANES spectrum. The recovered structure is found to be independent of the starting conditions, showing the theoretical uniqueness of the structural solution.