Stefano della Longa | Università Degli Studi Dell'Aquila (original) (raw)
Papers by Stefano della Longa
Biophysical Journal, 1999
Ferric iron protoporhyrin IX derivatives in SDS micelles have been investigated by means of visib... more Ferric iron protoporhyrin IX derivatives in SDS micelles have been investigated by means of visible absorption, resonance Raman, and XANES spectroscopies to establish specific correlations between the marker bands of the pentacoordinate derivatives obtained from the three different techniques. Hydroxyl and 1,2-dimethyl imidazole coordinated hemins display the typical spectroscopic marker bands of a pentacoordinate high-spin ferric iron derivative in both Raman and XANES spectra. In turn, the optical absorption spectra of these two derivatives are very different. This difference is in line with the assignment of hydroxyl as the fifth coordination ligand to free hemin in SDS micelles, as demonstrated by the isotopic shift of the frequency of Fe-OH bond with H218O. The present assignments are relevant to the identification of the coordination state and the nature of the fifth ligand in ferric heme proteins.
Physica C-superconductivity and Its Applications, 1991
The symmetry of the conduction bands over a range of 15 eV above the Fermi level in La2CuO4 has b... more The symmetry of the conduction bands over a range of 15 eV above the Fermi level in La2CuO4 has been studied by the joint analysis of the polarized X-ray absorption spectra at several edges: O K-edge, Cu K-edge, and Cu L3-edge. The partial density of states of the conduction bands DX (l, ml) projected on the atomic site X (Cu and O) with selected orbital angular momentum l, and its projection ml along the c-axis have been obtained. The oxygen K-edge X-ray absorption near edge structure (XANES) spectrum has been calculated by multiple scattering approach. A good agreement between the one-electron calculations in the fully relaxed final state potential and the experimental spectra for the final states in the high energy conduction bands has been found.
Archives of Biochemistry and Biophysics, 2008
Neuroglobin (Ngb) is a member of the globin family expressed in the vertebrate brain, involved in... more Neuroglobin (Ngb) is a member of the globin family expressed in the vertebrate brain, involved in neuroprotection. A combined approach of X-ray diffraction (XRD) on single crystal and X-ray absorption spectroscopy (XAS) in solution, allows to determine the oxidation state and the structure of the Fe–heme both in the bis-histidine and the CO-bound (NgbCO) states. The overall data demonstrate that under X-ray the iron is photoreduced fairly rapidly, and that the previously reported X-ray structure of ferric Ngb [B. Vallone, K. Nienhaus, M. Brunori, G.U. Nienhaus, Proteins 56 (2004) 85–92] very likely refers to a photoreduced species indistinguishable from the dithionite reduced protein. Results from the XAS analysis of NgbCO in solution are in good agreement with XRD data on the crystal. However prolonged X-ray exposure at 15 K determines CO release. This preliminary result paves the way to experiments aimed at the characterization of pentacoordinate ferrous Ngb, the only species competent in binding external ligands such as O2, CO or NO.
Physical Review B, 1991
The linearly polarized Cu K-edge x-ray-absorption near-edge structure (XANES) of Bi 2 Sr 2 CaCu 2... more The linearly polarized Cu K-edge x-ray-absorption near-edge structure (XANES) of Bi 2 Sr 2 CaCu 2 O 8+ δ (Bi 2: 2: 1: 2) has been measured, and the spectra are interpreted by the multiple-scattering approach in real space. The polarized spectra can be predicted in ...
Physical Review B, 1992
The polarized E⊥ c oxygen K-edge x-ray-absorption near-edge structure (XANES) spectrum of Bi 2 Sr... more The polarized E⊥ c oxygen K-edge x-ray-absorption near-edge structure (XANES) spectrum of Bi 2 Sr 2 CaCu 2 O 8+ δ (Bi 2: 2: 1: 2) has been calculated by a multiple-scattering approach and compared with experimental data. The symmetry of the conduction bands ...
Physica C-superconductivity and Its Applications, 1991
The polarized Cu K-edge X-ray Absorption Near Edge Structure (XANES) of La2CuO4 has been interpre... more The polarized Cu K-edge X-ray Absorption Near Edge Structure (XANES) of La2CuO4 has been interpreted by the multiple scattering approach. The size of the cluster of neighbouring atoms having good agreement with the XANES experimental data is determined by 45 atoms surrounding the absorbing Cu. The polarized spectra can be predicted in term of a one-electron dipole (Δl=+1) transition Cu 1s→ϵp, probing the unoccupied p-like (l=1) density of states projected on a Cu site with orbital angular momentum ml=0 in the E∥z spectra, and the ml=1 for the E⊤c spectra. Thus we show that the electronic structure of the high energy conduction bands, beyond the Cu 3d band, of La2CuO4 are well described in terms of the one-electron approximation. It is shown that XANES spectra are consistent with the contraction of the Cu-apex oxygen distance with doping.Final state effects induced by the core hole have been indentified: (i) the core transitions take place in the fully relaxed potential, (ii) the satellite at 7 eV above the main K-XANES peak in both polarizations is assigned to a multielectron shake up excitation. Finally the shoulder on the rising absorption edge, present in many Cu compounds and usually assigned to a shake down multi-electron excitation, is shown to be due to a one-electron transition to a state delocalized over a large cluster.
Journal of Synchrotron Radiation, 2002
Computational Materials Science, 1995
G4XANES, a software package calculating X-ray Absorption Near Edge Structure (XANES) spectra in t... more G4XANES, a software package calculating X-ray Absorption Near Edge Structure (XANES) spectra in the frame of the one-electron full multiple scattering formalism, is presented. The G4XANES package performs one-electron K,L-XANES “ab initio” simulations on different kinds of compounds (small molecules, crystals, free clusters, metal sites in biological compounds) by using a minimal set of input data. Polarized spectra as a function of the size of the scattering cluster are calculated, allowing to extract information on both the electronic and atomic structure around the selected absorbing atom. Recently reported spin-dependent XANES spectra have been also successfully treated. A description of the package, as well as its applications for such important classes of materials as high temperature superconductors, magnetic materials and metalloproteins, are presented.
Physica Scripta, 2005
In this paper we present a detailed quantitative analysis of the iron K-edge XANES data of potass... more In this paper we present a detailed quantitative analysis of the iron K-edge XANES data of potassium ferrocyanide in water solution. The right structural determination as been obtained from the XANES data by using the MXAN procedure to fit the experimental data despite the presence of small discrepancies between experimental data and best-fit calculations at low energy. The origin of such discrepancies is also discussed in terms of non muffin-tin corrections and the role of the right charge density of the cluster.
Biophysical Journal, 2004
European Biophysics Journal With Biophysics Letters, 1998
We present the results of a comparative study of the binding of carbon monoxide to myoglobin in g... more We present the results of a comparative study of the binding of carbon monoxide to myoglobin in glycerol/buffer solution with different concentrations of guanidine hydrochloride, under extended illumination over the temperature range 30 – 80 K. The changes in the Soret band indicate that the folding state of the protein is a key parameter in determining the photodissociation process and the relaxation rate of the protein.
Journal of Physical Chemistry B, 2006
A full multiple theoretical model (MXAN) is applied to fit picosecond difference X-ray absorption... more A full multiple theoretical model (MXAN) is applied to fit picosecond difference X-ray absorption spectra at the ruthenium L(3) edge upon photoexcitation of aqueous [RuII(bpy)3]2+. We show that fitting difference spectra allows an increase in sensitivity, such that slight structural changes can be retrieved, which are not detected in fitting full spectra. The Ru-N bond distances of the excited complex in the (3)MLCT state are in good agreement with recently published values. The implementation of the present approach to L-edge spectra and its high sensitivity opens opportunities for its extension to a large class of experiments where difference X-ray absorption spectra are recorded.
Biochimica Et Biophysica Acta-protein Structure and Molecular Enzymology, 1996
The Fe K-edge X-ray absorption near-edge structure (XANES) spectra of two irreversible human hemi... more The Fe K-edge X-ray absorption near-edge structure (XANES) spectra of two irreversible human hemichromes, spontaneously formed from HbA and HbMetSO (a hemoglobin derivative, where MetD6(55)β has been previously oxidized to sulfoxide by chloramine T) were determined. The results show that the hemichrome from HbMetSO is characterized by the distal histidyl imidazole moved within the bonding distance of the heme iron. Such structure is different from that of the hemichrome spontaneously produced from native human hemoglobin, which probably has a hydroxide group as sixth heme ligand.
Journal of Synchrotron Radiation, 2004
A general procedure which computes X-ray absorption near-edge structure (XANES) spectra starting ... more A general procedure which computes X-ray absorption near-edge structure (XANES) spectra starting from the individual configurations obtained from molecular dynamics (MD) simulations has been developed. This method allows one to perform a quantitative analysis of the XANES spectra of disordered systems and to estimate the effect of disorder on the low-energy region of the X-ray absorption spectra. As a test case, a Ni2+ aqueous solution has been investigated. The configurational averaged XANES theoretical spectrum obtained from the MD configurations compares well with the experimental data. This confirms simultaneously the reliability of the procedure and of the structural results obtained from the MD simulation.
Journal of Synchrotron Radiation, 1999
Visible light can break the Fe-CO bond in Fe (II) carbonmonoxy-myoglobin (MbCO) giving an unligat... more Visible light can break the Fe-CO bond in Fe (II) carbonmonoxy-myoglobin (MbCO) giving an unligated product (Mb*) that is almost stable at T< 30 K. Fe K-edge polarized X-ray absorption spectra (P-XAS) of the photoproduct (T= 20 K) of an oriented single crystal (0.2 ...
Archives of Biochemistry and Biophysics, 2007
The key structural features that define the reaction mechanism of the binuclear copper enzyme Tyr... more The key structural features that define the reaction mechanism of the binuclear copper enzyme Tyrosinase (Ty) from Streptomyces antibioticus were investigated by X-ray absorption spectroscopy. The data for the met form, the halide bound derivative and the adduct with the competitive inhibitor and transition state analogue Kojic acid were analysed using the recently developed MXAN package. This analysis permitted the definition of structural clusters that include all atoms within 5 Å from the metal ions of the active site. The data obtained for the different forms provide validation of the structural models previously proposed on the basis of the magnetic properties investigated by both pulsed EPR and paramagnetic NMR spectroscopies. The structural model of the reaction center obtained in this solution study is compared with the crystallographic structures recently proposed for several derivatives of bacterial Ty to suggest that only one of these structures is relevant to solution conditions.
Physical Review B, 2002
... P. D'Angelo Dipartimento di Chimica, Università di Roma La Sapienza, Piazz... more ... P. D'Angelo Dipartimento di Chimica, Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy INFM, UdR Camerino, Italy. ... NV Pavel Dipartimento di Chimica, Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy. ...
![Research paper thumbnail of The Solution Structure of [Cu(aq)] 2+ and Its Implications for Rack-Induced Bonding in Blue Copper Protein Active Sites](https://attachments.academia-assets.com/50063867/thumbnails/1.jpg)
](Inorganic Chemistry, 2007
Biophysical Journal, 2004
Biophysical Journal, 1999
Ferric iron protoporhyrin IX derivatives in SDS micelles have been investigated by means of visib... more Ferric iron protoporhyrin IX derivatives in SDS micelles have been investigated by means of visible absorption, resonance Raman, and XANES spectroscopies to establish specific correlations between the marker bands of the pentacoordinate derivatives obtained from the three different techniques. Hydroxyl and 1,2-dimethyl imidazole coordinated hemins display the typical spectroscopic marker bands of a pentacoordinate high-spin ferric iron derivative in both Raman and XANES spectra. In turn, the optical absorption spectra of these two derivatives are very different. This difference is in line with the assignment of hydroxyl as the fifth coordination ligand to free hemin in SDS micelles, as demonstrated by the isotopic shift of the frequency of Fe-OH bond with H218O. The present assignments are relevant to the identification of the coordination state and the nature of the fifth ligand in ferric heme proteins.
Physica C-superconductivity and Its Applications, 1991
The symmetry of the conduction bands over a range of 15 eV above the Fermi level in La2CuO4 has b... more The symmetry of the conduction bands over a range of 15 eV above the Fermi level in La2CuO4 has been studied by the joint analysis of the polarized X-ray absorption spectra at several edges: O K-edge, Cu K-edge, and Cu L3-edge. The partial density of states of the conduction bands DX (l, ml) projected on the atomic site X (Cu and O) with selected orbital angular momentum l, and its projection ml along the c-axis have been obtained. The oxygen K-edge X-ray absorption near edge structure (XANES) spectrum has been calculated by multiple scattering approach. A good agreement between the one-electron calculations in the fully relaxed final state potential and the experimental spectra for the final states in the high energy conduction bands has been found.
Archives of Biochemistry and Biophysics, 2008
Neuroglobin (Ngb) is a member of the globin family expressed in the vertebrate brain, involved in... more Neuroglobin (Ngb) is a member of the globin family expressed in the vertebrate brain, involved in neuroprotection. A combined approach of X-ray diffraction (XRD) on single crystal and X-ray absorption spectroscopy (XAS) in solution, allows to determine the oxidation state and the structure of the Fe–heme both in the bis-histidine and the CO-bound (NgbCO) states. The overall data demonstrate that under X-ray the iron is photoreduced fairly rapidly, and that the previously reported X-ray structure of ferric Ngb [B. Vallone, K. Nienhaus, M. Brunori, G.U. Nienhaus, Proteins 56 (2004) 85–92] very likely refers to a photoreduced species indistinguishable from the dithionite reduced protein. Results from the XAS analysis of NgbCO in solution are in good agreement with XRD data on the crystal. However prolonged X-ray exposure at 15 K determines CO release. This preliminary result paves the way to experiments aimed at the characterization of pentacoordinate ferrous Ngb, the only species competent in binding external ligands such as O2, CO or NO.
Physical Review B, 1991
The linearly polarized Cu K-edge x-ray-absorption near-edge structure (XANES) of Bi 2 Sr 2 CaCu 2... more The linearly polarized Cu K-edge x-ray-absorption near-edge structure (XANES) of Bi 2 Sr 2 CaCu 2 O 8+ δ (Bi 2: 2: 1: 2) has been measured, and the spectra are interpreted by the multiple-scattering approach in real space. The polarized spectra can be predicted in ...
Physical Review B, 1992
The polarized E⊥ c oxygen K-edge x-ray-absorption near-edge structure (XANES) spectrum of Bi 2 Sr... more The polarized E⊥ c oxygen K-edge x-ray-absorption near-edge structure (XANES) spectrum of Bi 2 Sr 2 CaCu 2 O 8+ δ (Bi 2: 2: 1: 2) has been calculated by a multiple-scattering approach and compared with experimental data. The symmetry of the conduction bands ...
Physica C-superconductivity and Its Applications, 1991
The polarized Cu K-edge X-ray Absorption Near Edge Structure (XANES) of La2CuO4 has been interpre... more The polarized Cu K-edge X-ray Absorption Near Edge Structure (XANES) of La2CuO4 has been interpreted by the multiple scattering approach. The size of the cluster of neighbouring atoms having good agreement with the XANES experimental data is determined by 45 atoms surrounding the absorbing Cu. The polarized spectra can be predicted in term of a one-electron dipole (Δl=+1) transition Cu 1s→ϵp, probing the unoccupied p-like (l=1) density of states projected on a Cu site with orbital angular momentum ml=0 in the E∥z spectra, and the ml=1 for the E⊤c spectra. Thus we show that the electronic structure of the high energy conduction bands, beyond the Cu 3d band, of La2CuO4 are well described in terms of the one-electron approximation. It is shown that XANES spectra are consistent with the contraction of the Cu-apex oxygen distance with doping.Final state effects induced by the core hole have been indentified: (i) the core transitions take place in the fully relaxed potential, (ii) the satellite at 7 eV above the main K-XANES peak in both polarizations is assigned to a multielectron shake up excitation. Finally the shoulder on the rising absorption edge, present in many Cu compounds and usually assigned to a shake down multi-electron excitation, is shown to be due to a one-electron transition to a state delocalized over a large cluster.
Journal of Synchrotron Radiation, 2002
Computational Materials Science, 1995
G4XANES, a software package calculating X-ray Absorption Near Edge Structure (XANES) spectra in t... more G4XANES, a software package calculating X-ray Absorption Near Edge Structure (XANES) spectra in the frame of the one-electron full multiple scattering formalism, is presented. The G4XANES package performs one-electron K,L-XANES “ab initio” simulations on different kinds of compounds (small molecules, crystals, free clusters, metal sites in biological compounds) by using a minimal set of input data. Polarized spectra as a function of the size of the scattering cluster are calculated, allowing to extract information on both the electronic and atomic structure around the selected absorbing atom. Recently reported spin-dependent XANES spectra have been also successfully treated. A description of the package, as well as its applications for such important classes of materials as high temperature superconductors, magnetic materials and metalloproteins, are presented.
Physica Scripta, 2005
In this paper we present a detailed quantitative analysis of the iron K-edge XANES data of potass... more In this paper we present a detailed quantitative analysis of the iron K-edge XANES data of potassium ferrocyanide in water solution. The right structural determination as been obtained from the XANES data by using the MXAN procedure to fit the experimental data despite the presence of small discrepancies between experimental data and best-fit calculations at low energy. The origin of such discrepancies is also discussed in terms of non muffin-tin corrections and the role of the right charge density of the cluster.
Biophysical Journal, 2004
European Biophysics Journal With Biophysics Letters, 1998
We present the results of a comparative study of the binding of carbon monoxide to myoglobin in g... more We present the results of a comparative study of the binding of carbon monoxide to myoglobin in glycerol/buffer solution with different concentrations of guanidine hydrochloride, under extended illumination over the temperature range 30 – 80 K. The changes in the Soret band indicate that the folding state of the protein is a key parameter in determining the photodissociation process and the relaxation rate of the protein.
Journal of Physical Chemistry B, 2006
A full multiple theoretical model (MXAN) is applied to fit picosecond difference X-ray absorption... more A full multiple theoretical model (MXAN) is applied to fit picosecond difference X-ray absorption spectra at the ruthenium L(3) edge upon photoexcitation of aqueous [RuII(bpy)3]2+. We show that fitting difference spectra allows an increase in sensitivity, such that slight structural changes can be retrieved, which are not detected in fitting full spectra. The Ru-N bond distances of the excited complex in the (3)MLCT state are in good agreement with recently published values. The implementation of the present approach to L-edge spectra and its high sensitivity opens opportunities for its extension to a large class of experiments where difference X-ray absorption spectra are recorded.
Biochimica Et Biophysica Acta-protein Structure and Molecular Enzymology, 1996
The Fe K-edge X-ray absorption near-edge structure (XANES) spectra of two irreversible human hemi... more The Fe K-edge X-ray absorption near-edge structure (XANES) spectra of two irreversible human hemichromes, spontaneously formed from HbA and HbMetSO (a hemoglobin derivative, where MetD6(55)β has been previously oxidized to sulfoxide by chloramine T) were determined. The results show that the hemichrome from HbMetSO is characterized by the distal histidyl imidazole moved within the bonding distance of the heme iron. Such structure is different from that of the hemichrome spontaneously produced from native human hemoglobin, which probably has a hydroxide group as sixth heme ligand.
Journal of Synchrotron Radiation, 2004
A general procedure which computes X-ray absorption near-edge structure (XANES) spectra starting ... more A general procedure which computes X-ray absorption near-edge structure (XANES) spectra starting from the individual configurations obtained from molecular dynamics (MD) simulations has been developed. This method allows one to perform a quantitative analysis of the XANES spectra of disordered systems and to estimate the effect of disorder on the low-energy region of the X-ray absorption spectra. As a test case, a Ni2+ aqueous solution has been investigated. The configurational averaged XANES theoretical spectrum obtained from the MD configurations compares well with the experimental data. This confirms simultaneously the reliability of the procedure and of the structural results obtained from the MD simulation.
Journal of Synchrotron Radiation, 1999
Visible light can break the Fe-CO bond in Fe (II) carbonmonoxy-myoglobin (MbCO) giving an unligat... more Visible light can break the Fe-CO bond in Fe (II) carbonmonoxy-myoglobin (MbCO) giving an unligated product (Mb*) that is almost stable at T< 30 K. Fe K-edge polarized X-ray absorption spectra (P-XAS) of the photoproduct (T= 20 K) of an oriented single crystal (0.2 ...
Archives of Biochemistry and Biophysics, 2007
The key structural features that define the reaction mechanism of the binuclear copper enzyme Tyr... more The key structural features that define the reaction mechanism of the binuclear copper enzyme Tyrosinase (Ty) from Streptomyces antibioticus were investigated by X-ray absorption spectroscopy. The data for the met form, the halide bound derivative and the adduct with the competitive inhibitor and transition state analogue Kojic acid were analysed using the recently developed MXAN package. This analysis permitted the definition of structural clusters that include all atoms within 5 Å from the metal ions of the active site. The data obtained for the different forms provide validation of the structural models previously proposed on the basis of the magnetic properties investigated by both pulsed EPR and paramagnetic NMR spectroscopies. The structural model of the reaction center obtained in this solution study is compared with the crystallographic structures recently proposed for several derivatives of bacterial Ty to suggest that only one of these structures is relevant to solution conditions.
Physical Review B, 2002
... P. D'Angelo Dipartimento di Chimica, Università di Roma La Sapienza, Piazz... more ... P. D'Angelo Dipartimento di Chimica, Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy INFM, UdR Camerino, Italy. ... NV Pavel Dipartimento di Chimica, Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy. ...
Inorganic Chemistry, 2007
Biophysical Journal, 2004