Measurement and simulation of nuclear inelastic-scattering spectra of molecular crystals

Paulsen, Hauke; Winkler, H.; Trautwein, Alfred X.; Grünsteudel, H.; Rusanov, V.; Toftlund, Hans

doi:10.1103/physrevb.59.975

Cited by 104 publications

(98 citation statements)

References 47 publications

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“…This gives rise to resonances only at those frequencies where the modulation is most pronounced, which are the peaks of J( ). Alternatively, the -dependent excitation could be achieved by nuclear inelastic scattering of synchrotron radiation at Mössbauer-active nuclei which is already established for intramolecular vibrational spectroscopy that is sensitive to exclusively those modes that involve Fe nuclei (43,44).…”

Section: Resultsmentioning

confidence: 99%

Dynamical magnetostructural properties of Anabaena ferredoxin

Schreiner

Nair

Pollet

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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A mixed quantum/classical investigation of the dynamical magnetostructural properties, that is, ''magnetodynamics,'' of oxidized Anabaena PCC7119 ferredoxin is carried out at room temperature in two distinct conformational states. This protein hosts a [2Fe-2S] cluster in which two iron centers are antiferromagnetically coupled to an overall low-spin electronic ground state that has a genuine multireference character. To study the magnetodynamics of this prosthetic group, an approximate spin projection method is formulated in the framework of density functional theory that allows for multideterminant ab initio molecular dynamics simulations to be carried out efficiently. By using this scheme, the influence of both thermal fluctuations and conformational motion on the structure of the [2Fe-2S] cluster and on the dynamics of the antiferromagnetic coupling constant, J(t), has been investigated. In addition to demonstrating how sensitively the shape of the [2Fe-2S] core itself is affected by hydrogen bonding, the analyses reveal a complex dynamical coupling of J to both local vibrations and large-amplitude motion. It is shown that this interplay can be understood in terms of specific vibrational modes and distinct hydrogen-bonding patterns between the iron-sulfur cluster and the protein backbone, respectively. This implies going beyond the Goodenough-Kanamori rules for angular magnetostructural correlations of oxidized iron-sulfur prosthetic groups.exchange coupling ͉ extended broken-symmetry ͉ hydrogen bonding ͉ iron-sulfur protein ͉ multideterminant hybrid molecular dynamics I ron-sulfur clusters are among the most ubiquitous, functionally versatile, and ancient prosthetic groups in proteins (1-4). One of the major classes of mobile electron carriers in contemporary biology is ferredoxin (Fd). Its fourfold cysteine-coordinated [2Fe-2S] core mediates electron transfer from photosystem I to ferredoxin-NADP ϩ -oxidoreductase, which reduces NADP ϩ to NADPH. A particularly interesting system is Fd from cyanobacterium Anabaena PCC7119 whose crystal structure was recently obtained at 1.3 and 1.17 Å resolution in the oxidized and the reduced forms (5), respectively. Most interestingly, it was found that two alternative conformations of Cys-46 exist, which is one of the four cysteinyl ligands of the [2Fe-2S] cluster (5). In the oxidized state Cys-46 adopts the so-called CO-in conformation, where the peptide oxygen points in the direction of the cluster, whereas, on reduction, the backbone flips to the CO-out conformation.Spin Coupling in Iron-Sulfur Clusters. In the ground state of the oxidized form of bioinorganic [mFe-nS] clusters, the Fe 3ϩ metal centers are typically in a local high-spin d 5 configuration [i.e., S Fe ϭ 5/2 for ferric Fe(III) centers], whereas they themselves are antiferromagnetically coupled to yield an overall low-spin state due to dominant superexchange interactions (6). In particular, the electronic ground state of [2Fe-2S] clusters in Fd has genuine multireference character and makes computational ...

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Section: Resultsmentioning

confidence: 99%

Dynamical magnetostructural properties of Anabaena ferredoxin

Schreiner

Nair

Pollet

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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“…Measurements on oriented samples, such as single crystals, also yield the direction of vibrational motions [10,12,14,18,23,20,26,28]. Other names used for this technique include phonon assisted Mössbauer effect [21,22,25,26], inelastic X-ray scattering of synchrotron radiation [11], nuclear inelastic scattering [18], nuclear inelastic absorption [9], and nuclear resonant inelastic X-ray scattering [29].…”

Section: Introductionmentioning

confidence: 99%

Vibrational dynamics of biological molecules: Multi-quantum contributions

Leu

Zgierski

Wyllie

et al. 2005

Journal of Physics and Chemistry of Solids

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High-resolution X-ray measurements near a nuclear resonance reveal the complete vibrational spectrum of the probe nucleus. Because of this, nuclear resonance vibrational spectroscopy (NRVS) is a uniquely quantitative probe of the vibrational dynamics of reactive iron sites in proteins and other complex molecules. Our measurements of vibrational fundamentals have revealed both frequencies and amplitudes of 57 Fe vibrations in proteins and model compounds. Information on the direction of Fe motion has also been obtained from measurements on oriented single crystals, and provides an essential test of normal mode predictions. Here, we report the observation of weaker two-quantum vibrational excitations (overtones and combinations) for compounds that mimic the active site of heme proteins. The predicted intensities depend strongly on the direction of Fe motion. We compare the observed features with predictions based on the observed fundamentals, using information on the direction of Fe motion obtained either from DFT predictions or from single crystal measurements. Two-quantum excitations may become a useful tool to identify the directions of the Fe oscillations when single crystals are not available.

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“…This technique provides the phonon excitation spectrum as seen by the probe nuclei, 3,4,5 and in most cases one can extract the partial vibrational frequency distribution, a function often referred to as the partial phonon density of states (PDOS). The NRIXS method has been applied to various materials, e.g., thin films and multilayers, 6,7,8 nanoparticles, 9,10 crystals with impurities, 11 organic molecules, 12,13,14,15 proteins, 16,17 samples under high pressures, 18 and samples of geophysical interests. 19,20 Most of these samples are compounds, and, while the obtained PDOS gives only part of the lattice dynamics, the low-energy portion of the PDOS provides the Debye sound velocity of the whole sample.…”

mentioning

confidence: 99%

Measuring velocity of sound with nuclear resonant inelastic x-ray scattering

et al. 2003

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Nuclear resonant inelastic x-ray scattering is used to measure the projected partial phonon density of states of materials. A relationship is derived between the low-energy part of this frequency distribution function and the sound velocity of materials. Our derivation is valid for harmonic solids with Debye-like low-frequency dynamics. This method of sound velocity determination is applied to elemental, composite, and impurity samples which are representative of a wide variety of both crystalline and noncrystalline materials. Advantages and limitations of this method are elucidated.PACS numbers: 61.10. Eq, 62.65.+k Mechanical properties form an important part of our understanding of condensed matter. In many areas of science, measurements of sound velocity are used to study materials of both natural occurence and artificial fabrications. For example, in the field of geophysics, the sound velocity is the most direct information we have about the Earth's interior. The standard approach to learn about the composition and structure of the Earth's interior entails measurements of sound velocities of candidate compounds. The results are then compared to seismological data to exclude or confirm a particular compound. In the following, we will describe the use of nuclear resonant inelastic x-ray scattering (NRIXS) to measure the velocity of sound.The NRIXS method was introduced to probe the lattice dynamics of materials by employing low-energy nuclear resonances.1,2 In NRIXS experiments, only signals from nuclear resonance absorption are monitored, and for this reason the extracted quantity is specific to the resonant isotope. This technique provides the phonon excitation spectrum as seen by the probe nuclei, 3,4,5 and in most cases one can extract the partial vibrational frequency distribution, a function often referred to as the partial phonon density of states (PDOS). The NRIXS method has been applied to various materials, e.g., thin films and multilayers, 19,20 Most of these samples are compounds, and, while the obtained PDOS gives only part of the lattice dynamics, the low-energy portion of the PDOS provides the Debye sound velocity of the whole sample. We will now show that, due to universal features of acoustic modes of harmonic solids, the low-energy portion of the PDOS is related to the Debye sound velocity in a simple way.The normalized phonon density of states is defined bywhere the energy eigenstates of lattice vibrations E l are labeled by quantum number l, and N is the total number of atoms in the solid. In the harmonic lattice approximation, a PDOS, which is more relevant to NRIXS experiments, is given bywhere ν enumerates resonant nuclei,Ñ is the total number of resonant nuclei,k is a unit vector in the incident photon direction, and e ν l are phonon polarization vectors. Equation (2) shows that the vibrational polarizations are projected onto the incident photon direction and in particular the vibrational modes with polarization perpendicular to the direction of the incident photon do not contribute...

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Measurement and simulation of nuclear inelastic-scattering spectra of molecular crystals

Cited by 104 publications

References 47 publications

Dynamical magnetostructural properties of Anabaena ferredoxin

Dynamical magnetostructural properties of Anabaena ferredoxin

Vibrational dynamics of biological molecules: Multi-quantum contributions

Measuring velocity of sound with nuclear resonant inelastic x-ray scattering

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