How nitrogenase shakes--initial information about P-cluster and FeMo-cofactor normal modes from nuclear resonance vibrational spectroscopy (NRVS)

Nitrogenase catalyzes a reaction critical for life, the reduction of N(2) to 2NH(3), yet we still know relatively little about its catalytic mechanism. We have used the synchrotron technique of (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the dynamics of the Fe-S clusters in this enzyme. The catalytic site FeMo-cofactor exhibits a strong signal near 190 cm(-)(1), where conventional Fe-S clusters have weak NRVS. This intensity is ascribed to cluster breathing modes whose frequency is raised by an interstitial atom. A variety of Fe-S stretching modes are also observed between 250 and 400 cm(-)(1). This work is the first spectroscopic information about the vibrational modes of the intact nitrogenase FeMo-cofactor and P-cluster.     

Characterization of the Fe site in iron-sulfur cluster-free hydrogenase (Hmd) and of a model compound via nuclear resonance vibrational spectroscopy (NRVS)

We have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the iron site in the iron-sulfur cluster-free hydrogenase Hmd from the methanogenic archaeon Methanothermobacter marburgensis. The spectra have been interpreted by comparison with a cis-(CO)2-ligated Fe model compound, Fe(S2C2H4)(CO)2(PMe3)2, as well as by normal mode simulations of plausible active site structures. For this model complex, normal mode analyses both from an optimized Urey-Bradley force field and from complementary density functional theory (DFT) calculations produced consistent results. For Hmd, previous IR spectroscopic studies found strong CO stretching modes at 1944 and 2011 cm(-1), interpreted as evidence for cis-Fe(CO)2 ligation. The NRVS data provide further insight into the dynamics of the Fe site, revealing Fe-CO stretch and Fe-CO bend modes at 494, 562, 590, and 648 cm(-1), consistent with the proposed cis-Fe(CO)2 ligation. The NRVS also reveals a band assigned to Fe-S stretching motion at approximately 311 cm(-1) and another reproducible feature at approximately 380 cm(-1). The (57)Fe partial vibrational densities of states (PVDOS) for Hmd can be reasonably well simulated by a normal mode analysis based on a Urey-Bradley force field for a five-coordinate cis-(CO)2-ligated Fe site with additional cysteine, water, and pyridone cofactor ligands. A "truncated" model without a water ligand can also be used to match the NRVS data. A final interpretation of the Hmd NRVS data, including DFT analysis, awaits a three-dimensional structure for the active site.     

General theory of vibrational mode mixing and frequency shifts in resonance raman scattering

A general formalism is given for treating vibrational mode mixing, frequency shifts, and atomic equilibrium position shifts under electronic excitation in resonance Raman scattering. The theory is exact for first-order scattering at T = 0 K for all linear and quadratic electron-phonon coupling strengths. Numerical results illustrating mode mixing are presented.     

Characterization of a synthetic peroxodiiron(III) protein model complex by nuclear resonance vibrational spectroscopy

The vibrational spectrum of an η(1),η(1)-1,2-peroxodiiron(III) complex was measured by nuclear resonance vibrational spectroscopy and fit using an empirical force field analysis. Isotopic (18)O(2) labelling studies revealed a feature involving motion of the {Fe(2)(O(2))}(4+) core that was not previously observed by resonance Raman spectroscopy.     

Dynamics of an [Fe4S4(SPh)4]2- cluster explored via IR, Raman, and nuclear resonance vibrational spectroscopy (NRVS)-analysis using 36S substitution, DFT calculations, and empirical force fields

We have used four vibrational spectroscopies--FT-IR, FT-Raman, resonance Raman, and 57Fe nuclear resonance vibrational spectroscopy (NRVS)--to study the normal modes of the Fe-S cluster in [(n-Bu)4N]2[Fe4S4(SPh)4]. This [Fe4S4(SR)4]2- complex serves as a model for the clusters in 4Fe ferredoxins and high-potential iron proteins (HiPIPs). The IR spectra exhibited differences above and below the 243 K phase transition. Significant shifts with 36S substitution into the bridging S positions were also observed. The NRVS results were in good agreement with the low temperature data from the conventional spectroscopies.The NRVS spectra were interpreted by normal mode analysis using optimized Urey-Bradley force fields (UBFF) as well as from DFT theory. For the UBFF calculations, the parameters were refined by comparing calculated and observed NRVS frequencies and intensities. The frequency shifts after 36S substitution were used as an additional constraint. A D 2d symmetry Fe4S4S'4 model could explain most of the observed frequencies, but a better match to the observed intensities was obtained when the ligand aromatic rings were included for a D 2d Fe4S4(SPh)4 model. The best results were obtained using the low temperature structure without symmetry constraints. In addition to stretching and bending vibrations, low frequency modes between approximately 50 and 100 cm(-1) were observed. These modes, which have not been seen before, are interpreted as twisting motions with opposing sides of the cube rotating in opposite directions. In contrast with a recent paper on a related Fe4S4 cluster, we find no need to assign a large fraction of the low frequency NRVS intensity to 'rotational lattice modes'. We also reassign the 430 cm(-1) band as primarily an elongation of the thiophenolate ring, with approximately 10% terminal Fe-S stretch character. This study illustrates the benefits of combining NRVS with conventional Raman and IR analysis for characterization of Fe-S centers. DFT theory is shown to provide remarkable agreement with the experimental NRVS data. These results provide a reference point for the analysis of more complex Fe-S clusters in proteins.     

Normal vibrational analysis of poly(vinylidene chloride)

Normal coordinate calculations have been performed for poly(vinylidene chloride) employing a TXTX′ conformational model (X and X′ denote torsional angles of equal value but opposite sign). A valence force field previously determined from the model compounds 2,2-dichloropropane and 2,2-dichlorobutane was directly transferred to the chain conformation of the polymer. The results are in excellent agreement with the observed vibrational spectra and we have been able to satisfactorily assign all the major normal modes.     

Solid-state vibrational spectroscopy: Part 11. An infrared and raman vibrational spectroscopic study of metal(II) halide aniline complexes

Infrared (4000?200 cm^?1) and Raman (3500?50 cm^?1) spectra are reported for metal(II) halide aniline complexes of the following stoichiometries: (MX₂an₂) (M  Co, Ni or Hg, X  Cl; M  Mn, X  Cl or Br; M  Zn or Cd, X  Cl, Br or I); (MX₂an₃) (M  Mn, X  Cl or Br; M  Ni, X  Cl); (CdCl₂an) and an assignment is proposed for all the observed bands. Low-temperature (83 K) IR spectra are also reported and it is noted that whilst the aniline ring and CH mode values are virtually insensitive to temperature, the NH₂ rocking and metal-ligand stretching mode values increase with decreasing temperature, whilst the NH₂ stretching mode values decrease with decreasing temperature.     

Conformational analysis of poly(ethylene oxide) and model compounds by nuclear magnetic resonance spectroscopy

In order to determine the conformation of poly(ethylene oxide) (PEO), ¹³C satellite spectra of PEO, 1,2-dimethoxyethane (DME), and dioxane were measured at various temperatures in various solvents, and analyzed. Relations between the coupling constants were derived from the linearity between the parameters N = J_AB + J_A′B and L = J_A′B in AA′BB′ spectra of PEO and DME. The vicinal coupling constants for the individual rotational isomers were obtained from the above relations and the temperature dependences of N and L and the enthalpy differences were calculated in each solvent. The gauche rotamer is more stable than the trans isomer by 250–500 cal/mole in all cases examined.     

Preparation and dynamics of vibrational hot spots in polyatomics via raman scttering

We exploit a recent time dependent formulation of resonance Raman scattering to examine vibrational hot spot production in molecules which have dissociative excited states. The excited-state dynamics are described by a Raman wavefunction which is used to obtain the resonance Raman (RR) spectrum. The RR spectrum will contain the spectral signature of the subsequent dynamics and decay of the hot spot initial condition.     

Vibrational assignments of six-coordinate ferrous heme nitrosyls: new insight from nuclear resonance vibrational spectroscopy

This Communication addresses a long-standing problem: the exact vibrational assignments of the low-energy modes of the Fe-N-O subunit in six-coordinate ferrous heme nitrosyl model complexes. This problem is addressed using nuclear resonance vibrational spectroscopy (NRVS) coupled to (15)N(18)O isotope labeling and detailed simulations of the obtained data. Two isotope-sensitive features are identified at 437 and 563 cm(-1). Normal coordinate analysis shows that the 437 cm(-1) mode corresponds to the Fe-NO stretch, whereas the 563 cm(-1) band is identified with the Fe-N-O bend. The relative NRVS intensities of these features determine the degree of vibrational mixing between the stretch and the bend. The implications of these results are discussed with respect to the trans effect of imidazole on the bound NO. In addition, a comparison to myoglobin-NO (Mb-NO) is made to determine the effect of the Mb active site pocket on the bound NO.     

Surface enhanced raman and resonance raman spectroscopy in a non-aqueous electrochemical environment: Tris(2,2′-bipyridine)ruthenium(II) adsorbed on silver from acetonitrile

This letter reports the first observation of both surface enhanced Raman scattering (SERS) and surface enhanced resonance Raman scattering (SERRS) from the transition metal complex tris(2,2′-bipyridine)ruthenium (II), Ru(bpy)₃²⁺, adsorbed on a silver electrode from acetonitrile (ACN). The assignment of these spectra as valid examples of SERS and SERRS in a non-aqueous environment is based on the following criteria: (1) in situ demonstration of monolayer surface coverage of Ru(bpy)₃²⁺ using double potential step chronocoulometry (DPSCC); (2) the Raman signals are most intense after surface roughening by anodization; (3) the Raman spectra are potential dependent in the non-faradaic potential region; (4) the measured enhancement factors are greater ilian 10⁶; (5) the surface spectra are frequency shifted relative to their bulk counterpart; and (6) several other molecules also exhibit non-aqueous SERS and SERRS behavior. These results are highly significant in that generality of surface enhanced Raman spectroscopy has been extended into the rich domain of nonaqueous electrochemistry.     

Solid-state vibrational spectroscopy: Part VI. An infrared and raman spectroscopic study of transition metal(II)4-methylpyridine complexes

Infrared (4000–200 cm^?1) and Raman (3500–300 cm^?1 ) spectra are reported for metal(II) halide and thiocyanate 4-methylpyridine complexes of the following stoichiometries: (MX₂(4-Mepy)₂) {M = Mn, Co, Cu or Zn, X = Cl or Br; M = Mn, Ni or Zn, X = NCS}; (MX₂(4-Mepy)₄) {M = Mn, Fe, Co or Ni, X = Cl or Br; M = Mn, Fe, Co, W or Cu, X = NCS}. For a given series of isomorphous complexes there is a correlation between the sum of the differences between the liquid and ligand values of the ν₁, ν₂, ν₃, ν₄, ν₅, ν₆, ν₇, ν₈, ν₉, ν₁₀, ν₁₂, ν₁₃ and ν₁₄ modes of 4-methylpyridine and the strength of the metal-nitrogen bond. Comparison of the shift values of pyridine and 4-methylpyridine complexes supports the suggestion that, unlike the situation in the pyridine complexes, back-donation from the metal to the ligand is unimportant in the 4-methylpyridine complexes.     

Interpretation of nuclear resonant vibrational spectra of rubredoxin using a combined quantum mechanics and molecular mechanics approach

Nuclear resonant vibrational spectra of the reduced and oxidized form of a mutant of rubredoxin from Pyrococcus abyssii were measured and are compared with simulated spectra that were calculated by a combined quantum mechanics (QM) and molecular mechanics (MM) method. Density functional theory was used for the QM level. Calculations were performed for different models of rubredoxin. Realistic spectra were simulated with reduced models that include at least the iron center, the four cysteins coordinating it, and the residues connected to the cysteins together with a QM layer that comprises the first two coordination shells of the iron center. Larger QM layers did not lead to significant changes of the simulated spectra.     

Ultrafast infrared spectroscopy of riboflavin: dynamics, electronic structure, and vibrational mode analysis

Femtosecond time-resolved infrared spectroscopy was used to study the vibrational response of riboflavin in DMSO to photoexcitation at 387 nm. Vibrational cooling in the excited electronic state is observed and characterized by a time constant of 4.0 +/- 0.1 ps. Its characteristic pattern of negative and positive IR difference signals allows the identification and determination of excited-state vibrational frequencies of riboflavin in the spectral region between 1100 and 1740 cm (-1). Density functional theory (B3LYP), Hartree-Fock (HF) and configuration interaction singles (CIS) methods were employed to calculate the vibrational spectra of the electronic ground state and the first singlet excited pipi* state as well as respective electronic energies, structural parameters, electronic dipole moments and intrinsic force constants. The harmonic frequencies of the S 1 excited state calculated by the CIS method are in satisfactory agreement with the observed band positions. There is a clear correspondence between computed ground- and excited-state vibrations. Major changes upon photoexcitation include the loss of the double bond between the C4a and N5 atoms, reflected in a downshift of related vibrations in the spectral region from 1450 to 1720 cm (-1). Furthermore, the vibrational analysis reveals intra- and intermolecular hydrogen bonding of the riboflavin chromophore.     

Formation constant and stoichiometry of the acetonitrile:18-crown-6 complex by nuclear magnetic resonance, raman and infrared spectroscopy

Crown ethers are increasingly used in a variety of chemical applications. While crown ether complexes with alkali-metal cations have been extensively studied, relatively little is known about their complexes with neutral molecules to form so-called host: guest complexes. The use of NMR is reported for the determination of the formation constant (2.1 +/- 0.1) for the acetonitrile: 18-crown-6 complex. The suitability of Raman spectroscopy for studies of the solid-phase complex is demonstrated and limitations in the use of infrared spectroscopy are discussed.     

Applications of surface-enhanced raman scattering (SERS) spectroscopy in biochemistry

Conclusion These results demonstrate that SERS spectroscopy creates a new and powerful method to study the vibrational behaviour of biomolecules at rather dilute aqueous solutions down to 10^–7M.

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Anwendung der Oberflächenverstärkten-Raman-Spektroskopie in der Biochemie

     

Electrochemical processes of meso-tetrakis (4-sulfonatophenyl) porphine at a silver electrode studied by surface-enhanced resonance raman spectroscopy

The potential dependence of surface-enhanced resonance Roman spectra of meso-tetrakis (4-sulfonatophenyl) porphine (TSPP) in 0.05 M H₂SO₄ reveals two electrochemical processes at a silver electrode surface. One which begins around ?0.3 V is interpreted as dissociation of aggregated TSPP to monomers. The other which occurs near ?0.4 V is ascribed to a partial Ag incorporation of TSPP molecules.     

Quantitative analysis in pharmacy and pharmaceutical chemistry by nuclear magnetic resonance spectroscopy

The applications of n.m.r. to the quantitative analysis of pharmaceutical formulations and products of interest to the pharmacist and pharmaceutical analyst are reviewed. Special attention is paid to the accuracy of the method, the coefficients of variation being quoted (or calculated from data in the original paper) where possible. An elementary knowledge of n.m.r. is assumed.     

Model aluminum-poly(p-phenylenevinylene) interfaces studied by surface raman spectroscopy

Polymeric organic light-emitting diodes (OLEDs) have emerged as inexpensive and versatile alternatives to traditional inorganic-based display technologies. Further advances in this field depend on extending device lifetimes and improving electroluminescence efficiencies, both of which are strongly coupled to the integrity of the electrode/organic contacts. Therefore, the deposition of low-work function metals on organic materials has been extensively studied by X-ray photoelectron spectroscopy (XPS), ultraviolet photoemission spectroscopy (UPS), and near-edge X-ray adsorption fine structure (NEXAFS) to ascertain information about the chemical and electronic states within the interfacial region. However, to date, the only molecular structural information about metal-organic species formed in these regions has come from fits of theoretical models to existing XPS and UPS data. Very little direct structural information exists about the potential multitude of metal-organic species formed during cathode deposition. We report the use of surface Raman spectroscopy to study the interactions between aluminum and trans-stilbene, a model for poly(p-phenylenevinylene) (PPV). The Raman spectral data suggest preferential formation of covalent Al-C bonds at the vinylene carbons as opposed to the phenyl carbons of PPV.