Characterization of temperature-dependent iron-imidazole vibrational modes in far infrared

The active site of several oxygen binding proteins can be mimicked with the ferric iron protoporphyrin IX derivative hemin, coordinating two imidazole molecules and embedded in sodium dodecyl sulfate (SDS) micelles; the detergent simulates the hydrophobic cavity of heme proteins. We studied the low-frequency vibrational modes of the porphyrin-iron-imidazole bonding in infrared absorbance spectra. Assignment of the metal-ligand vibrations to signals at 396, 387, and 378 cm(-1) was performed by isotope labeling of the imidazole ligand. These modes were also found to be temperature-dependent and to display a linear increase of signal intensity between 25 and 150 K and, with a different slope, between 150 and 300 K. The modes at 396 and 399 cm(-1) show for 25 K an up-shift about 4 cm(-1) and the signal at 378 cm(-1) a small downshift, indicating the involvement of antisymmetric stretching modes and, in the latter, of bending motions. Anharmonic couplings to doming modes are discussed, and the doming mode and hydrogen-bonding signature spectral range between 300 and 100 cm(-1) is presented.     

Probing the Hydrogen Bonding Structure in the Rieske Protein

The use of the far‐infrared spectral range presents a novel approach for analysis of the hydrogen bonding in proteins. Here it is presented for the analysis of Fe? S vibrations (500–200 cm^?1) and of the intra‐ and intermolecular hydrogen bonding signature (300–50 cm^?1) in the Rieske protein from Thermus thermophilus as a function of temperature and pH. Three pH values were adequately chosen in order to study all the possible protonation states of the coordinating histidines. The Fe? S vibrations showed pH‐dependent shifts in the FIR spectra in line with the change of protonation state of the histidines coordinating the [2Fe? 2S] cluster. Measurements of the low‐frequency signals between 300 and 30 K demonstrated the presence of a distinct overall hydrogen bonding network and a more rigid structure for a pH higher than 10. To further support the analysis, the redox‐dependent shifts of the secondary structure were investigated by means of an electrochemically induced FTIR difference spectroscopic approach in the mid infrared. The results confirmed a clear pH dependency and an influence of the immediate environment of the cluster on the secondary structure. The results support the hypothesis that structure‐mediated changes in the environment of iron? sulfur centers play a critical role in regulating enzymatic catalysis. The data point towards the role of the overall internal hydrogen bonding organization for the geometry and the electronic properties of the cluster.     

Temperature-dependent spin crossover in neuronal nitric oxide synthase bound with the heme-coordinating thioether inhibitors

A series of L-arginine analogue nitric oxide synthase inhibitors with a thioether tail have been shown to form an Fe-S thioether interaction as evidenced by continuous electron density between the Fe and S atoms. Even so, the Fe-S thioether interaction was found to be far less important for inhibitor binding than the hydrophobic interactions between the alkyl group in the thioether tail and surrounding protein (Martell et al. J. Am. Chem. Soc. 2010 , 132 , 798). However, among the few thioether inhibitors that showed Fe-S thioether interaction in crystal structures, variations in spin state (high-spin or low-spin) were observed dependent upon the heme iron oxidation state and temperature. Since modern synchrotron X-ray data collection is typically carried out at cryogenic temperatures, we reasoned that some of the discrepancies between cryo-crystal structures and room-temperature UV-visible spectroscopy could be the result of temperature-dependent spin-state changes. We, therefore, have characterized some of these neuronal nitric oxide synthase (nNOS)-thioether inhibitor complexes in both crystal and solution using EPR and UV-visible absorption spectrometry as a function of temperature and the heme iron redox state. We found that some thioether inhibitors switch from high to low spin at lower temperatures similar to the "spin crossover" phenomenon observed in many transition metal complexes.     

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.     

The quadruplex-duplex structural transition of polyriboguanylic acid

The vibrational infrared (IR) absorption and vibrational circular dichroism (VCD) spectral changes of polyriboguanylic acid (polyG) as a function of time, temperature and pH have been investigated to establish how changes in spectral features relate to the structural modifications of polyG. From the progression of IR and VCD spectral features with respect to time, it is observed that stabilization of the quadruplex structure at pH 6.4 (near-neutral environment) takes place within 5 days. This stabilization process is most clearly evidenced by a downshift of the carbonyl absorption band and the corresponding positive VCD couplet, from 1689 to approximately 1682 cm(-1) in time. Time-induced spectral modifications also indicated that, in an acidic environment (pH 3.1) and within a 5 day waiting period, polyG develops a duplex structure. An additional positive VCD couplet associated with an absorption band at 1589 cm(-1) is identified as a marker of the polyG duplex structure. From the progression of spectral features with respect to temperature at pH 6.4, it is found that heating induces structural changes that favor the formation of a duplex structure. This duplex structure, at pH 6.4, would not form at room temperature simply by the passage of time. When polyG is in an acidic environment (pH 3.1), heating accelerates the conversion to the duplex structure that could also be obtained with passage of time at that pH. On the basis of the comparison of experimental and quantum theoretical VCD spectra for polyG, the key spectral signature for the quadruplex form is considered to be a single positive VCD couplet, while the spectral signature for a duplex form is considered to contain an additional positive VCD couplet at a lower frequency.     

铜分子筛Cu(Ⅰ)物种上吸附CO的漫反射红外光谱

应用漫反射红外光谱测定了不同的铜分子筛经真空自还原后吸附ＣＯ的基频,组频和泛频谱带,结果表明,ＣＯ压力较低时,形成Ｃｕ（Ⅰ）（ＣＯ）吸附物种,其种类与分子筛的结构特性有关。随ＣＯ２压力增高,部分吸附物种转变为Ｃｕ（Ⅰ）（ＣＯ）２,分析Ｃｕ（Ⅰ）（ＣＯ）基频和组频谱带可得到比Ｃ－Ｏ伸缩振动更灵敏的反映Ｃｕ（Ⅰ）和ＣＯ作用的Ｃｕ（Ⅰ）－Ｃ伸缩振动频率。     

Theoretical IR spectra for water clusters (H2O)n (n = 6-22, 28, 30) and identification of spectral contributions from different H-bond conformations in gaseous and liquid water

The vibrational IR spectra in the O-H stretching region are computed for water clusters containing 6-22, 28, and 30 molecules using quantum-chemical calculations (B3LYP and an augmented basis set). For the cluster with 20 molecules, several different structures were studied. The vibrational spectrum was partitioned into contributions from different molecules according to their coordination properties. The frequency shifts depend on the number of donated/accepted H-bonds primarily of the two molecules participating in the H-bond, but also of the surrounding molecules H-bonding to these molecules. The frequencies of H-bonds between two molecules of the same coordination type are spread over a broad interval. The most downshifted hydrogen-bond vibrations are those donated by a single-donor 3-coordinated molecule where the H-bond is accepted by a single-acceptor molecule. The H-bonded neighbors influence the downshift, and their contribution can be rationalized in the same way as for the central dimer. Single donors/acceptors cause larger downshifts than 4-coordinated molecules, and the least downshift is obtained for double donors/acceptors. This result is at variance with the conception that experimental liquid water spectra may be divided into components for which larger downshifts imply higher H-bond coordination. A mean spectral contribution for each coordination type for the donor molecule was derived and fitted to the experimental liquid water IR spectrum, which enabled an estimation of the distribution of H-bond types and average number of H-bonds (3.0 +/- 0.2) in the liquid.     

Terahertz time-domain and Raman spectroscopy of the sulfur-containing peptide dimers: Low-frequency markers of disulfide bridges

The terahertz time-domain and Raman spectra of sulfur-containing cystein-based peptides in the region of the low-frequency infrared vibrations have been measured at room temperature. The low-frequency bands that can be assigned to the S–S bridges are observed. The vibrational modes found in molecular crystalline materials should be described as phonon modes with strong coupling to the intra molecular vibrations.     

Sulfur K-edge XAS and DFT calculations on P450 model complexes: effects of hydrogen bonding on electronic structure and redox potentials

Hydrogen bonding (H-bonding) is generally thought to play an important role in tuning the electronic structure and reactivity of metal-sulfur sites in proteins. To develop a quantitative understanding of this effect, S K-edge X-ray absorption spectroscopy (XAS) has been employed to directly probe ligand-metal bond covalency, where it has been found that protein active sites are significantly less covalent than their related model complexes. Sulfur K-edge XAS data are reported here on a series of P450 model complexes with increasing H-bonding to the ligated thiolate from its substituent. The XAS spectroscopic results show a dramatic decrease in preedge intensity. DFT calculations reproduce these effects and show that the observed changes are in fact solely due to H-bonding and not from the inductive effect of the substituent on the thiolate. These calculations also indicate that the H-bonding interaction in these systems is mainly dipolar in nature. The -2.5 kcal/mol energy of the H-bonding interaction was small relative to the large change in ligand-metal bond covalency (30%) observed in the data. A bond decomposition analysis of the total energy is developed to correlate the preedge intensity change to the change in Fe-S bonding interaction on H-bonding. This effect is greater for the reduced than the oxidized state, leading to a 260 mV increase in the redox potential. A simple model shows that E degrees should vary approximately linearly with the covalency of the Fe-S bond in the oxidized state, which can be determined directly from S K-edge XAS.     

Some Attempts to Employ the Singlet Oxygen Generated from H2O2

Some attempts to employ the singlet oxygen generated from molybdate-catalyzed decomposition of hydrogen peroxide are presented. Reduction of ascaridole with diimide is also described, along with the preliminary results of the cleavage study using Fe-cysteinate as a simple model for Fe-S type redox species. There were strong indications that S-alkylation occurred as observed in similar cleavage of the potent antimalarial qinghaosu.     

铁硫蛋白及其模型化合物中铁硫共价性研究

铁硫团簇中金属和配体间强的共价性在决定其反应特性中具有重要作用。基于Phillips理论发展的一个半经验模型被应用于铁硫团蔟共价性的定量计算。结果表明穆斯堡尔谱和吸收光谱对铁硫团簇的共价性能够提供一个直接的实验探测。     

Theoretical studies of [FeFe]-hydrogenase: infrared fingerprints of the dithiol-bridging ligand in the active site

An unresolved structural issue for [FeFe]-hydrogenases is the nature of the dithiol-bridging ligand in the diiron subcluster of the active site. The two most probable candidates are 1,3-dithiopropane (propane dithiol, PDT) and di-(thiomethyl)-amine (DTN). In the latter case, the dithiol-bridging ligand is assumed to play a major role in the reaction cycle. We report density-functional theory studies of the differing roles of these dithiol-bridging ligands in the infrared spectra of synthetic models and of computational representations of the diiron cluster of the active site. Our analysis shows distinct spectral features associated with the dithiol-bridging NH mode for compounds having a DTN bridge, which, however, would have been obscured by the H2O vibrations in existing measurements. However, if indeed nitrogen is present in the dithiol-bridging ligand, a combination of selective deuteration and chemical inactivation with CO would create a unique signature in an accessible region of the infrared spectrum, whose position and intensity are predicted.     

Infrared spectroscopy of SO2 aqueous solutions

The chemistry of SO2 solutions was studied with infrared transmission and total internal reflection (ATR) spectroscopy. The cross-sections of the SO2 stretching vibrations v1, v3 and the combination band of v1 + v3 were obtained and found to be slightly different from their gas phase values. Six features we associate with sulfur-containing ions were observed. We present the first infrared evidence for the bisulfite ion HOSO2- through detection of its OH stretching vibration. Other features may be associated with HSO3-, another isomer of the bisulfite ion, and a new compound we propose to be H2S2O6(2-). We found no evidence for sulfurous acid H2SO3.     

Infrared spectrum and absorption coefficient of the cofactor flavin in water

Flavins play a key role as redox cofactors of enzymes involved in important metabolic processes. Moreover, they undergo photochemical reactions as chromophores in sensors of blue light or magnetic field in many organisms. The reaction mechanisms of flavoproteins have been investigated by infrared spectroscopy and theoretical studies. However, basic information on flavins in the infrared spectral range has been missing, such as absorption spectra in water and absorption coefficients. Here, the cofactors flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) were investigated in aqueous medium by Fourier transform infrared spectroscopy. Transmission and attenuated total reflection (ATR) configuration were employed in direct comparison. Absorption spectra in the range of 920–1800 cm⁻¹ were determined after accurate subtraction of the contributions from the water vibrations. The important carbonyl vibrations were resolved at 1661 and 1712 cm⁻¹. The absorption spectra may serve as a reference for theoretical and experimental studies on the effect of the microenvironment on the flavin cofactor. Furthermore, the molar absorption coefficient of FAD at 1547 cm⁻¹ was determined to 2200 L mol⁻¹ cm⁻¹ with an integral absorption coefficient of ∼50,000 L mol⁻¹ cm⁻². These values are prerequisite for the determination of reaction yields in flavoproteins from reaction-induced difference spectra.     

Adsorption structures of water in NaX studied by DRIFT spectroscopy and neutron powder diffraction

Diffuse reflectance infrared Fourier transform spectroscopic (DRIFTS) measurements (4000-1500 cm(-1)) and the results of neutron powder diffraction have been combined to study the structure of adsorption complexes of water in a NaX zeolite at different water loadings (25, 48, 72, and 120 water molecules per unit cell, respectively). Sharp bands corresponding to non-hydrogen-bonded OH groups of water molecules and broad associate bands due to hydrogen-bonded molecules are observed in the DRIFT spectra. We observe a remarkable downshift of the high-frequency associate band in a narrow temperature interval when the water amount decreases from 120 to 72 molecules per unit cell, which could signify some kind of "phase transition" for the water inside the zeolite cavities. Neutron powder diffraction results show that water molecules are predominantly localized in or near the 12-ring windows. Water molecules with hydrogen-bonded and non-hydrogen-bonded OH groups were found, in agreement with the observation of sharp and broad bands in the DRIFT spectra. We find strong evidence for the formation of cyclic hexamers of water molecules localized in the 12-ring windows, which are further stabilized by hydrogen bonds to framework oxygen atoms.     

Raman and UV-visible absorption spectra of ion-paired aggregates of copper porphyrins

Raman and UV-visible absorption spectra of ion-paired aggregate constructed from two copper porphyrins, copper tetrakis(4-N-methylpyridyl)porphyrin (CuTMPyP) and copper tetrakis(4-sulfonatophenyl)pophyrin (CuTSPP), are reported in this paper. The absorption bands of the aggregate was found exhibiting obvious shift and broadening, which are attributed to the excitonic coupling between the two paired porphyrin rings. The excitonic coupling in the aggregates also induces evident alteration for Raman intensities compared with monomer spectrum. Aggregation results in only small shifts (2-3 cm(-1)) for Raman lines connecting with the vibrations of porphyrin rings, manifesting only slight structural change of porphyrin skeletons. On the other hand, evident downshift (5 cm(-1)) was observed for the Cm-pyridyl stretch mode (1254 cm(-1)) of CuTMPyP, suggesting weakening of the Cm-pyridyl bonds by aggregation. Raman depolarization ratios of the aggregates are different from those of the monomers, implying a lowering of effective symmetry due to the molecular packing in the aggregates.     

Zum konformationsverhalten einiger halogenalkane

The rotational isomerism of 1-bromopropane, 1-chloro-2-methylpropane and 1-bromo-2-methylpropane has been studied in the liquid phase by infrared spectroscopy. For the corresponding conformers the enthalpy differences were obtained from the temperature dependences of the intensities of the CX-stretching and some CCC-deformation vibrations. It was found that only the CX-stretching vibrations are suitable for enthalpy determinations. In the liquid phase those conformers with a gauche position of the methyl group and halogen atom are slightly preferred.     

Casting New Physicochemical Light on the Fundamental Biological Processes in Single Living Cells by Using Raman Microspectroscopy

This Personal Account highlights the capabilities of spontaneous Raman microspectroscopy for studying fundamental biological processes in a single living cell. Raman microspectroscopy provides time‐ and space‐resolved vibrational Raman spectra that contain detailed information on the structure and dynamics of biomolecules in a cell. By using yeast as a model system, we have made great progress in the development of this methodology. The results that we have obtained so far are described herein with an emphasis placed on how three cellular processes, that is, cell‐division, respiration, and cell‐death, are traced and elucidated with the use of time‐ and space‐resolved structural information that is extracted from the Raman spectra. For cell‐division, compositional‐ and structural changes of various biomolecules are observed during the course of the whole cell cycle. For respiration, the redox state of mitochondrial cytochromes, which is inferred from the resonance Raman bands of cytochromes, is used to evaluate the respiration activity of a single cell, as well as that of isolated mitochondrial particles. Special reference is made to the “Raman spectroscopic signature of life”, which is a characteristic Raman band at 1602 cm^?1 that is found in yeast cells. This signature reflects the cellular metabolic activity and may serve as a measure of mitochondrial dysfunction. For cell‐death, “cross‐talk” between the mitochondria and the vacuole in a dying cell is suggested. DOI 10.1002/tcr.201200008     

Infrared and Raman spectra of terephthalonitrile and terephthalonitrile-15N2. Force field for out-of-plane vibrations

A general assignment of the vibrational spectra of terephthalonitrile and terephthalonitrile-¹⁵N₂ is proposed on the basis of their infrared and Raman spectra. The relevant symmetry is found to be D_2h. The force field for the out-of-plane vibrations of these molecules was calculated by refining the general quadratic force field obtained by the semi-empirical MINDO/3 method, starting with a geometry optimized by this method. The refined force field reproduces the observed frequencies of the out-of-plane vibrations to better than ±0.5 cm⁻¹.     

Characterization of lattice disorder in the low-temperature phase of irradiated PTFE by vibrational spectroscopy

In an effort to elucidate the structure of the low-temperature phase of PTFE, a spectroscopic study of the effect of progressive irradiation on the low-frequency infrared spectrum was undertaken. Previous infrared and Raman measurements indicated that irradiation of PTFE decreases its crystalline content, resulting in a lowering of the 19°C phase transition temperature due to the introduction of disorder and defect structures into the lattice by chain scission. Far-infrared studies of virgin and irradiated PTFE at liquid nitrogen temperatures show that the medium to strong bands at 45, 54, 58, and 71 cm^?1, attributed to lattice vibrations, decrease in intensity as the crystalline content decreases. These findings support the assignment of these bands to intermolecular vibrations of the crystalline lattice and are an indication of the presence of more than one molecule in the crystallographic unit cell.