CuI and H2 O2 Inactivate and FeII Inhibits [Fe]-Hydrogenase at Very Low Concentrations

[Fe]-Hydrogenase (Hmd) catalyzes reversible hydride transfer from H₂ . It harbors an iron-guanylylpyridinol as a cofactor with an Fe^II that is ligated to one thiolate, two COs, one acyl-C, one pyridinol-N, and solvent. Here, we report that Cu^I and H₂ O₂ inactivate Hmd (half-maximal rates at 1 μM Cu^I and 20 μM H₂ O₂ ) and that Fe^II inhibits the enzyme with very high affinity (K_i =40 nM). Infrared and EPR studies together with competitive inhibition studies with isocyanide indicated that Cu^I exerts its inhibitory effect most probably by binding to the active site iron-thiolate ligand. Using the same methods, it was found that H₂ O₂ binds to the active-site iron at the solvent-binding site and oxidizes Fe^II to Fe^III . Also it was shown that Fe^II reversibly binds away from the active site iron, with binding being competitive to the organic hydride acceptor; this inhibition is specific for Fe^II and is reminiscent of that for the [FeFe]-hydrogenase second iron, which specifically interacts with H₂ .

The biocompatibility of carbon hydroxyapatite/β-glucan composite for bone tissue engineering studied with Raman and FTIR spectroscopic imaging

The spectroscopic approaches of FTIR imaging and Raman mapping were applied to the characterisation of a new carbon hydroxyapatite/β-glucan composite developed for bone tissue engineering. The composite is an artificial bone material with an apatite-forming ability for the bone repair process. Rabbit bone samples were tested with an implanted bioactive material for a period of several months. Using spectroscopic and chemometric methods, we were able to determine the presence of amides and phosphates and the distribution of lipid-rich domains in the bone tissue, providing an assessment of the composite's bioactivity. Samples were also imaged in transmission using an infrared microscope combined with a focal plane array detector. CaF2 lenses were also used on the infrared microscope to improve spectral quality by reducing scattering artefacts, improving chemometric analysis. The presence of collagen and lipids at the bone/composite interface confirmed biocompatibility and demonstrate the suitability of FTIR microscopic imaging with lenses in studying these samples. It confirmed that the composite is a very good background for collagen growth and increases collagen maturity with the time of the bone growth process. The results indicate the bioactive and biocompatible properties of this composite and demonstrate how Raman and FTIR spectroscopic imaging have been used as an effective tool for tissue characterisation.

A new linear bismuth coordination polymer based on 1,10-phenanthroline-2,9-dicarboxylic acid: ionothermal synthesis, crystal structure and fluorescence properties

A new linear bismuth(III) coordination polymer, catena-poly[[chloridobismuth(III)]-μ3-1,10-phenanthroline-2,9-dicarboxylato-κ(6)O(2):O(2),N(1),N(10),O(9):O(9)], [Bi(C14H6N2O4)Cl]n, has been obtained by an ionothermal method and characterized by elemental analysis, energy-dispersive X-ray spectroscopy, IR spectroscopy, thermal stability studies and single-crystal X-ray diffraction. The structure is constructed by Bi(C14H6N2O4)Cl fragments in which each Bi(III) centre is seven-coordinated by one Cl atom, four O atoms and two N atoms. The coordination geometry of the Bi(III) cation is distorted pentagonal-bipyramidal (BiO4N2Cl), with one bridging carboxylate O atom and one Cl atom located in the axial positions. The Bi(C14H6N2O4)Cl fragments are further extended into a one-dimensional linear polymeric structure via subsequent but different centres of symmetry (bridging carboxylate O atoms). Neighbouring linear chains are assembled via weak C-H···O and C-H···Cl hydrogen bonds, forming a three-dimensional supramolecular architecture. Intermolecular π-π stacking interactions are observed, with centroid-to-centroid distances of 3.678 (4) Å, which further stabilize the structure. In addition, the solid-state fluorescence properties of the title coordination polymer were investigated.

Unusual hydrogen bonding in L-cysteine hydrogen fluoride

L-Cysteine hydrogen fluoride, or bis(L-cysteinium) difluoride-L-cysteine-hydrogen fluoride (1/1/1), 2C3H8NO2S(+)·2F(-)·C3H7NO2S·HF or L-Cys(+)(L-Cys···L-Cys(+))F(-)(F(-)...H-F), provides the first example of a structure with cations of the 'triglycine sulfate' type, i.e. A(+)(A···A(+)) (where A and A(+) are the zwitterionic and cationic states of an amino acid, respectively), without a doubly charged counter-ion. The salt crystallizes in the monoclinic system with the space group P2(1). The dimeric (L-Cys···L-Cys(+)) cation and the dimeric (F(-)···H-F) anion are formed via strong O-H···O or F-H···F hydrogen bonds, respectively, with very short O···O [2.4438 (19) Å] and F···F distances [2.2676 (17) Å]. The F···F distance is significantly shorter than in solid hydrogen fluoride. Additionally, there is another very short hydrogen bond, of O-H···F type, formed by a L-cysteinium cation and a fluoride ion. The corresponding O···F distance of 2.3412 (19) Å seems to be the shortest among O-H···F and F-H···O hydrogen bonds known to date. The single-crystal X-ray diffraction study was complemented by IR spectroscopy. Of special interest was the spectral region of vibrations related to the above-mentioned hydrogen bonds.

N-(6-Methylpyridin-2-yl)mesitylenesulfonamide and acetic acid--a salt, a cocrystal or both?

In the solid obtained from N-(6-methylpyridin-2-yl)mesitylenesulfonamide and acetic acid, the constituents interact via two N-H···O hydrogen bonds. The H atom situated in one of these short contacts is disordered over two positions: one of these positions is formally associated with an adduct of the neutral sulfonamide molecule and the neutral acetic acid molecule, and corresponds to a cocrystal, while the alternative site is associated with salt formation between a protonated sulfonamide molecule and deprotonated acetic acid molecule. Site-occupancy refinements and electron densities from difference Fourier maps suggest a trend with temperature, albeit of limited significance; the cocrystal is more relevant at 100 K, whereas the intensity data collected at room temperature match the description as cocrystal and salt equally well.

Spectroelectrochemical Studies on Quinacridone by Using Poly(vinyl alcohol) Coating as Protection Layer

Spectroscopic measurements in the infrared range combined with electrochemistry are a powerful technique for investigation of organic semiconductors to track changes during oxidation and reduction (p- and n-doping) processes. For these measurements it is important that the studied material, mostly deposited as a thin film on an internal reflection element, does not dissolve during this characterization. In this study we introduce a technique that allows infrared spectroelectrochemical characterization of films of these materials for the first time. In many cases so far this has been impossible, due to solubility in the oxidized and/or reduced form. This novel technique is shown on thin films of quinacridone by adding a protection layer of poly(vinyl alcohol) (PVA).

The Nature of Bonding between Argon and Mixed Gold-Silver Trimers

The controversial nature of chemical bonding between noble gases and noble metals is addressed. Experimental evidence of exceptionally strong Au-Ar bonds in Ar complexes of mixed Au-Ag trimers is presented. IR spectra reveal an enormous influence of the attached Ar atoms on vibrational modes, particularly in Au-rich trimers, where Ar atoms are heavily involved owing to a relativistically enhanced covalency. In Ag-rich trimers, vibrational transitions of the metal framework predominate, indicating a pure electrostatic character of the Ag-Ar bonds. The experimental findings are analyzed by means of DFT calculations, which show how the relativistic differences between Au and Ag are manifested in stronger Au-Ar binding energies. Because of the ability to vary composition and charge distribution, the trimers serve as ideal model systems to study the chemical nature of the bonding of noble gases to closed-shell systems containing gold.

Comparative study of halogen- and hydrogen-bond interactions between benzene derivatives and dimethyl sulfoxide

The halogen bond, similar to the hydrogen bond, is an important noncovalent interaction and plays important roles in diverse chemistry-related fields. Herein, bromine- and iodine-based halogen-bonding interactions between two benzene derivatives (C6 F5 Br and C6 F5 I) and dimethyl sulfoxide (DMSO) are investigated by using IR and NMR spectroscopy and ab initio calculations. The results are compared with those of interactions between C6 F5 Cl/C6 F5 H and DMSO. First, the interaction energy of the hydrogen bond is stronger than those of bromine- and chlorine-based halogen bonds, but weaker than iodine-based halogen bond. Second, attractive energies depend on 1/r(n) , in which n is between three and four for both hydrogen and halogen bonds, whereas all repulsive energies are found to depend on 1/r(8.5) . Third, the directionality of halogen bonds is greater than that of the hydrogen bond. The bromine- and iodine-based halogen bonds are strict in this regard and the chlorine-based halogen bond only slightly deviates from 180°. The directional order is iodine-based halogen bond>bromine-based halogen bond>chlorine-based halogen bond>hydrogen bond. Fourth, upon the formation of hydrogen and halogen bonds, charge transfers from DMSO to the hydrogen- and halogen-bond donors. The CH3 group contributes positively to stabilization of the complexes.

The Melibiose Transporter of Escherichia coli: CRITICAL CONTRIBUTION OF LYS-377 TO THE STRUCTURAL ORGANIZATION OF THE INTERACTING SUBSTRATE BINDING SITES

We examine the role of Lys-377, the only charged residue in helix XI, on the functional mechanism of the Na(+)-sugar melibiose symporter from Escherichia coli. Intrinsic fluorescence, FRET, and Fourier transform infrared difference spectroscopy reveal that replacement of Lys-377 with either Cys, Val, Arg, or Asp disables both Na(+) and melibiose binding. On the other hand, molecular dynamics simulations extending up to 200-330 ns reveal that Lys-377 (helix XI) interacts with the anionic side chains of two of the three putative ligands for cation binding (Asp-55 and Asp-59 in helix II). When Asp-59 is protonated during the simulations, Lys-377 preferentially interacts with Asp-55. Interestingly, when a Na(+) ion is positioned in the Asp-55-Asp-59 environment, Asp-124 in helix IV (a residue essential for melibiose binding) reorients and approximates the Asp-55-Asp-59 pair, and all three acidic side chains act as Na(+) ligands. Under these conditions, the side chain of Lys-377 interacts with the carboxylic moiety of these three Asp residues. These data highlight the crucial role of the Lys-377 residue in the spatial organization of the Na(+) binding site. Finally, the analysis of the second-site revertants of K377C reveals that mutation of Ile-22 (in helix I) preserves Na(+) binding, whereas that of melibiose is largely abolished according to spectroscopic measurements. This amino acid is located in the border of the sugar-binding site and might participate in sugar binding through apolar interactions.

Complete Proton Transfer Cycle in GFP and Its T203V and S205V Mutants

Proton transfer is critical in many important biochemical reactions. The unique three-step excited-state proton transfer in avGFP allows observations of protein proton transport in real-time. In this work we exploit femtosecond to microsecond transient IR spectroscopy to record, in D₂O, the complete proton transfer photocycle of avGFP, and two mutants (T203V and S205V) which modify the structure of the proton wire. Striking differences and similarities are observed among the three mutants yielding novel information on proton transfer mechanism, rates, isotope effects, H-bond strength and proton wire stability. These data provide a detailed picture of the dynamics of long-range proton transfer in a protein against which calculations may be compared.

Mechanism of Decomposition of Surface Ethoxy Species to Ethene and Acidic OH Groups on H-ZSM-5

The reaction mechanism of the decomposition of ethoxy species to ethene and acidic OH groups on H-ZSM-5 was studied by IR spectroscopy using isotope-labeled ethanol. The concerted mechanism occurring on both the ethoxy (acid) site and the counterpart lattice oxygen was suggested by GC-MS analysis of evolved d2-ethene and IR observation of the recovery of OH s groups on acid sites from the decomposition of CH3CD2O- ethoxy species. The concerted mechanism was further confirmed by the estimation of activation energy for decomposition of CH3CH2O-, CH3CD2O-, and CD3CD2O- ethoxy species, 122 ± 3, 125 ± 3, and 140 ± 5 kJ mol(-1), respectively, where the kinetic isotope effect was observed for the cleavage of the CH or CD bond of the methyl group of the ethoxy species.

Infrared Spectroscopy During Electrocatalytic Turnover Reveals the Ni-L Active Site State During H2 Oxidation by a NiFe Hydrogenase

A novel in situ IR spectroscopic approach is demonstrated for the characterization of hydrogenase during catalytic turnover. E. coli hydrogenase 1 (Hyd-1) is adsorbed on a high surface-area carbon electrode and subjected to the same electrochemical control and efficient supply of substrate as in protein film electrochemistry during spectral acquisition. The spectra reveal that the active site state known as Ni-L, observed in other NiFe hydrogenases only under illumination or at cryogenic temperatures, can be generated reversibly in the dark at ambient temperature under both turnover and non-turnover conditions. The observation that Ni-L is present at all potentials during turnover under H2 suggests that the final steps in the catalytic cycle of H2 oxidation by Hyd-1 involve sequential proton and electron transfer via Ni-L. A broadly applicable IR spectroscopic technique is presented for addressing electrode-adsorbed redox enzymes under fast catalytic turnover.

Vibrational spectroscopy, ab initio calculations and Frontier Orbital analysis of 4,5,6,8,9-pentachloropyrimido-[1,2-a][1,8]naphthyridin-10-one

In this work we present a study of the vibrational spectra of 4,5,6,8,9-pentachloropyrimido-[1,2-a][1,8]naphthyridin-10-one, C11H2Cl5N3O, a substance belonging to the important pharmacological class of 1,8-naphthyridine derivatives. The Fourier transform infrared and the Fourier transform Raman spectra of the crystal were recorded at room temperature in the regions 400-4000 and 50-4000 cm(-1), respectively. Vibrational wavenumbers were predicted using Density Functional Theory calculations with the B3LYP functional on 6-31G(d,p) and 6-311++G(d,p) basis sets. The descriptions of the normal modes were made after calculating the potential energy distribution. Additionally, potential reaction sites were evaluated through Mulliken population and Frontier Orbital analysis.

Sub-terahertz frequency-domain spectroscopy reveals single-grain mobility and scatter influence of large-area graphene

The response of individual domains in wafer-sized chemical vapor deposition graphene is measured by contactless sub-terahertz interferometry, observing the intrinsic optical conductance and reaching very high mobility values. It is shown that charged scatterers limit the mobility, validating previous theoretical predictions, and sub-terahertz quality assessment is demonstrated, as necessary for large-scale applications in touchscreens, as well as wearable and optoelectronic devices.

Formation of Water Chains on CaO(001): What Drives the 1D Growth?

Formation of partly dissociated water chains is observed on CaO(001) films upon water exposure at 300 K. While morphology and orientation of the 1D assemblies are revealed from scanning tunneling microscopy, their atomic structure is identified with infrared absorption spectroscopy combined with density functional theory calculations. The latter exploit an ab initio genetic algorithm linked to atomistic thermodynamics to determine low-energy H2O configurations on the oxide surface. The development of 1D structures on the C4v symmetric CaO(001) is triggered by symmetry-broken water tetramers and a favorable balance between adsorbate-adsorbate versus adsorbate-surface interactions at the constraint of the CaO lattice parameter.

The exploration of hydrogen bonding properties of 2,6- and 3,5-diethynylpyridine by IR spectroscopy

Hydrogen bonding properties of 2,6- and 3,5-diethynylpyridine were analyzed by exploring of their interactions with trimethylphosphate, as hydrogen bond acceptor, or phenol, as hydrogen bond donor, in tetrachloroethene C2Cl4. The employment of IR spectroscopy enabled unravelling of their interaction pattern as well as the determination of their association constants (Kc) and standard reaction enthalpies (ΔrH(⦵)). The association of diethynylpyridines with trimethylphosphate in stoichiometry 1:1 is established through CH⋯O hydrogen bond, accompanied by the secondary interaction between CC moiety and CH3 group of trimethylphosphate. In the complexes with phenol, along with the expected OH⋯N interaction, CC⋯HO interaction is revealed. In contrast to 2,6-diethynylpyridine where the spatial arrangement of hydrogen bond accepting groups enables the simultaneous involvement of phenol OH group in both OH⋯N and OH⋯CC hydrogen bond, in the complex between phenol and 3,5-diethynylpyridine this is not possible. It is postulated that cooperativity effects, arisen from the certain type of resonance-assisted hydrogen bonds, contribute the stability gain of the latter. Associations of diethynylpyridines with trimethylphosphate are characterized as weak (Kc≈0.8-0.9mol(-1)dm(3); -ΔrH(⦵)≈5-8kJmol(-1)), while their complexes with phenol as medium strong (Kc≈5mol(-1)dm(3); -ΔrH(⦵)≈15-35kJmol(-1)). Experimental findings on the studied complexes are supported with the calculations conducted at B3LYP/6-311++G(d,p) level of theory in the gas phase. Two conformers of diethynylpyridine⋯trimethylphosphate dimers are formed via CH⋯O interaction, whereas dimers between phenol and diethynylpyridines are established through OH⋯N interaction.

Calcium tartrate esahydrate, CaC4H4O6·6H2O: a structural and spectroscopic study

The crystal structure of calcium tartrate esahydrate, CaC4H4O6·6H2O, has been solved by the charge-flipping method from single-crystal X-ray diffraction data and refined to R = 0.021, based on 1700 unique observed diffractions. Salient crystallographic data are: a = 7.7390 (1), b = 12.8030 (2), c = 5.8290 (1) Å, Z = 2, and space group P2₁2₁2. During the refinement step it was possible to locate all H atoms by difference Fourier synthesis. The tartrate molecule has a (-)-gauche conformation and is coordinated to two calcium ions to form infinite chains along the a axis which alternate Ca polyhedra with tartrate molecules. The chains are interlinked by a three-dimensional network of hydrogen bonds from four water molecules surrounding the Ca ion, reinforced by hydrogen bonds from one interstitial water molecule. Micro-Raman and FT-IR spectroscopic data are provided.

Determination of N-acetylation degree in chitosan using Raman spectroscopy

Application of Raman spectroscopy in determination of the acetylation degree (DA) of chitosan has been developed. The spectra of several chitosan samples characterized by different DD (degree of deacetylation) in the range 50-100% have been measured. The integral intensities of the bands assigned to the vibrations of amine group and glucosidic ring were used to calculate the DA from the intensity ratio. The assignment of the bands to the respective normal modes of chitosan was based on the DFT quantum chemical calculations. This method has a number of advantages over other techniques. It is fast and does not require purification of the sample nor require dissolution of the chitosan in any solvent.

Thermal treatment of magnetite nanoparticles

This paper presents the results of a thermal treatment process for magnetite nanoparticles in the temperature range of 50-500 °C. The tested magnetite nanoparticles were synthesized using three different methods that resulted in nanoparticles with different surface characteristics and crystallinity, which in turn, was reflected in their thermal durability. The particles were obtained by coprecipitation from Fe chlorides and decomposition of an Fe(acac)3 complex with and without a core-shell structure. Three types of ferrite nanoparticles were produced and their thermal stability properties were compared. In this study, two sets of unmodified magnetite nanoparticles were used where crystallinity was as determinant of the series. For the third type of particles, a Ag shell was added. By comparing the coated and uncoated particles, the influence of the metallic layer on the thermal stability of the nanoparticles was tested. Before and after heat treatment, the nanoparticles were examined using transmission electron microscopy, IR spectroscopy, differential scanning calorimetry, X-ray diffraction and Mössbauer spectroscopy. Based on the obtained results, it was observed that the fabrication methods determine, to some extent, the sensitivity of the nanoparticles to external factors.

Early formation of the ion-conducting pore in channelrhodopsin-2

Channelrhodopsins (ChRs) are light-gated ion channels that are widely used in optogenetics. They allow precise control of neuronal activity with light, but a detailed understanding of how the channel is gated and the ions are conducted is still lacking. The recent determination of the X-ray structural model in the closed state marks an important milestone. Herein the open state structure is presented and the early formation of the ion conducting pore is elucidated in atomic detail using time-resolved FTIR spectroscopy. Photo-isomerization of the retinal-chromophore causes a downward movement of the highly conserved E90, which opens the pore. Molecular dynamic (MD) simulations show that water molecules invade through this opened pore, Helix 2 tilts and the channel fully opens within ms. Since E90 is a highly conserved residue, the proposed E90-Helix2-tilt (EHT) model might describe a general activation mechanism and provides a new avenue for further mechanistic studies and engineering.

SN2P2: a neutral five-membered sulfur-pnictogen(III) ring

The novel aromatic ring compound 2,4-diphospha-3,5-diaza-thiole (cyclo-SNPNP) was synthesized via flash pyrolysis of SP(N3)3 and characterized by IR spectroscopy and (15)N isotope labeling. Quantum chemical computations indicate its formation by head-to-tail dimerization of SNP and subsequent elimination of a sulfur atom from the highly unstable boatlike six-membered-ring compound cyclo-SNPSNP.

Monitoring solid oxide CO2 capture sorbents in action

The separation, capture, and storage of CO2 , the major greenhouse gas, from industrial gas streams has received considerable attention in recent years because of concerns about environmental effects of increasing CO2 concentration in the atmosphere. An emerging area of research utilizes reversible CO2 sorbents to increase conversion and rate of forward reactions for equilibrium-controlled reactions (sorption-enhanced reactions). Little fundamental information, however, is known about the nature of the sorbent surface sites, sorbent surface-CO2 complexes, and the CO2 adsorption/desorption mechanisms. The present study directly spectroscopically monitors Na2 O/Al2 O3 sorbent-CO2 surface complexes during adsorption/desorption with simultaneous analysis of desorbed CO2 gas, allowing establishment of molecular level structure-sorption relationships between individual surface carbonate complexes and the CO2 working capacity of sorbents at different temperatures.

Carbon dioxide adsorption in amine-functionalized mixed-ligand metal-organic frameworks of UiO-66 topology

A series of mixed-ligand [1,4-benzenedicarboxylic acid (BDC)/2-amino-1,4-benzenedicarboxylic acid (ABDC)] UiO-66 metal-organic frameworks (MOFs) synthesized through two different methods (low (LT) and high temperature (HT)) have been investigated for their carbon dioxide adsorption properties from 0 to 1 bar to clarify the role of amino loading on carbon dioxide uptake. Volumetric CO2 isotherms show that the CO2 capacity (normalized to the Langmuir surface area) increases with a degree of functionalization of about 46%; for similar NH2 contents, the same values are found for both synthetic procedures. Microcalorimetric isotherms reveal that amino-functionalized materials have a larger differential heat of adsorption (q(diff) ) towards CO2 ; reaching 27(25) and 20(22) kJ mol(-1) on HT(LT)-UiO-66-NH2 and UiO-66, respectively, at the lowest equilibrium pressures used in this study. All experimental results are supported by values obtained through quantum mechanical calculations.

Vibrational circular dichroism and theoretical study of the conformational equilibrium in (-)-S-nicotine

We report an extensive study of the molecular and electronic structure of (-)-S-nicotine, to deduce the phenomenon that controls its conformational equilibrium and to solve its solution-state conformer population. Density functional theory, ab initio, and molecular mechanics calculations were used together with vibrational circular dichroism (VCD) and Fourier transform infrared spectroscopies. Calculations and experiments in solution show that the structure and the conformational energy profile of (-)-S-nicotine are not strongly dependent on the medium, thus suggesting that the conformational equilibrium is dominated by hyperconjugative interactions rather than repulsive electronic effects. The analysis of the first recorded VCD spectra of (-)-S-nicotine confirmed the presence of two main conformers at room temperature. Our results provide further evidence of the hypersensitivity of vibrational optical activity spectroscopies to the three-dimensional structure of chiral samples and prove their suitability for the elucidation of solution-state conformer distribution.

Ionic strength and composition govern the elasticity of biological membranes. A study of model DMPC bilayers by force- and transmission IR spectroscopy

Infrared (IR) spectroscopy was used to quantify the ion mixture effect of seawater (SW), particularly the contribution of Mg(2+) and Ca(2+) as dominant divalent cations, on the thermotropic phase behaviour of 1,2-dimyristoyl-sn-glycero-3-posphocholine (DMPC) bilayers. The changed character of the main transition at 24 °C from sharp to gradual in films and the 1 °C shift of the main transition temperature in dispersions reflect the interactions of lipid headgroups with the ions in SW. Force spectroscopy was used to quantify the nanomechanical hardness of a DMPC supported lipid bilayer (SLB). Considering the electrostatic and ion binding equilibrium contributions while systematically probing the SLB in various salt solutions, we showed that ionic strength had a decisive influence on its nanomechanics. The mechanical hardness of DMPC SLBs in the liquid crystalline phase linearly increases with the increasing fraction of all ion-bound lipids in a series of monovalent salt solutions. It also linearly increases in the gel phase but almost three times faster (the corresponding slopes are 4.9 nN/100 mM and 13.32 nN/100 mM, respectively). We also showed that in the presence of divalent ions (Ca(2+) and Mg(2+)) the bilayer mechanical hardness was unproportionally increased, and that was accompanied with the decrease of Na(+) ion and increase of Cl(-) ion bound lipids. The underlying process is a cooperative and competitive ion binding in both the gel and the liquid crystalline phase. Bilayer hardness thus turned out to be very sensitive to ionic strength as well as to ionic composition of the surrounding medium. In particular, the indicated correlation helped us to emphasize the colligative properties of SW as a naturally occurring complex ion mixture.

The study of hydrogen bonding and π⋯π interactions in phenol⋯ethynylbenzene complex by IR spectroscopy

Weak hydrogen bonds between phenol and ethynylbenzene in tetrachloroethene were explored by using FTIR spectroscopy. Association constants (Kc) were determined by high dilution method at two temperatures, 20°C and 26°C, and they are, respectively, 0.54±0.09 mol(-1) dm3 and 0.36±0.08 mol(-1) dm3. The position of ethynylbenzene stretching band, when in hydrogen bonding complex with phenol (CC⋯), is proposed to be governed by the interplay of OH⋯π (CC moiety or phenyl ring of ethynylbenzene) and π⋯π (phenyl ring of phenol⋯CC moiety or phenyl ring of ethynylbenzene) interactions. This conclusion is supported by the findings on the complex between ethanol and ethynylbenzene; in the latter, CC⋯ stretching band is shifted to the higher wavenumbers, as expected when ethynylbenzene interacts with hydrogen bond donor. Geometries and energies of the presumed complexes, as well as their vibrational spectra, are predicted by using ab initio calculations. The spectroscopic and thermodynamic data obtained here offer the missing pieces in the present picture of migration of H-atom of phenol OH group between competing hydrogen bond accepting centers on ethynylbenzene.

N-alkylacylamides in thin films display infrared spectra of 3₁₀-, α-, and π-helices with visible static and dynamic growth phases

A peptide model is a physical system containing a CONH group, the simplest being HCONHCH3 , N-methylformamide (NMF). We have discovered that NMF and N-methylacetamide (NMA), which form hydrogen-bonded oligomers in thin films on a planar AgX fiber, display infrared (IR) spectra with peaks like those of polypeptide helices. Structures can be assigned by their amide I maxima near 1672 (3(10)), 1655 (3(10)), 1653 (α), 1655 (π), and 1635 cm(-1) (π), which are the first IR data for the π-helix. Sharp peaks are an outcome of immobilization of polar species on the polar surface of silver halides. We report the first use of expanded thin-film IR spectroscopy, in which plots of every spectrum over the amide I-II range show pauses or slow stages in the increase or decrease of absorption. These are identified as static phases followed by dynamic phases, with the incremental gain or loss of a helix turn. A general theory can be stated for such processes. Density functional calculations show that the NMA α-helix pentamer (crystal structure geometry) is transformed into a π-helix-like form. For the first time, an entire sequence (3(10)-helix, α-helix, π-helix, quasiplanar species) of spectra has been recorded for NMA.

N-methyl-trimethylacetamide in thin films displays infrared spectra of π-helices, with visible static and dynamic growth phases, and then a β-sheet

The simplest (minimal) peptide model is HCONHCH3. An increase in the π-helix content with increased substitution in the acyl portion suggested the examination of N-methyl-trimethylacetamide) (NMT). NMT displays spectra, in which there is evolution of a set of helices defined by their amide I maxima near 1686 (3(10)), 1655 (first π), and, most importantly, at 1637 cm(-1) (π). Expanded thin-film infrared spectroscopy (XTFIS) shows pauses or slow stages, which are identified as static phases followed by dynamic phases with the incremental gain or loss of a helix turn. In addition, absorbance at 1637 cm(-1) suddenly increases at 82.1 s (30% over 0.3 s), indicating a phase change and crystallization of the π-helix, along with a coincidental decrease in the absorbance for the first π-helix. A sharp peak occurs at the maximum of the phase change at 82.5 s, representing a pure NMT π-helix. The spectra then undergo a decreasing general absorption loss over 150 s, with the π-helix evolving further to an antiparallel β-sheet fragment. The spectral quality arises from the immobilization of polar molecules on polar surfaces. The crystal structure is that of an antiparallel β-sheet.

In situ synchrotron IR microspectroscopy of CO2 adsorption on single crystals of the functionalized MOF Sc2(BDC-NH2)3

Synchrotron radiation (SR) IR microspectroscopy has enabled determination of the thermodynamics, kinetics, and molecular orientation of CO₂ adsorbed in single microcrystals of a functionalized metal–organic framework (MOF) under conditions relevant to carbon capture from flue gases. Single crystals of the small-pore MOF, Sc₂(BDC-NH₂)₃, (BDC-NH₂=2-amino-1,4-benzenedicarboxylate), with well-defined crystal form have been investigated during CO₂ uptake at partial pressures of 0.025-0.2 bar at 298–373 K. The enthalpy and diffusivity of adsorption determined from individual single crystals are consistent with values obtained from measurements on bulk samples. The brilliant SR IR source permits rapid collection of polarized spectra. Strong variations in absorbance of the symmetric stretch of the NH₂ groups of the MOF and the asymmetric stretch of the adsorbed CO₂ at different orientations of the crystals relative to the polarized IR light show that CO₂ molecules align along channels in the MOF.

Defining the Proton Topology of the Zr6-Based Metal-Organic Framework NU-1000

Metal-organic frameworks (MOFs) constructed from Zr6-based nodes have recently received considerable attention given their exceptional thermal, chemical, and mechanical stability. Because of this, the structural diversity of Zr6-based MOFs has expanded considerably and in turn given rise to difficulty in their precise characterization. In particular it has been difficult to assign where protons (needed for charge balance) reside on some Zr6-based nodes. Elucidating the precise proton topologies in Zr6-based MOFs will have wide ranging implications in defining their chemical reactivity, acid/base characteristics, conductivity, and chemical catalysis. Here we have used a combined quantum mechanical and experimental approach to elucidate the precise proton topology of the Zr6-based framework NU-1000. Our data indicate that a mixed node topology, [Zr6(μ3-O)4(μ3-OH)4(OH)4 (OH2)4](8+), is preferred and simultaneously rule out five alternative node topologies.

Metal-carbonyl units for vibrational and luminescence imaging: towards multimodality

Metal-carbonyl complexes are attractive structures for bio-imaging. In addition to unique vibrational properties due to the CO moieties enabling IR and Raman cell imaging, the appropriate choice of ancillary ligands opens up the opportunity for luminescence detection. Through a classification by techniques, past and recent developments in the application of metal-carbonyl complexes for vibrational and luminescence bio-imaging are reviewed. Finally, their potential as bimodal IR and luminescent probes is addressed.

Crystal structure of (NH4)2[Fe(II) 5(HPO3)6], a new open-framework phosphite

Di-ammonium hexa-phosphito-penta-ferrate(II), (NH4)2[Fe5(HPO3)6], was synthesized under mild hydro-thermal conditions and autogeneous pressure, yielding twinned crystals. The crystal structure exhibits an [Fe(II) 5(HPO3)6](2-) open framework with NH4 (+) groups as counter-cations. The anionic skeleton is based on (001) sheets of [FeO6] octa-hedra (one with point-group symmetry 3.. and one with .2.) linked along [001] through [HPO3](2-) oxoanions. Each sheet is constructed from 12-membered rings of edge-sharing [FeO6] octa-hedra, giving rise to channels with a radius of ca 3.1 Å in which the disordered NH4 (+) cations are located. The IR spectrum shows vibrational bands typical for phosphite and ammonium groups.

Spectroscopic identification of a bidentate binding motif in the anionic magnesium-CO2 complex ([ClMgCO2 ](-))

A magnesium complex incorporating a novel metal-CO2 binding motif is spectroscopically identified. Here we show with the help of infrared photodissociation spectroscopy that the complex exists solely in the [ClMg(η(2) -O2 C)](-) form. This bidentate double oxygen metal-CO2 coordination has previously not been observed in neutral nor in charged unimetallic complexes. The antisymmetric CO2 stretching mode in [ClMg(η(2) -O2 C)](-) is found at 1128 cm(-1) , which is considerably redshifted from the corresponding mode in bare CO2 at 2349 cm(-1) , suggesting that the CO2 moiety has a considerable negative charge (∼1.8 e(-) ). We also employed electronic structure calculations and kinetic analysis to support the interpretation of the experimental results.

Intramolecular H/D Exchange of Ethanol Catalyzed by Acidic OH Groups on H-ZSM-5 Zeolite

IR observation of ethanol adsorption clarified the presence of the apparent intramolecular isotope exchange from CD3CH2OH to CHD2CH2OD on acidic OH groups of H-ZSM-5 zeolite. This reaction did not proceed with CD3OH nor CH3CD2OH, implying that the β-hydrogen of alcohol had interaction with the lattice oxygen adjacent to Al and that the reaction was mediated by isotope exchange of CD3 groups of ethanol and OH groups on zeolite.

Characterization and optical studies of 90/10 (wt/wt%) PVA/β-chitin blend irradiated with γ-rays

X-ray diffraction, IR spectroscopy and UV/visible spectra were studied as a function of gamma irradiation doses (5-100kGy) for 90/10 (wt/wt%) PVA/β-chitin. A new intense reflection peak at 2θ=21.5° appeared in the X-ray spectrum of the sample irradiated at 50kGy γ-dose. Besides, the band centered at 2931cm(-1) in IR spectrum splits into two clearly separated bands around 2919 and 2941cm(-1) for the sample irradiated at 10kGy γ-dose. The disappearance of the absorption band at 280nm of PVA in the blend sample indicates that the ligand PVA becomes opaque in the UV region and provides evidence for the miscibility between homopolymers. The value of absorbance, in UV/visible range, at 10kGy γ-dose was the highest one compared to the other γ-doses. The location of the γ-doses on the chromaticity diagram was different, indicating the change in the spectral colors of the investigated blend. In addition, the absorption edge, band tail and color parameters values were determined as a function of γ-doses.

Control of the transition between Ni-C and Ni-SI(a) states by the redox state of the proximal Fe-S cluster in the catalytic cycle of [NiFe] hydrogenase

[NiFe] hydrogenase catalyzes the reversible cleavage of H2. The electrons produced by the H2 cleavage pass through three Fe-S clusters in [NiFe] hydrogenase to its redox partner. It has been reported that the Ni-SI(a), Ni-C, and Ni-R states of [NiFe] hydrogenase are involved in the catalytic cycle, although the mechanism and regulation of the transition between the Ni-C and Ni-SI(a) states remain unrevealed. In this study, the FT-IR spectra under light irradiation at 138-198 K show that the Ni-L state of [NiFe] hydrogenase is an intermediate between the transition of the Ni-C and Ni-SI(a) states. The transition of the Ni-C state to the Ni-SI(a) state occurred when the proximal [Fe4S4]p(2+/+) cluster was oxidized, but not when it was reduced. These results show that the catalytic cycle of [NiFe] hydrogenase is controlled by the redox state of its [Fe4S4]p(2+/+) cluster, which may function as a gate for the electron flow from the NiFe active site to the redox partner.

SDS-PAGE and IR spectroscopy to evaluate modifications in the viral protein profile induced by a cationic porphyrinic photosensitizer

Reactive oxygen species can be responsible for microbial photodynamic inactivation due to its toxic effects, which include severe damage to proteins, lipids and nucleic acids. In this study, the photo-oxidative modifications of the proteins of a non-enveloped T4-like bacteriophage, induced by the cationic porphyrin 5,10,15-tris(1-methylpyridinium-4-yl)-20-(pentafluorophenyl)porphyrin tri-iodide were evaluated. Two methods were used: sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) and infrared spectroscopy. SDS-PAGE analysis showed that the phage protein profile was considerably altered after photodynamic treatment. Seven protein bands putatively corresponding to capsid and tail tube proteins were attenuated and two other were enhanced. Infrared spectroscopy confirmed the time-dependent alteration on the phage protein profile detected by SDS-PAGE, indicative of a response to oxidative damage. Infrared analysis showed to be a promising and rapid screening approach for the analysis of the modifications induced on viral proteins by photosensitization. In fact, one single infrared spectrum can highlight the changes induced to all viral molecular structures, overcoming the delays and complex protocols of the conventional methods, in a much simple and cost effective way.

Kinetic, spectroscopic, and theoretical assessment of associative and dissociative methanol dehydration routes in zeolites

Mechanistic interpretations of rates and in situ IR spectra combined with density functionals that account for van der Waals interactions of intermediates and transition states within confining voids show that associative routes mediate the formation of dimethyl ether from methanol on zeolitic acids at the temperatures and pressures of practical dehydration catalysis. Methoxy-mediated dissociative routes become prevalent at higher temperatures and lower pressures, because they involve smaller transition states with higher enthalpy, but also higher entropy, than those in associative routes. These enthalpy-entropy trade-offs merely reflect the intervening role of temperature in activation free energies and the prevalence of more complex transition states at low temperatures and high pressures. This work provides a foundation for further inquiry into the contributions of H-bonded methanol and methoxy species in homologation and hydrocarbon synthesis reactions from methanol.

Investigating the thermostability of succinate: quinone oxidoreductase enzymes by direct electrochemistry at SWNTs-modified electrodes and FTIR spectroscopy

Succinate: quinone reductases (SQRs) are the enzymes that couple the oxidation of succinate and the reduction of quinones in the respiratory chain of prokaryotes and eukaryotes. Herein, we compare the temperature-dependent activity and structural stability of two SQRs, the first from the mesophilic bacterium Escherichia coli and the second from the thermophilic bacterium Thermus thermophilus, using a combined electrochemical and infrared spectroscopy approach. Direct electron transfer was achieved with full membrane protein complexes at single-walled carbon nanotube (SWNT)-modified electrodes. The possible structural factors that contribute to the temperature-dependent activity of the enzymes and, in particular, to the thermostability of the Thermus thermophilus SQR are discussed.

The cellular environment of cancerous human tissue. Interfacial and dangling water as a "hydration fingerprint"

Despite a large number of publications, the role of water in the cellular environment of biological tissue has not been clarified. Characterizing the biological interface is a key challenge in understanding the interactions of water in the tissue. Although we often assume that the properties of the bulk water can be translated to the crowded biological environment, this approach must be considerably revised when considering the biological interface. To our knowledge, few studies have directly monitored the interactions and accumulation of water in the restricted environments of the biological tissue upon realistic crowding conditions. The present study focuses on a molecular picture of water molecules at the biological interface, or specifically, water molecules adjacent to the hydrophobic and hydrophilic surfaces of normal and cancerous tissues. We recorded and analyzed the IR and Raman spectra of the νs(OH) stretching modes of water at the biological interfaces of the human breast and neck tissues. The results revealed dramatic changes in the water content in the tissue and are potentially relevant to both the fundamental problems of interfacial water modeling and the molecular diagnostics of cancer as a 'hydration fingerprint'. Herein, we will discuss the origin of the vibrational substructures observed for the νs(OH) stretching modes of water, showing that the interfacial water interacting via H-bond with other water molecules and biomolecules at the biological surface and free OH vibration of the dangling water are sensitive indicators of the pathology between the normal (noncancerous) and cancerous tissue and cancer types.

Mechanistic insight into oxide-promoted palladium catalysts for the electro-oxidation of ethanol

Recent advancements in the development of alternatives to proton exchange membrane fuel cells utilizing less-expensive catalysts and renewable liquid fuels, such as alcohols, has been observed for alkaline fuel cell systems. Alcohol fuels present the advantage of not facing the challenge of storage and transportation encountered with hydrogen fuel. Oxidation of alcohols has been improved by the promotion of alloyed or secondary phases. Nevertheless, currently, there is no experimental understanding of the difference between an intrinsic and a synergistic promotion effect in high-pH environments. This report shows evidence of different types of promotion effects on palladium electrocatalysts obtained from the presence of an oxide phase for the oxidation of ethanol. The correlation of mechanistic in situ IR spectroscopic studies with electrochemical voltammetry studies on two similar electrocatalytic systems allow the role of either an alloyed or a secondary phase on the mechanism of oxidation of ethanol to be elucidated. Evidence is presented for the difference between an intrinsic effect obtained from an alloyed system and a synergistic effect produced by the presence of an oxide phase.

Ester carbonyl vibration as a sensitive probe of protein local electric field

The ability to quantify the local electrostatic environment of proteins and protein/peptide assemblies is key to gaining a microscopic understanding of many biological interactions and processes. Herein, we show that the ester carbonyl stretching vibration of two non-natural amino acids, L-aspartic acid 4-methyl ester and L-glutamic acid 5-methyl ester, is a convenient and sensitive probe in this regard, since its frequency correlates linearly with the local electrostatic field for both hydrogen-bonding and non-hydrogen-bonding environments. We expect that the resultant frequency-electric-field map will find use in various applications. Furthermore, we show that, when situated in a non-hydrogen-bonding environment, this probe can also be used to measure the local dielectric constant (ε). For example, its application to amyloid fibrils formed by Aβ(16-22) revealed that the interior of such β-sheet assemblies has an ε value of approximately 5.6.

Probing protonation sites of isolated flavins using IR spectroscopy: from lumichrome to the cofactor flavin mononucleotide

Infrared spectra of the isolated protonated flavin molecules lumichrome, lumiflavin, riboflavin (vitamin B2), and the biologically important cofactor flavin mononucleotide are measured in the fingerprint region (600-1850 cm(-1)) by means of IR multiple-photon dissociation (IRMPD) spectroscopy. Using density functional theory calculations, the geometries, relative energies, and linear IR absorption spectra of several low-energy isomers are calculated. Comparison of the calculated IR spectra with the measured IRMPD spectra reveals that the N10 substituent on the isoalloxazine ring influences the protonation site of the flavin. Lumichrome, with a hydrogen substituent, is only stable as the N1-protonated tautomer and protonates at N5 of the pyrazine ring. The presence of the ribityl unit in riboflavin leads to protonation at N1 of the pyrimidinedione moiety, and methyl substitution in lumiflavin stabilizes the tautomer that is protonated at O2. In contrast, flavin mononucleotide exists as both the O2- and N1-protonated tautomers. The frequencies and relative intensities of the two C=O stretch vibrations in protonated flavins serve as reliable indicators for their protonation site.

Defects in surface chemistry--reductive coupling of benzaldehyde on rutile TiO₂(110)

The surface chemistry of oxygen and oxygenates on Rutile TiO2(110) is of great interest for various applications such as heterogeneous catalysis and photo catalysis. Though it is generally accepted that surface defects are active sites, the role of subsurface defects is under debate. We have therefore investigated the influence of the bulk defect density on the reductive coupling of benzaldehyde to stilbene as a model system. Using IRRAS we identify stilbene diolate as a reduction intermediate. The concentration of this intermediate is proportional to the bulk defect density, whereas adsorption of benzaldehyde at lower temperatures is not affected, which indicates a dominant role of Ti interstitials at temperatures above 400 K.

Temperature-dependent IR spectroscopic and structural study of 18-crown-6 chelating ligand in the complexation with sodium surfactant salts and potassium picrate

18-crown-6 ether (18C6) complexes with the following anionic surfactants: sodium n-dodecylsulfate (18C6-NaDS), sodium 4-(1-pentylheptyl)benzenesulfonate (18C6-NaDBS); and potassium picrate (18C6-KP) were synthesized and studied in terms of their thermal and structural properties. Physico-chemical properties of new solid 1:1 coordination complexes were characterized by infrared (IR) spectroscopy, thermogravimetry and differential thermal analysis, differential scanning calorimetry, X-ray diffraction and microscopic observations. The strength of coordination between Na(+) and oxygen atoms of 18C6 ligand does not depend on anionic part of the surfactant, as established by thermodynamical parameters obtained by temperature-dependent IR spectroscopy. Each of these complexes exhibit different kinds of endothermic transitions in heating scan. Diffraction maxima obtained by SAXS and WAXS, refer the behavior of the compounds 18C6-NaDS and 18C6-NaDBS as smectic liquid crystalline. Distortion of 18C6-NaDS and 18C6-KP complexes occurs in two steps. Temperature of the decomplexation of solid crystal complex 18C6-KP is considerably higher than of mesophase complexes, 18C6-NaDS, and 18C6-NaDBS. The structural and liquid crystalline properties of novel 18-crown-ether complexes are function of anionic molecule geometry, type of chosen cation (Na(+), K(+)), as well as architecture of self-organized aggregates. A good combination of crown ether unit and amphiphile may provide a possibility for preparing new functionalized materials, opening the research field of ion complexation and of host-guest type behavior.

Complex formation of Sn(II) with L-cysteine: an IR, DTA/TGA and DFT investigation

The novel complex of Sn(II) with L-cysteine (L-H2Cys) has been synthesized and characterized by elemental analysis, TGA and IR spectroscopy. Vibrational assignment and DFT/PBE0/def2-TZVP ab initio simulation give evidence of cysteine molecule being coordinated to Sn(II) as three-dentate chelating N,O,S-donor ligand. The four Perdew density functionals TPSS, PBE0, PBE, TPSSh have been tested to provide consistency of simulated and experimental IR spectra, the best result is provided by unweighted Hartree-Fock density functionals (PBE, TPSS). On the contrary, the Hartree-Fock weighted functionals (PBE0, TPPSh) provide the most accurate geometry optimization. Unharmonic frequencies are obtained via ab initio vibrational self-consistent field (PT2-VSCF) calculations at DFT/TPSS/Def2-TZVP level, the vibrational assignment of IR spectra has been carried out.

Thermal stability and reduction of iron oxide nanowires at moderate temperatures

BACKGROUND

The thermal stability of iron oxide nanowires, which were obtained with a hard template method and are promising elements of Li-ion based batteries, has been investigated by means of thermogravimetry, infrared and photoemission spectroscopy measurements.

RESULTS

The chemical state of the nanowires is typical of the Fe2O3 phase and the stoichiometry changes towards a Fe3O4 phase by annealing above 440 K. The shape and morphology of the nanowires is not modified by moderate thermal treatment, as imaged by scanning electron microscopy.

CONCLUSION

This complementary spectroscopy-microscopy study allows to assess the temperature limits of these Fe2O3 nanowires during operation, malfunctioning or abuse in advanced Li-ion based batteries.

Spin-coupling in dimers of 2,3-dicyano-5,6-dichlorosemiquinone radical anions in the crystalline state

A crystal engineering approach is used to stabilize a radical anion in the crystalline state and to modulate the separation distance within π-stacks of anion radicals. Alkali metal salts of 2,3-dicyano-5,6-dichlorosemiquinone (C8Cl2N2O2, DDQ∙- radical anions were prepared and their crystal structures determined: LiDDQ·2H2O·(CH3)2CO, RbDDQ·2H2O and CsDDQ·2H2O. In these structures, stacked dimers of radical anions are formed within π-stacked columns. Within the stacked dimers, interplanar separation distances are significantly shorter than the sum of the van der Waals radii for two C atoms; the shortest is 2.812 Å for the Li salt and the longest is 2.925 Å for the Cs salt. Diamagnetic character, observed by electron paramagnetic resonance spectroscopy, indicates spin-coupling of the unpaired electrons within the radical anion dimer. The electron-rich cyano substituents on DDQ∙- influence the electron redistribution within the ring skeleton. The crystalline compounds are also characterized by IR spectroscopy, complemented by quantum-chemical calculations based on both isolated and periodic models.

Phosphatation of zeolite H-ZSM-5: a combined microscopy and spectroscopy study

A variety of phosphated zeolite H-ZSM-5 samples are investigated by using a combination of Fourier transfer infrared (FTIR) spectroscopy, single pulse (27)Al, (29)Si, (31)P, (1)H-(31)P cross polarization (CP), (27)Al-(31)P CP, and (27)Al 3Q magic angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy, scanning transmission X-ray microscopy (STXM) and N2 physisorption. This approach leads to insights into the physicochemical processes that take place during phosphatation. Direct phosphatation of H-ZSM-5 promotes zeolite aggregation, as phosphorus does not penetrate deep into the zeolite material and is mostly found on and close to the outer surface of the zeolite, acting as a glue. Phosphatation of pre-steamed H-ZSM-5 gives rise to the formation of a crystalline tridymite AlPO4 phase, which is found in the mesopores of dealuminated H-ZSM-5. Framework aluminum species interacting with phosphorus are not affected by hydrothermal treatment. Dealuminated H-ZSM-5, containing AlPO4 , retains relatively more framework Al atoms and acid sites during hydrothermal treatment than directly phosphated H-ZSM-5.