Phonon modes controlled by primary chemical structure of partially fluorinated dimyristoylphosphatidylcholine (DMPC) revealed by multiple-angle incidence resolution spectrometry (MAIRS).

Partially fluorinated dimyristoylphosphatidylcholines (DMPCs) involving double alkyl chains are employed to control the phonon generation in thin films, which is examined by infrared (IR) spectroscopy coupled with multiple-angle incidence resolution spectrometry (MAIRS). technique. Compounds having perfluoroalkyl (Rf) chains are known to exhibit phonon bands in IR spectra because of the strong dipole-dipole interactions. Since the phonon bands of an organic matter have a similar shape to the normal absorption bands, however, recognition of the phonon modes is difficult and confusing for IR spectroscopists. Here, we show that MAIRS works out for finding phonon modes in monolayers: the Berreman shift is readily captured by the MAIRS in-plane and out-of-plane (OP) spectra. By measuring the longitudinal-optic (LO) energy-loss function spectrum of a bulk sample, the degree of molecular aggregation in the monolayer is also revealed by comparing the OP spectrum of the monolayer to the LO one. In addition, partially fluorinated DMPC compounds having both hydrocarbon and Rf chains are prepared, and they are used to obstruct the self-aggregation of the Rf groups in the film. As a result, the phonon characteristics are mostly lost in the MAIRS spectra as expected.

Simultaneous Analysis of Molecular Orientation and Quantity Change of Constituents in a Thin Film Using pMAIRS.

Spectral analysis using chemometrics is extensively used for quantitative chemical analysis in a mixture, but it works powerfully only when the peak intensity is solely proportional to the quantity of chemical components. In this sense, thin films on a solid substrate are not suitable for chemometric analysis, because the molecular orientation also influences the peak intensity via the surface selection rules. In the present study, this long-term analytical issue has readily been overcome by using p-polarized multiple-angle incidence resolution spectrometry (pMAIRS), which has a characteristic that the in-plane (IP) and out-of-plane (OP) vibrational spectra of a thin-film sample are obtained simultaneously in a common ordinate scale. Thanks to this unique power of pMAIRS, the average of the IP and OP spectra annihilates optical anisotropy, yielding an orientation-free spectrum, which enables us to perform the simultaneous quantitative analysis of both quantity change and molecular orientation of the constituents in a thin film. Now, we are ready to examine chemical reactions quantitatively in a thin film.

Infrared active surface modes found in thin films of perfluoroalkanes reveal the dipole-dipole interaction and surface morphology.

Infrared (IR) spectra of an organic thin film are mostly understood by considering the normal modes of a single molecule, if the dipole-dipole (D-D) interaction is ignorable in the film. When the molecules have a chemical group having a large permanent dipole moment such as the C=O and C-F groups, the D-D interaction induces vibrational couplings across the molecules, which produces an extra band as a surface phonon or polariton band because of the small thickness. Since the dipole moment of an organic compound is much less than that of an inorganic ionic crystal, we have a problem that the extra band looks like a normal-mode band, which are difficult to be discriminated from each other. In fact, this visual similarity sometimes leads us to a wrong direction in chemical discussion because the direction of the transition moment of the extra band is totally different from those of the normal modes. Here, we show useful selection rules for discussing IR spectra of a thin film without performing the permittivity analysis. The apparent change in the spectral shape on decrease in the thickness of the sample can be correlated with the morphological change in the film surface, which can also be discussed with changes in the molecular packing. This analytical technique has effectively been applied for studying the chemical properties of perfluoroalkanes as a chemical demonstration, which readily supports the stratified dipole-array theory for perfluoroalkyl compounds.

Rational Method of Monitoring Molecular Transformations on Metal-Oxide Nanowire Surfaces.

Metal-oxide nanowires have demonstrated excellent capability in the electrical detection of various molecules based on their material robustness in liquid and air environments. Although the surface structure of the nanowires essentially determines their interaction with adsorbed molecules, understanding the correlation between an oxide nanowire surface and an adsorbed molecule is still a major challenge. Herein, we propose a rational methodology to obtain this information for low-density molecules adsorbed on metal oxide nanowire surfaces by employing infrared p-polarized multiple-angle incidence resolution spectroscopy and temperature-programmed desorption/gas chromatography-mass spectrometry. As a model system, we studied the surface chemical transformation of an aldehyde (nonanal, a cancer biomarker in breath) on single-crystalline ZnO nanowires. We found that a slight surface reconstruction, induced by the thermal pretreatment, determines the surface chemical reactivity of nonanal. The present results show that the observed surface reaction trend can be interpreted in terms of the density of Zn ions exposed on the nanowire surface and of their corresponding spatial arrangement on the surface, which promotes the reaction between neighboring adsorbed molecules. The proposed methodology will support a better understanding of complex molecular transformations on various nanostructured metal-oxide surfaces.

Amyloid-ß fibrils assembled on ganglioside-enriched membranes contain both parallel ß-sheets and turns.

Some protein and peptide aggregates, such as those of amyloid-ß protein (Aß), are neurotoxic and have been implicated in several neurodegenerative diseases. Aß accumulates at nanoclusters enriched in neuronal lipids called gangliosides in the presynaptic neuronal membrane, and the resulting oligomeric and/or fibrous forms accelerate the development of Alzheimer's disease. Although the presence of Aß deposits at such nanoclusters is known, the mechanism of their assembly and the relationship between Aß secondary structure and topography are still unclear. Here, we first confirmed by atomic force microscopy that Aß40 fibrils can be obtained by incubating seed-free Aß40 monomers with a membrane composed of sphingomyelin, cholesterol, and the ganglioside GM1. Using Fourier transform infrared (FTIR) reflection-absorption spectroscopy, we then found that these lipid-associated fibrils contained parallel ß-sheets, whereas self-assembled Aß40 molecules formed antiparallel ß-sheets. We also found that the fibrils obtained at GM1-rich nanoclusters were generated from turn Aß40 Our findings indicate that Aß generally self-assembles into antiparallel ß-structures but can also form protofibrils with parallel ß-sheets by interacting with ganglioside-bound Aß. We concluded that by promoting the formation of parallel ß-sheets, highly ganglioside-enriched nanoclusters help accelerate the elongation of Aß fibrils. These results advance our understanding of ganglioside-induced Aß fibril formation in neuronal membranes and may help inform the development of additional therapies for Alzheimer's disease.

Probing the Molecular Structure and Orientation of the Leaf Surface of Brassica oleracea L. by Polarization Modulation-Infrared Reflection-Absorption Spectroscopy.

The surface of most aerial plant organs is covered with the cuticle, a membrane consisting of a variety of organic compounds, including waxes, cutin (a polyester) and polysaccharides. The cuticle serves as the multifunctional interface between the plant and the environment, and plays a major role in protecting plants against various environmental stress factors. Characterization of the molecular arrangements in the intact cuticle is critical for the fundamental understanding of its physicochemical properties; however, this analysis remains technically challenging. Here, we describe the nondestructive characterization of the intact cuticle of Brassica oleracea L. leaves using polarization modulation-infrared (IR) reflection-absorption spectroscopy (PM-IRRAS). PM-IRRAS has a probing depth of less than several hundreds of nanometers, and reveals the crystalline structure of the wax covering the cuticle surface (epicuticular wax) and the nonhydrogen-bonding character of cutin. Combined analysis using attenuated total reflection-IR spectra suggested that hemicelluloses xylan and xyloglucan are present in the outer cuticle region close to the epicuticular wax, whereas pectins are dominant in the inner cuticle region (depth of ≤2 µm). PM-IRRAS can also determine the average orientation of the cuticular molecules, as indicated by the positive and negative spectral peaks. This unique advantage reveals the orientational order in the intact cuticle; the hydrocarbon chains of the epicuticular wax and cutin and the backbones of hemicelluloses are oriented perpendicular to the leaf surface. PM-IRRAS is a versatile, informative and easy-to-use technique for studying plant cuticles because it is nondestructive and does not require sample pretreatment and background measurements.

Second Generation of Multiple-Angle Incidence Resolution Spectrometry.

Infrared surface spectroscopic techniques commonly have long-term issues that (1) the multiple reflections of light in the substrate yield optical interference fringes in the absorption spectrum and (2) the double modulation of light at the interferometer in a Fourier transform infrared spectrometer makes the water-vapor subtraction impossible. These measurement troubles often disturb the quantitative analysis of chemical bands of the analyte thin film. Multiple-angle incidence resolution spectrometry (MAIRS) is not an exception in this matter, either. In the present study, the long-term common issues have first been resolved by fixing the angle of incidence at a large angle, whereas the polarization angle is changed. With this simple conceptual change of MAIRS, as a result, we are ready for concentrating on spectral analysis only without concerning about the measurement troubles.

Raman Optical Activity on a Solid Sample: Identification of Atropisomers of Perfluoroalkyl Chains Having a Helical Conformation and No Chiral Center.

Perfluoroalkyl (Rf) chains have a specific helical conformation due to the steric repulsion between the adjacent CF2 units. Although Rf chains have no chiral center, two chiral structures, i.e., the right-handed (R) and left-handed (L) helices, are available as the most stable conformations, which are atropisomers to each other. According to the stratified dipole array (SDA) theory, the helical structure about the chain axis plays a key role in the spontaneous molecular aggregation of Rf chains in a two-dimensional manner, and the Rf chains having the same chirality tend to be aggregated spontaneously to generate molecular domains. This implies that an Rf compound in a solid state should be a mixture of the R and L domains, and each domain should exhibit distinguishable optical activity. To identify molecular domains with different atropisomers, in this study, Raman optical activity (ROA) measurements were performed on a Raman imaging spectrometer. Through the ROA measurements of recrystallized solid samples of an Rf compound, each particle exhibits an apparent optical activity, and the two atropisomers were readily distinguished. As a result, an Rf compound with the same helicity is found to be spontaneously aggregated as expected by the SDA theory.

Study of Perfluoroalkyl Chain-Specific Band Shift in Infrared Spectra on the Chain Length.

The CF2 symmetric stretching vibration (νs(CF2)) band of a perfluoroalkyl (Rf) group in an infrared (IR) spectrum exhibits a unique character, that is, an apparent high wavenumber shift with increasing the chain length, which is an opposite character to that of the CH stretching vibration band of a normal alkyl chain. To reveal the mechanism of the unusual IR band shift, two vibrational characters of an Rf chain are focused: (1) a helical conformation of an Rf chain, (2) the carbon (C) atoms having a smaller mass than the fluorine (F) atom dominantly vibrate as a coupled oscillator leaving F atoms stay relatively unmoved. These indicate that a "coupled oscillation of the skeletal C atoms" of an Rf chain should be investigated considering the helical structure. In the present study, therefore, the coupled oscillation of the Rf chain dependent on the chain length is investigated by Raman spectroscopy, which is suitable for investigating a skeletal vibration. The Raman-active νs(CF2) band is found to be split into two bands, the splitting is readily explained by considering the helical structure and length with respect to group theory, and the unusual peak shift is concluded to be explained by the helical length.

Comprehensive Understanding of Structure-Controlling Factors of a Zinc Tetraphenylporphyrin Thin Film Using pMAIRS and GIXD Techniques.

The performance of an organic electronic device is significantly influenced by the anisotropic molecular structure in the film, which has long been difficult to predict especially for a solution process. In the present study, a zinc tetraphenylporphyrin (ZnTPP) thin film prepared by a solution process was chosen to comprehensively explore the molecular-arrangement mechanism as a function of representative film-preparation parameters: solvent, film-preparation technique, and thermal annealing. The anisotropic structure was first analyzed by using a combination of infrared p-polarized multiple-angle incidence resolution spectrometry (pMAIRS) and grazing incidence X-ray diffraction (GIXD), which readily revealed the molecular orientation and crystal structure, respectively. As a result, the real dominant factor was found to be the evaporation time of the solvent that determines the initial two different molecular arrangements, types-I and -II, while the thermal annealing was found to play an additional role of improving the molecular order. The correlation between the molecular orientation and the crystal structure was also revealed through the individual orientation analysis of the porphyrin and phenyl rings.

Surface selection rule of infrared diffuse reflection spectrometry for analysis of molecular adsorbates on a rough surface of a nonabsorbing medium.

The surface selection rule (SSR) for discussing the molecular orientation in a thin film adsorbed on a rough surface is determined by analyzing a surface monolayer by defining the angle of incidence and polarizations. As the standard sample, a highly organized self-assembled monolayer (SAM) on a rough alumina surface is employed. By introducing crossed-Nicol polarizers in the incident and detection paths, the specular reflection and diffuse reflection components are readily separated. To fully understand the spectra of the SAM, a new idea is proposed that the incidental light can be excluded from the discussion when the angle of incidence is small, which is named the pseudotransmission (pd-Tr) model. Another important idea is that a part of a spectrum is degraded in the signal-to-noise ratio by the suppression of incidental light on the rough surface via a deconstructive interference, which can experimentally be revealed by the crossed-Nicol measurements of single-beam spectra depending on the angle of incidence. Through the experiments of all the combinations of polarizations and angles of incidence, the pd-Tr model and the light suppression are found to be an important base to fully understand the SSR of molecular adsorbates on a rough surface of a nonabsorbing medium.

Analysis of the hydration process and rotational dynamics of water in a Nafion membrane studied by 1H NMR spectroscopy.

(1)H NMR spectroscopy is employed to reveal the hydration process of a Nafion membrane by measuring both the chemical shift and the spin-lattice relaxation time. In a former study, the hydration process was suggested to comprise two steps: the molecular adsorption of water on the sulfonic acid groups and wetting with liquid water. The present study has revealed the first step can further be divided into two steps. By introducing a new experimental technique, the quantitatively reliable NMR measurements of protons ((1)H) of water involved in the polymer membrane are realized. In addition, a new analytical procedure is developed using a reciprocal concentration on a saturation-adsorption model, and the hydration is clearly revealed to have three individual steps. Both the chemical shift and the relaxation time plots against the reciprocal concentration exhibit three linear parts with apparently different slopes. Of great interest is that the initial hydration is divided into two stages: the first hydration is a very strong adsorption of water probably on the hydroxyl group of the sulfonic acid group, and the second one is a relatively weak adsorption on another site of the sulfonic acid group. The third hydration is readily assigned to excess bulk (liquid-like) water as expected. These adsorption processes are readily correlated with the rotational motion of water by converting the spin-lattice relaxation time to the rotational correlation time.

Infrared spectroscopic study of stereo-controlled poly(N-isopropylacrylamide) with an extended chain conformation induced by adsorption on a gold surface.

Poly(N-isopropylacrylamide) (PNiPAM) compounds with various diad tacticities were prepared, and the molecular interaction properties in a thin film deposited on a gold surface were analyzed using infrared spectroscopy. The intramolecular and intermolecular interactions were found to depend on the tacticity, and only atactic (diad ratio 46 %) PNiPAM exhibits poor molecular interaction even in the bulk sample. On the other hand, the same series of compounds dissolved in an acetone solution were spread on a gold surface to form a thin film. In the dissolution process, the polymer molecules are relaxed via solvation, and they are bound to the gold surface by a molecular interaction to form a submonolayer thin film. In the thin film, the molecular interaction with the gold surface via the N-H group was monitored in the infrared spectra only for a nearly isotactic (m = 90) PNiPAM by an apparent shift of the N-H stretching vibration band. This shift was confirmed by changing the degree of hydrophilicity of the gold surface: a larger shift is found on a gold surface with stronger hydrophilicity. As a result, the conformation of a nearly isotactic molecule is found to be extended by the interaction with the gold surface, which works to immobilize the molecule.

Perfluoroalkanes remain on water surface even after volatilization: Affinity analysis of fluorinated solvent with water surface.

Perfluoroalkyl (Rf) compounds are known to have a poor solubility for most solvents except fluorinated solvents, which is known as a fluorous property. In Langmuir (L) film studies of Rf compounds, fluorinated solvents such as perfluoro-n-alkanes are generally used as a good solvent for depositing a sample monolayer on the water surface. On the other hand, a single Rf chain with a short length such as C6F13- is known to exhibit a totally different character from a condensed matter to have a strong affinity to a water molecule on the water surface via the dipole-dipole interaction, which is known as the dipole interactive (DI) property. On considering the DI property, the solvents of perfluoro-n-alkanes would remain on water for a long time, which may disturb the formation of L film on water. In the present study, details of a liquid layer of perfluoro-n-alkanes on water are investigated by using infrared external reflection (IR ER) spectrometry. Although the perfluoro-n-alkanes are highly volatile, the relevant vibration bands did not disappear even after two hours, which means that they remain on the water surface. Fortunately, however, the remained solvent, C6F14, has been found no disturbing factor for preparation of L films.

Control of supramolecular organizations by coordination bonding in tetrapyridylporphyrin thin films.

Coordination bonding has been employed for the first time to control molecular orientation in thin films and is demonstrated by using tetrapyridylporphyrin. Changing the central metal ion of porphyrin controls the balance of the coordination bonding and hydrogen bonding, and edge-on orientation has been realized for the first time as well as face-on orientation. The mechanism of the film structure formation is comprehensively explained based on the electron configuration of the central metal ion.

Stereoisomer-dependent conversion of dinaphthothienothiophene precursor films.

Soluble precursor materials of organic semiconductors are employed for fabricating solution-processable thin film devices. While the so-called precursor approach has already been tried for various organic electronic devices such as transistors and solar cells, understanding of the conversion process in the film lags far behind. Here, we report that molecular aggregation of the precursor compound significantly influences the thermal conversion reaction in the film. For this study, two stereoisomers of a dinaphthothienothiophene (DNTT) precursor that are the endo- and exo-DNTT-phenylmaleimide monoadducts are focused on. The structural change during the thermal conversion process has been investigated by a combination of infrared spectroscopy and X-ray diffraction techniques. The results show that the endo-isomer is readily converted to DNTT in the film by heating, whereas the exo-isomer exhibits no reaction at all. This reaction suppression is found to be due to the self-aggregation property of the exo-isomer accompanying the intermolecular C-H[Formula: see text]O interactions. This finding shows a new direction of controlling the on-surface reaction, as well as the importance of analyzing the film structure at the initial stage of the reaction.

Conformational Change of Alkyl Chains at Phase Transitions in Thin Films of an Asymmetric Benzothienothiophene Derivative.

Among many promising organic semiconducting materials, 2-decyl-7-phenyl[1]benzothieno[3,2-b][1]benzothiophene (Ph-BTBT-C10) shows outstanding device performances for organic field-effect transistors. This compound has a highly ordered liquid crystalline state, i.e., the smectic E (SmE) phase. Although the transition from the crystalline state to the SmE phase is believed to accompany melting of the alkyl chains, no spectroscopic evidence has been found so far. In this study, the conformational change of the decyl chains in Ph-BTBT-C10 films across the phase transition is analyzed by temperature-dependent measurements in situ using infrared spectroscopy. The spectral analysis reveals that the polycrystalline film has latent conformational disorder (the gauche conformer), the rate of which becomes more pronounced with the heat treatment. As expected, melting of the decyl chains is observed above the transition temperature to the SmE phase. This study also highlights the discovery of some key bands sensitive to the phase transitions in liquid crystalline organic semiconductors.

Blue shift of the isolated CD stretching band of CH2DOH in water induced by changes in the hydrogen-bonding pattern.

The wavenumber shift in the CD stretching (ν(CD)) band of the monodeuterated methanol (CH(2)DOH) has been monitored in water-methanol mixtures. For the pure liquid, two dominant bands are observed at 2148 and 2176 cm(-1) in the ν(CD) region. The matrix isolation technique and spectral simulation based on quantum chemical calculations have revealed that these two bands are categorized into the C(1) mode and originate from methanol molecules participating in different hydrogen(H)-bonding patterns. The simulation results for methanol clusters have suggested that the 2148 cm(-1) band is concerned with the end-donor species in the H-bonding network. The relative intensity of the band near 2148 cm(-1) decreases with increasing water concentration, indicating that the population of the end-donor species decreases by the addition of water. This spectral change causes the blue shift in the mean center of the ν(CD) band of CH(2)DOH in water.

In vivo characterization of the structures of films of a fatty acid and an alcohol adsorbed on the skin surface.

An in vivo analysis of stearyl alcohol and stearic acid films on the skin surface using polarized infrared-external reflection spectroscopy revealed that whether the sample molecules adopt an energetically stable conformation and orientation strongly depends on the molecular functionalities and sample preparation conditions. For stearic acid, even the difference in solute concentration between 0.1 and 0.5 wt% results in a different molecular conformation and orientation. This illustrates that the molecular organization of the adsorbate on the skin surface is sensitively determined by the kinetics of the sample film growth, not by the simple thermodynamic equilibrium with the skin temperature.

Quantitative Anisotropic Analysis of Molecular Orientation in Amorphous N2O at 6 K by Infrared Multiple-Angle Incidence Resolution Spectrometry.

The existence of molecular orientational order in nanometer-thick films of molecules has long been implied by surface potential measurements. However, direct quantitative determination of the molecular orientation is challenging, especially for metastable amorphous thin films at low temperatures. This study quantifies molecular orientation in amorphous N2O at 6 K using infrared multiple-angle incidence resolution spectrometry (IR-MAIRS). The intensity ratio of the weak antisymmetric stretching vibration band of the 14N15NO isotopomer between the in-plane and out-of-plane IR-MAIRS spectra provides an average molecular orientation angle of 65° from the surface normal. No discernible change is observed in the orientation angle when a different substrate material is used (Si and Ar) at 6 K or the Si substrate temperature is changed in the range of 6-14 K. This suggests that the transient mobility of N2O during physisorption is key in governing the molecular orientation in amorphous N2O.