Infra-red Dichroism Research Articles

Conformational distributions of tetrahydro-2-turoic acid in water at different pH values by their IR and vibrational circular dichroism spectra

Infrared (IR) and vibrational circular dichroism (VCD) spectra of tetrahydro-2-furoic acid (THFA) in aqueous solutions under several different pH conditions were recorded. To interpret the IR and VCD spectra of THFA obtained in highly acidic and basic aqueous solutions, extensive and systematic conformational searches were conducted to acquire the low-energy minima for both the neutral and deprotonated forms of THFA species, as well as their hydrated clusters. This was accomplished by using the conformer-rotamer ensemble sampling tool (CREST) with an implicit solvation model for water. The CREST candidates were further optimized at the B3LYP-D3BJ/def2-TZVP level of theory. The simulated VCD spectra of the neutral THFA conformers in the polarizable continuum model (PCM) of water alone exhibit little agreement with the experimental data under highly acidic conditions. Applying the clusters-in-a-liquid solvation model by considering the monohydrate THFA conformers in the PCM of water, significantly improved agreement with the experimental data. Similarly, the deprotonated THFA species solvated with one to four explicit water molecules in the PCM of water were considered. While the IR and VCD spectra of the deprotonated THFA monohydrate conformers offer the best agreement with the experimental data, other larger hydrated clusters, particularly the dihydrates, also contribute to the spectra. Through the synergistic combined experimental and theoretical approach used in the study, comprehensive conformational distributions of the predominant THFA species across various pH conditions were extracted.

Characterization of dragonfly wing membranes using FTIR imaging and IR dichroism imaging

We characterized dragonfly wings from three species, Sympetrum frequens, Orthetrum albistylum speciosum, and Sympetrum infuscatum, collected in Chitose City using Fourier transform infrared (FTIR) imaging and infrared (IR) dichroism imaging. In the FTIR images, the distribution of amide I and II bands derived from the chitin was observed across the entire vein domain; however, strong absorption for the amide bands was observed in the thicker vein domain membrane: approximately 23% of the total vein domain membrane in the wing. IR dichroism images indicated that the chitin in the thinner vein domain membrane was oriented along the primary vein.

Fast-Tracking of the Segmental Orientation in Poly(ethylene oxide)-based Polyurethane Urea by Mechano-optical (Infrared Dichroism and Birefringence) Properties: Degree of the Soft-Segment Ordering Effect

The orientation behavior of segment-specific chemical groups of NH and CH was investigated for poly(ethylene oxide) (PEO)-based polyurethane urea (PUU) during uniaxial stretching using a uniaxial stretching system integrated with spectral birefringence and ultrafast IR spectrometers that capture two polarization states simultaneously. PUUs with 30% by-weight urethane-urea hard segment content were prepared using PEO oligomers with number average molecular weights of 2000, 4600, and 8000 g/mol. High-molecular weight PEO-based PUUs exhibited microphase morphologies with sharp interfaces between the PEO matrix and urethane-urea hard segments, while low-molecular weight PEO-2000 (2000 g/mol)-based PUU exhibited a gradient interphase. This is primarily due to substantial hydrogen-bonding interactions between the urea hard segments and ether groups of highly amorphous PEO-2000 compared with highly crystalline soft segments in PEO-4600 and PEO-8000, which lack significant hydrogen-bonding interactions with urea groups and hence a sharper interface and improved microphase separation. The segment-specific chemical group orientation study revealed that the relaxation and reorganization behaviors are closely dependent on the initial morphology. In microphase-separated PUU with a gradient interphase, responses of the hard and soft segments to deformation are similar even at lower strain levels. For the microphase-separated PUUs with a sharp interface, the low-strain level orientation is localized in the soft-segment regions until the connection with the hard segments drive the orientation in the chain axis toward the stretching direction. This network transition is also reflected in the mechano-optical behavior as a change from a high-strain optical constant to a lower-strain optical constant.

Thermal Behaviors, Interfacial Microstructure and Molecular Orientation of Shape Memory Polyurethane/SiO2 Based Sealant for Concrete Pavement.

Expansion joint failure is one of the main causes that lead to the damages of concrete pavement. The silicon dioxide/shape memory polyurethane (SiO2/SMPU) is a new kind of sealant which can use its shape memory performance to adapt to the width of the expansion joint with the change of pavement temperature, and it can effectively prolong the service life of the pavement and reduce maintenance costs. In this study, the effects of programming and the addition of SiO2 particles to the thermodynamic properties of the specimens were detected using differential scanning calorimetry (DSC), the optimal shape memory programming temperature of which is 72.9 °C. Combined with scanning electron microscopy (SEM) and shape memory effect test, the particles are evenly distributed between the two phases, and the shape fixation rate (Rf) of 98.15% and the shape recovery rate (Rr) of 97.31% show that the composite has a good shape memory effect. Fourier transform infrared spectroscopy (FTIR) and dynamic infrared dichroism illustrate the change of the hydrogen bond of soft and hard segments with the SiO2 particles in the shape memory cycle, revealing the optimal shape memory programming process. This study provides an insight into the reinforcement mechanism of SiO2 nanoparticles in SMPU matrix and verify whether it can meet the engineering requirements of expansion joints when used as a sealant of concrete pavement.

The combined use of amide I bands in polarized Raman, IR, and vibrational dichroism spectra for the structure analysis of peptide fibrils and disordered peptides and proteins

AbstractRaman spectroscopy is generally a versatile tool to explore the structure of proteins and peptides in solution. However, in spite of the development of ultraviolet (UV) resonance Raman spectroscopy as a tool that allows for the investigation of samples with lower concentrations, Raman has not played the same role as infrared (IR) spectroscopy with regard to secondary structure analysis. Reported UV Raman studies have recently focused on the ψ‐dependence of amide III as a useful tool for the structural analysis even of disordered peptides. Amide I based structural analysis generally uses visible excitation. Rather than describing the traditional secondary structure analysis of proteins, this review focusses on work that used Raman in conjunction with other vibrational spectroscopies such as IR and vibrational circular dichroism to probe the conformational distribution of amino acid residues in unfolded peptides and the self‐assembling of peptides into fibrils. We argue against the use of spectral decomposition into Gaussian bands particularly if this type of analysis is exclusively applied to either IR or Raman band profiles. The article emphasizes the delocalized excitonic character of amide I wavefunctions which has to be accounted for in any attempt to use the respective bands for structure analysis.

Degree of orientations of collagen fibers and bone apatite crystals in rat femora by infrared dichroism imaging

ObjectivesThe degree of orientations of collagen fibers and bone apatite crystals affects bone strength. We demonstrated that collagen fibers were aligned along the long axis of bone and that the degree of collagen fiber orientation changed with aging using infrared (IR) dichroism imaging. In this study, we developed a technique for evaluating bone apatite crystal orientation using IR dichroism imaging to investigate the relationships between collagen fiber and bone apatite crystal orientations. MethodsFemora were harvested from male Sprague Dawley rats of different ages (6, 12, and 33 weeks); they were then embedded in poly (methyl methacrylate) and sectioned with a microtome into 3-μm longitudinal sections. The angle-dependent Fourier transform infrared (FTIR) spectra for sections were collected using FTIR imaging, and collagen fiber and bone apatite crystal orientations in the sections were assessed using IR dichroism imaging. ResultsCollagen fibers and poorly crystalline apatite in the femoral cortical bone were longitudinally aligned; however, the stoichiometric hydroxyapatite crystal and all of the bone apatite were not aligned. The degree of poorly crystalline apatite orientation was higher in 33-week-old rats than in 6-week-old rats. ConclusionsPoorly crystalline apatite in the rat femoral cortical bone was aligned along the collagen fibers. The degree of poorly crystalline apatite orientation and collagen fiber orientation in the femoral cortical bone increased until at least 33 weeks; meanwhile, on aging, the stoichiometric hydroxyapatite crystal was not longitudinally aligned.

Analysis of Collagen Fiber Orientation in Bone of Different Aged Rats Using FTIR Imaging

Bone is mainly composed of type I collagen, hydroxyapatite, and water. Bone strength is increased in bone formation and reflects 70% bone mineral density (BMD) and 30% bone quality; however, BMD is clinically used to assess bone strength. In this work, we analyzed collagen fiber orientation in femur of different aged rats using infrared (IR) dichroism image due to assess consequences of collagen fiber orientation for bone strength. IR dichroism images indicated that the degree of collagen fiber orientation in rat femur was increased until 33 weeks old at least, and it can affect bone strength.

Enhanced stability of the columnar matrix in a discotic liquid crystal by insertion of ZnO nanoparticles

An experimental characterisation of dispersions of ZnO nanoparticles (NPs) in the columnar matrix of a discotic liquid crystal has been carried out. Thermophysical properties have been investigated by absorbance spectroscopy, differential scanning calorimetry, polarising optical microscopy, dielectric measurements, dc conductivity, X-ray diffraction and infrared (IR) dichroism technique. The experimental results show that inclusion of ZnO NPs into the columnar matrix enhances the orientational order in the columnar phase and does not affect the two-dimensional hexagonal lattice. The alignment in homeotropic samples is also found to be better with the addition of the NPs. The real (ϵ′) and imaginary parts (ϵ′′) of the permittivity increase by a small amount in the dispersions. The order parameter measured using the IR dichroism technique in the face-on geometry (homeotropic alignment) shows an enhancement for the composite system. The dc conductivity is also found to increase by an order of magnitude by addition of the NPs. These results suggest an improved stacking of the disc-like molecules within the columns by the insertion of the ZnO NPs possessing high charge mobility. Such composite systems would be highly beneficial for potential applications such as organic conductors.

The strong dimerization of the transmembrane domain of the fibroblast growth factor receptor (FGFR) is modulated by C‐terminal juxtamembrane residues

The fibroblast growth factor receptor 3 (FGFR3) is a member of the FGFR subfamily of the receptor tyrosine kinases (RTKs) involved in signaling across the plasma membrane. Generally, ligand binding leads to receptor dimerization and activation. Dimerization involves the transmembrane (TM) domain, where mutations can lead to constitutive activation in certain cancer types and also in skeletal malformations. Thus, it has been postulated that FGFR homodimerization must be inherently weak to allow regulation, a feature reminiscent of alpha and beta integrin TM interactions. However, we show herein that in FGFR3-TM, four C-terminal residues, CRLR, have a profound destabilizing effect in an otherwise strongly dimerizing TM peptide. In the absence of these four residues, the dimerizing propensity of FGFR3-TM is comparable to glycophorin, as shown using various detergents. In addition, the expected enhanced dimerization induced by the mutation associated to the Crouzon syndrome A391E, was observed only when these four C-terminal residues were present. In the absence of these four residues, A391E was dimer-destabilizing. Finally, using site specific infrared dichroism and convergence with evolutionary conservation data, we have determined the backbone model of the FGFR3-TM homodimer in model lipid bilayers. This model is consistent with, and correlates with the effects of, most known pathological mutations found in FGFR-TM.

Protein−Lipid Interactions with Fusobacterium nucleatum Major Outer Membrane Protein FomA: Spin-Label EPR and Polarized Infrared Spectroscopy

FomA, the major outer membrane protein of Fusobacterium nucleatum, was expressed and purified in Escherichia coli and reconstituted from detergent in bilayer membranes of phosphatidylcholines with chain lengths from C(12:0) to C(17:0). The conformation and orientation of membrane-incorporated FomA were determined from polarized, attenuated total reflection, infrared (IR) spectroscopy, and lipid-protein interactions with FomA were characterized by using electron paramagnetic resonance (EPR) spectroscopy of spin-labeled lipids. Approximately 190 residues of membranous FomA are estimated to be in a beta-sheet configuration from IR band fitting, which is consistent with a 14-strand transmembrane beta-barrel structure. IR dichroism of FomA indicates that the beta-strands are tilted by approximately 45 degrees relative to the sheet/barrel axis and that the order parameter of the latter displays a discontinuity corresponding to hydrophobic matching with fluid C(13:0) lipid chains. The stoichiometry ( N b = 23 lipids/monomer) of lipid-protein interaction from EPR demonstrates that FomA is not trimeric in membranes of diC(14:0) phosphatidylcholine and is consistent with a monomeric beta-barrel of 14-16 strands. The pronounced selectivity of interaction found with anionic spin-labeled lipids places basic residues of the protein in the vicinity of the polar-apolar membrane interfaces, consistent with current topology models. Comparison with similar data from the 8- to 22-stranded E. coli outer membrane proteins, OmpA, OmpG, and FhuA, supports the above conclusions.

Mechanical properties and linear infrared dichroism of thin films of polyurethane nanocomposites

Morphological, mechanical, and Fourier transform infrared dichroic investigations were performed on neat polyurethane (PU) polymer matrix and PU+CaCO3 nanocomposite thin films to determine how the nanofiller influenced the mechanical properties. The measurements were performed on strips that were cut from the prepared films in parallel and perpendicular directions with respect to the direction of film preparation. Optical microscopy of PU and the PU+CaCO3 nanocomposite revealed the strain-induced transition from a continuous spherulitic morphology to a fiberlike structure. The stress–strain behavior of the neat PU and PU+CaCO3 nanocomposite films showed significant differences at large strain regimes. The experimental results suggest that the mechanical properties were strongly related to the orientational behavior of the separated phases. The orientation of the hard and soft segments was analyzed by the orientation function calculated from the IR absorbances. A correlation between the orientations of segments, tensile properties, and hardness of the investigated polymer films was established. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008

Differences in mechanical behavior between alternating and random styrene-methyl methacrylate copolymers

The viscoelastic behavior of an alternating copolymer styrene-methyl methacrylate (S-alt-M) of composition 50:50 mol% has been investigated over a wide temperature range covering the glassy state, the glass transition region (governed by the mechanical relaxation α), and the rubbery plateau. Data were discussed by comparison with the styrene-methyl methacrylate random copolymer (S-r-M) of same composition. These studies based on tensile and shear DMTA measurements, were carried out at various temperatures and frequencies. In addition, stress-strain curves in compression mode were recorded at various temperatures and strain rates in the glassy state. The activation enthalpy and activation volume of the plastic deformation process with temperature was measured for both S-alt-M and S-r-M. Data analysis was performed on a molecular scale, by putting emphasis on the correlation existing between the amplitude of relaxation and the β -relaxation character associated to the sequence length distribution of the copolymers. From the orientation measurements of SM copolymers, carried out by infra-red dichroism, on films stretched at various gaps (T − Tα) from the main relaxation temperature and at various strain rates, it turned out that the M segments stayed even more oriented than the S segments. Two distinct orientation relaxation curves were obtained for each type of segments, irrespective of the type of copolymer. It was shown that they could be reduced to unique ones after normalization by the zero time or zero (T − Tα) orientation value. All these results were interpreted in relation to the role of polar-polar intermolecular interactions between M-M units, which are likely to occur in the S-r-M copolymer, but were quite lacking in the S-alt-M copolymer. However, the influence of the triad MSM on the mechanical properties was shown to progressively decrease as long as the testing temperature approaches or exceeds Tα.

Segmental Orientations and Deformation Mechanism of Poly(ether-block-amide) Films

Simultaneous measurements of microscopic infrared (MicIR) dichroism, mesoscale deformation, and macroscopic stress during uniaxial stretching are made to four microphase-separated poly(ether-block-amide) (PEBA) films quenched form melt. Before the onset of microstructural alterations, poly(tetramethylene oxide) (PTMO) blocks in soft domains undergo affine deformation, and the true stress−strain relationship on the mesoscale of 500 μm can be described using an interpenetrating network model combining the Matsuoka viscoelastic constitutive equation and the affine deformation equation for mechanically hard and soft networks, respectively. Beyond a threshold strain at which PTMO blocks in the soft network are fully extended, plastic deformation occurs in the hard domain composed of polyamide-12 (PA), which is accompanied by depression of the true stress toward values lower than the prediction of the interpenetrating network model and also by deviation of the molecular orientation of PTMO blocks in the soft domain from the affine deformation mode. The deformation in the hard domain is characterized by a three-stage molecular orientation of hard PA blocks being present in either a fibrillar or a lamellar form. Alignment of PTMO blocks along the draw axis is predominantly observed for the sample with the lowest PA fraction, followed by rotation of the lamellae and then by the plastic deformation leading to fibrillation at high strains.

Direct decoration of disclinations by solidification-induced band texture for a nematic side chain liquid crystalline polymer

For a nematic polymethacrylate side chain liquid crystalline polymer, g 154 N 298 I (°C), the solidification-induced band texture has been observed aligned along the disclination under a polarizing optical microscope, when the specimen was quenched from 280°C to room temperature. The decoration technique of solidification-induced band texture, which is usually reported for main chain liquid crystalline polymers, was then introduced to reveal the director field pattern along a disclination for this side chain liquid crystalline polymer. It was found by infra-red dichroism measurements that the director orientation is parallel with the direction of the band. On this basis, disclinations with strength s=±1/2 and s=±1 were mapped according to the corresponding pattern of solidification-induced band texture. In addition, two types of inversion wall, loop-like and splay-type walls, were also found to be decorated by the solidification-induced band texture.

Deformation Mechanisms of Polymer Thin Films by Simultaneous Kinetic Measurement of Microscopic Infrared Dichroism and Macroscopic Stress. 2. Molecular Orientation during Necking Process of Isotactic Polypropylene

The molecular orientations in the crystalline and the amorphous phases in a quenched isotactic polypropylene (iPP) film with a smectic structure are studied using an instrument constructed for simultaneous kinetic measurement of microscopic infrared (MicIR) dichroism from a predetermined sampling area with a size of 200 × 200 μm2 and macroscopic stress of film uniaxially stretched at a constant elongation rate at 30 °C. Local deformation behavior in the sampling area is determined for one sample using a method of photogrammetry. During the passage of the necking through the sampling area, the local extension ratio λ(t) increases fast from 1.5 to 5, which induces the rapid orientation of iPP chains in both the crystalline and the amorphous phases. The orientation function of the amorphous phase, fam, from the mesoscale deformation of the sampling area is found to be well described by the pseudo-affine deformation mechanism, since the local area shrinks anisotropically during the passage of the neck shoulder. The orientation function fc in the crystalline phase increases linearly with fam up to fam = 0.3 with a slope of 1.85 for all samples tested. In the neck entity, the crystal orientation may lag behind the amorphous chain orientation due to the enhanced plastic deformations. It is shown that the behavior of the amorphous phase is essential for the averaged lamellar orientation on the mesoscale.

The Molecular Architecture of Lipid Membranes—New Insights from Hydration-Tuning Infrared Linear Dichroism Spectroscopy

A new, precise method of adjustment and variation of the hydration degree of materials, is presented. This humidity-titration technique has proved to be practical, relatively fast to achieve, accurate, and, last but not least, well-defined in a thermodynamic sense. It is used in combination with infrared (IR) attenuated total reflection (ATR) spectroscopy to study the hydration of selected phospholipids on a molecular level. Examples of hydration-driven, lyotropic phase transitions are presented and discussed. The second part of the article deals with the relationship between polarised IR absorption spectroscopy and the degree of molecular order in macroscopically oriented samples. The basic formulae for the analysis of IR dichroism data in terms of molecular order parameters are given. Aspects of the molecular order of lipid membranes, such as the orientation and conformation of phosphocholine (PC) headgroups before and after interaction with ions (Ca2+ and Mg2+), the segmential order of the acyl chains in fluid and solid phases, complex formation between water and the PC headgroups and the ordering of lipid-bound water are presented in the third part of this publication. These examples illustrate the effect of the hydration degree on the molecular architecture of lipid assemblies.

Deformation Mechanisms of Polymer Thin Films by Simultaneous Kinetic Measurement of Microscopic Infrared Dichroism and Macroscopic Stress. Part III: Influence of Morphology on Molecular Orientation of Isotactic Polypropylene Films Subjected to Uniaxial Stretching

Molecular orientations of the crystalline and the amorphous phases are studied in relation to morphology using an instrument constructed for simultaneous kinetic measurement of microscopic infrared (MicIR) dichroism from a pre-determined sampling area and macroscopic stress of isotactic polypropylene (iPP) thin film uniaxially stretched at a constant strain rate at room temperature. The morphology imposes important influences on profiles of MicIR dichroism as a function of stretching time and also on a relationship between the orientation functions, fc and f am, of the crystalline and the amorphous phases. Linear relationships between fc and fam are found for the local areas without giant spherulite inclusions when f am<0.3~0.4, suggesting the harmonious developments of amorphous chain deformation and lamellar orientation during the necking propagation. The proportionality constant between fc and fam is not universal but is strongly dependent on the morphology of the surrounding area where the local area under examination is located. The linear relationship between fc and fam is completely invalidated for describing the relationship between the amorphous chain deformation and the lamellar orientation inside the spherulites, which reveals that the deformation mechanism in the spherulite is different from that in the microcrystalline region.

Computational analysis of side-chain conformations in polyaspartates exhibiting reversible helical sense inversion in the solid state

Poly(β-phenylpropyl l-aspartate), poly(β-phenylbutyl l-aspartate), and poly(β-phenylpentyl l-aspartate) exhibit a reversible transformation from a right-handed α-helix (αR) to a left-handed ω-helix (ωL) in the solid state. During this transition, the infrared (IR) dichroism of the side-chain ester group and the birefringence change drastically, showing that the side-chain conformations are different for these two helices. In the present study, for the purpose of elucidating the preferred side-chain conformation in each helix, we performed the computational analyses. The energy contours, the directions of the IR transition moments and the anisotropies in polarizability as functions of the first two dihedral angles of the side chain, χ1 and χ2 were calculated. Then, comparing them with the experimental IR dichroism and birefringence data, we elucidated the specific side-chain conformation preferred for each αR or ωL skeleton. The preferred values of (χ1, χ2) were found to be (−75, −60°) for αR and (180, 45°) for ωL.

Study by Polarization Modulation Infrared Spectroscopy of an Oriented PTFE Film and Its Effect on the Organization of a Thin Chiral Smectic Adsorbed Layer

PTFE deposited by friction at 300°C is known to align crystals. We have used infrared modulation linear dichroism (MLD) and polarization modulation infrared reflection absorption spectroscopy (PMIRRAS) to study the PTFE layer itself and coated with a very thin layer of a chiral smectic liquid crystal. From the experimental and simulation results of a spectra we deduce that the PTFE chains are perfectly parallel to the deposition direction. Whatever the thickness of liquid crystal (0.1–100 nm), the organization is very well defined and reproducible. We give the angles of the main vibrations of the liquid crystalline molecules with the PTFE chains and with the plane of the substrate. The liquid crystal can be considered as quasi-epitaxied on the PTFE-oriented chains.

Evidence from infrared dichroism, x-ray diffraction, and atomistic computer simulation for a “zigzag” molecular shape in tilted smectic liquid crystal phases

Infrared dichroism (IR) and atomistic computer simulation are employed to probe molecular shape in smectic liquid crystal phases where the optic axis is tilted relative to the layer normal. Polar plots of absorption profiles due to core (phenyl, C-C) and tail (alkyl or methylene, CH2) vibrations in the tilted synclinic (smectic-C) phase of a variety of materials show the phenyl (core) IR absorbance symmetry axes to be consistently tilted at larger angle from the layer normal than the alkyl or methylene (tail). This suggests that, on average, the tails are less tilted than the cores. Furthermore, we find that optic axis tilt angle is close to the core tilt angle measured by IR dichroism, as expected, since liquid crystal birefringence arises primarily from the cores. These results are in accord with the "zigzag" model of Bartolino, Doucet, and Durand. However, we find that only a small fraction of the tail, the part nearest the core, is tilted, and only this part contributes significantly to layer contraction upon molecular tilt.