Linear Dichroism Spectroscopy Research Articles

Role of isotropic lipid phase in the fusion of photosystem II membranes.

It has been thoroughly documented, by using 31P-NMR spectroscopy, that plant thylakoid membranes (TMs), in addition to the bilayer (or lamellar, L) phase, contain at least two isotropic (I) lipid phases and an inverted hexagonal (HII) phase. However, our knowledge concerning the structural and functional roles of the non-bilayer phases is still rudimentary. The objective of the present study is to elucidate the origin of I phases which have been hypothesized to arise, in part, from the fusion of TMs (Garab et al. 2022 Progr Lipid Res 101,163). We take advantage of the selectivity of wheat germ lipase (WGL) in eliminating the I phases of TMs (Dlouhý et al. 2022 Cells 11: 2681), and the tendency of the so-called BBY particles, stacked photosystem II (PSII) enriched membrane pairs of 300-500nm in diameter, to form large laterally fused sheets (Dunahay et al. 1984 BBA 764: 179). Our 31P-NMR spectroscopy data show that BBY membranes contain L and I phases. Similar to TMs, WGL selectively eliminated the I phases, which at the same time exerted no effect on the molecular organization and functional activity of PSII membranes. As revealed by sucrose-density centrifugation, magnetic linear dichroism spectroscopy and scanning electron microscopy, WGL disassembled the large laterally fused sheets. These data provide direct experimental evidence on the involvement of I phase(s) in the fusion of stacked PSII membrane pairs, and strongly suggest the role of non-bilayer lipids in the self-assembly of the TM system.

Linear dichroism reveals the perpendicular orientation of DNA bases in the RecA and Rad51 recombinase filaments: A possible mechanism for the strand exchange reaction.

Linear dichroism spectroscopy is used to investigate the structure of RecA family recombinase filaments (RecA and Rad51 proteins) with DNA for clarifying the molecular mechanism of DNA strand exchange promoted by these proteins and its activation. The measurements show that the recombinases promote the perpendicular base orientation of single-stranded DNA only in the presence of activators, indicating the importance of base orientation in the reaction. We summarize the results and discuss the role of DNA base orientation.

Orbital ordering and ultrafast carrier dynamics anisotropies in orientation-engineered orthorhombic YMnO3 films

The rich physical properties unveiled in a plethora of transition and rare-earth metal oxides have been attributed to the intricate interplays between the orbital, charge, and spin degrees of freedom. Among them, rare-earth manganites (RMnO3) have been attracting tremendous attention owing to the ionic size-induced lattice distortion dictated by the Goldschmidt tolerance factor and the substantial Jahn–Teller distortion unique to Mn3+ ions, which evidently have resulted in a variety of emergent characteristics in electronic, magnetic, and orbital ordering. In this work, we deliberately engineered the orientation of a series of orthorhombic YMnO3 (o-YMO) films grown on SrTiO3(100) [STO(100)] and SrTiO3(110) [STO(110)] substrates by means of pulsed laser deposition. The x-ray diffraction (XRD) and reciprocal space mapping revealed that o-YMO/STO(100) is c-axis-oriented and o-YMO/STO(110) is a-axis-oriented, respectively. The XRD ϕ-scans further indicate that both films have excellent in-plane crystallinity, allowing the exploration of anisotropies along the respective crystallographic orientations. Indeed, the x-ray absorption linear dichroism spectroscopy taken along the respective crystallographic orientations evidently exhibited substantial anisotropy. Theoretical fitting with configuration interaction cluster calculations suggests that the d3z2−r2 orbitals are parallel to YMO[001]/(100), leading to stronger electron scattering along the c-axis. Independent polarization-dependent Δ R/R spectra obtained using the femtosecond pump–probe method exhibited substantial anisotropic behaviors in carrier relaxation dynamics when probing along different crystallographic orientations, presumably due to orbital ordering anisotropies.

Circular and Linear Dichroism for the Analysis of Small Noncoding RNA Properties.

Useful structural information about the conformation of nucleic acids can be quickly acquired by circular and linear dichroism (CD/LD) spectroscopy. These techniques, rely on the differentialabsorption of polarised light andare indeed extremely sensitive to subtle changes in the structure of chiralbiomolecules. Many CD analyses of DNA or DNA:protein complexes have beenconducted with substantial data acquisitions. Conversely, CDRNA analysisare still scarce, despite the fact that RNA plays a wide cellular function. This chapter seeks to introduce the reader to the use of circular, lineardichroism and in particular the use of Synchrotron Radiation for such samples. The use of these techniques on small noncoding RNA (sRNA) will be exemplified by analyzing changes in base stacking and/or helical parameters for the understanding of sRNA structure and function, especially by translating the dynamics of RNA:RNA annealing but also to access RNA stability or RNA:RNA alignment. The effect of RNA remodeling proteins will also be addressed. These analyses are especially useful to decipher the mechanisms by which sRNA will adopt the proper conformation thanks to the action of proteins such as Hfq or ProQ in the regulation of the expression of their target mRNAs.

Photoinduced Reactions of Styrylpyridine Derivatives for the In Situ Formation of Selective Ligands for Apyrimidinic DNA

AbstractThe photocyclization reaction of sterically demanding styrylpyridine derivatives was investigated and shown to depend on the type of substituent. With this method, a 2,2‐diphenyl‐1,3‐benzodioxolo‐annelated benzo[c]quinolizinium was synthesized, and its association with regular and abasic site‐containing DNA (AP‐DNA) was investigated by absorption, fluorescence, circular and linear dichroism spectroscopy. Specifically, this ligand binds preferentially to AP‐DNA relative to regular duplex DNA, and the AP‐DNA/ligand complex is formed in situ upon irradiation of the styrylpyridine substrate in the presence of the DNA.

Excited states of trans-stilbene and 1,4-diphenylbutadiene. Near and vacuum UV polarization spectroscopy

The UV absorbance spectra of trans-stilbene ((E)-1,2-diphenylethene, DPE) and (E,E’)-1,4-diphenyl-1,3-butadiene (DPB) are investigated by Synchrotron Radiation Linear Dichroism (SRLD) spectroscopy using stretched polyethylene as an anisotropic solvent. The investigation covers the range 58,000–25,000 cm–1 (172–400 nm). The observed polarization data provide information on the transition moment directions of the observed spectral features. The wavenumbers, intensities, and polarization directions of the observed spectral bands are compared with the results of quantum chemical calculations using the semiempirical all-valence-electrons method LCOAO and Time-Dependent Density Functional Theory (TD–DFT) with the functional CAM-B3LYP.

A plug-and-play aptamer diagnostic platform based on linear dichroism spectroscopy.

A plug-and-play sandwich assay platform for the aptamer-based detection of molecular targets using linear dichroism (LD) spectroscopy as a read-out method has been demonstrated. A 21-mer DNA strand comprising the plug-and-play linker was bioconjugated onto the backbone of the filamentous bacteriophage M13, which gives a strong LD signal due to its ready alignment in linear flow. Extended DNA strands containing aptamer sequences that bind the protein thrombin, TBA and HD22, were then bound to the plug-and-play linker strand via complementary base pairing to generate aptamer-functionalised M13 bacteriophages. The secondary structure of the extended aptameric sequences required to bind to thrombin was checked using circular dichroism spectroscopy, with the binding confirmed using fluorescence anisotropy measurements. LD studies revealed that this sandwich sensor design is very effective at detecting thrombin down to pM levels, indicating the potential of this plug-and-play assay system as a new label-free homogenous detection system based on aptamer recognition.

Irradiation Temperature Dependence of Shape Elongation of Metal Nanoparticles in Silica: Counterevidence to Ion Hammering Related Scenario

Irradiation temperature (IT) dependence of the elongation efficiency of vanadium nanoparticles (NPs) in SiO2 was evaluated: The samples were irradiated with 120 MeV Ag9+ ions to a fluence of 1.0 × 1014 ions/cm2 each at ITs of 300, 433, 515, and 591 K, while the measurements were performed at room temperature. The vanadium was selected for the NP species because of the highest bulk m.p. of 1910 °C (2183 K) among all the species of the elemental metal NPs in which the shape elongation was observed. The highest m.p. could contribute negligible size changes of NPs against inevitable exposure to high temperatures for the IT dependence measurements. The elongation of V NPs was evaluated qualitatively by transmission electron microscopy (TEM) and quantitatively by optical linear dichroism (OLD) spectroscopy. The electron microscopy studies showed a pronounced elongation of NPs with ion irradiation at the elevated temperatures. The OLD signal was almost constant, or even slightly increased with increasing the IT from 300 to 591 K. This IT dependence provides a striking contrast to that of the ion hammering (IH) effect, which predicts a steep decrease with increasing IT. Combined with the other two counterevidence previously reported, the IH-related effect is excluded from the origin of the shape elongation of metal NPs in SiO2.

Near and vacuum UV polarization spectroscopy of 1,4-distyrylbenzene

The UV absorbance bands of 1,4-distyrylbenzene (1,4-Bis[(E)-2-phenylethenyl]benzene, DSB) are investigated by Synchrotron Radiation Linear Dichroism (SRLD) spectroscopy using stretched polyethylene as an anisotropic solvent. The observed polarization data provide information on the transition moment directions of the observed spectral features. The investigation covers the range 15,000–58,000 cm−1 (667–172 nm), thereby providing new information on the transitions of DSB in the vacuum UV region. The observed spectrum is characterized by four main band systems centered at 27,600, 41,000, 49,800, and 57,500 cm−1 (362, 244, 201, and 174 nm). In general, the observed bands and their polarization directions are well predicted by the results of quantum chemical calculations using Time-Dependent Density Functional Theory (TD–DFT) with the functional CAM-B3LYP, and with the semiempirical all-valence-electrons method LCOAO.

One‐Dimensional Photonic Crystal for Surface Mode Polarization Control

AbstractBloch surface waves sustained by truncated 1D photonic crystals (1DPCs) are well known tools for surface‐enhanced spectroscopy. They provide strongly confined fields with uniform distribution over a large surface area, a characteristic exploited in standard refractometric sensing. However, their application to polarization‐sensitive investigations is not straightforward because the transverse electric (TE) and magnetic (TM) surface modes possess distinct dispersion relations, therefore their relative phase is not conserved along propagation and the polarization state of any wave obtained by combining these modes is ill‐defined. In this work, a novel design of a 1DPC is realized in which the TE and TM modes exhibit the same phase velocity over a broadband spectral range and thus their dispersion relations overlap. The capability to simultaneously excite TE and TM modes with a well‐defined phase relation allows the generation of surface waves with a controlled polarization state. This paves the way to polarization‐resolved surface‐enhanced analysis, including, for example, linear and circular dichroism spectroscopy of grafted molecular layers at the photonic crystal surface.

On the complexity of the 1,3-dithiole-2-thione chromophore. UV-Vis polarization spectroscopy and theoretical calculations

• Excited electronic states of 1,3-dithiole-2-thione. • UV-Vis Linear Dichroism (LD) spectroscopy. • Stretched polyethylene as an anisotropic solvent. • Time-Dependent Density Functional Theory (TD-DFT) calculations. • Low-energy virtual orbitals with large non-valence character. The electronic transitions of 1,3-dithiole-2-thione (DTT) are investigated by Linear Dichroism (LD) spectroscopy in the near-UV and visible regions and by quantum chemical calculations. The LD experiments are performed in the spectral region 46,000–20,000 cm –1 (217 - 500 nm) using stretched polyethylene (PE) as an anisotropic solvent. The observed spectral features are compared with electronic transitions calculated by Time-Dependent Density Functional Theory (TD-DFT) considering different functionals and a variety of basis sets. The DTT chromophore is complex and a full elucidation may require the application of more advanced theoretical models with consideration of multiply excited electronic configurations and evaluation of multi-state vibronic couplings.

Temperature-induced orbital polarizations and tunable charge dynamics in layered double perovskite thin films

The realization of lead-free all-inorganic perovskites in emergent materials requires an in-depth understanding of strongly correlated systems toward optoelectronics or spintronics applications. Herein, we report the electronic and optical variation of the <111>-oriented layered double perovskites (LDP) family with the formula of Cs4MIIBi2Br12 thin films (where MII: Cu, Mn, Pb, or Sr). The element and shell-specific orbital polarization based on soft X-ray linear dichroism spectroscopy probes the Cs M4,5- and Mn L2,3- edges of Cs4MnBi2Br12 thin films as a function of temperature. A strong reversal orbital polarization at the respective edges at 150 K indicates a thermally induced orbital-selective rearrangement at low temperature. In addition, the valence band analysis indicates different orbital admixtures of Br 4p and MIId states, corroborated by the density functional theory calculations. In terms of the transient charge dynamics, we observe the photoluminescence peak maxima position trend line is shifted toward a longer wavelength. In addition, the longest average lifetime is recorded for Cs4CuBi2Br12 at 27.40 ± 1 μs. As the LDP structural integrity is lead-free, therefore, these all-inorganic perovskites hold promising potentials as sustainable and green materials for photophysics applications.

Linear Dichroism Activity of Chiral Poly(p-Aryltriazole) Foldamers.

Controllable higher-order assembly is a central aim of macromolecular chemistry. An essential challenge to developing these molecules is improving our understanding of the structures they adopt under different conditions. Here, we demonstrate how flow linear dichroism (LD) spectroscopy is used to provide insights into the solution structure of a chiral, self-assembled fibrillar foldamer. Poly(para-aryltriazole)s fold into different structures depending on the monomer geometry and variables such as solvent and ionic strength. LD spectroscopy provides a simple route to determine chromophore alignment in solution and is generally used on natural molecules or molecular assemblies such as DNA and M13 bacteriophage. In this contribution, we show that LD spectroscopy is a powerful tool in the observation of self-assembly processes of synthetic foldamers when complemented by circular dichroism, absorbance spectroscopy, and microscopy. To that end, poly(para-aryltriazole)s were aligned in a flow field under different solvent conditions. The extended aromatic structures in the foldamer give rise to a strong LD signal that changes in sign and in intensity with varying solvent conditions. A key advantage of LD is that it only detects the large assemblies, thus removing background due to monomers and small oligomers.

Charge Carrier Screening in Photoexcited Epitaxial Semiconductor Nanorods Revealed by Transient X-ray Absorption Linear Dichroism.

Understanding the electronic structure and dynamics of semiconducting nanomaterials at the atomic level is crucial for the realization and optimization of devices in solar energy, catalysis, and optoelectronic applications. We report here on the use of ultrafast X-ray linear dichroism spectroscopy to monitor the carrier dynamics in epitaxial ZnO nanorods after band gap photoexcitation. By rigorously subtracting out thermal contributions and conducting ab initio calculations, we reveal an overall depletion of absorption cross sections in the transient X-ray spectra caused by photogenerated charge carriers screening the core-hole potential of the X-ray absorbing atom. At low laser excitation densities, we observe phase-space filling by excited electrons and holes separately. These results pave the way for carrier- and element-specific probing of charge transfer dynamics across heterostructured interfaces with ultrafast table-top and fourth-generation X-ray sources.

Orientation of α-Synuclein at Negatively Charged Lipid Vesicles: Linear Dichroism Reveals Time-Dependent Changes in Helix Binding Mode

The neuronal protein α-synuclein, linked to Parkinson’s disease, binds to negatively charged vesicles adopting a partial α-helix structure, but helix arrangement at the vesicle surface is not fully understood. Using linear dichroism spectroscopy (LD), we study the interaction of monomeric α-synuclein with large unilamellar vesicles of 1,2-dioleoyl-sn-glycero-3-phospho-l-serine (DOPS), 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine (POPS), and 1,2-dioleoyl-sn-glycero-3-phospho-(1′-rac-glycerol) (DOPG) under mild shear flow. The LD data of oriented lipid vesicles show that the long axis of the protein helix is oriented preferentially perpendicular to the membrane normal but deviates from a uniform in-plane distribution. Upon initial binding, a fraction of helices are oriented in the direction of least curvature for all ellipsoid-shaped vesicles at a lipid:protein molar ratio of 100. However, at a lower protein concentration the helices distribute uniformly on DOPS and POPS vesicles. In all cases, the α-synuclein helices rearrange with time (minute time scale) in the shear flow and begin to tilt into the vesicle membrane. Faster reorientation kinetics in the presence of flow suggests that modulation of membrane dynamics, by thermal or shear-dynamic activation, may overcome steric barriers by what may be called “flow catalysis”.

Biphenyl-Induced Superhelix in l -Phenylalanine-Based Supramolecular Self-Assembly with Dynamic Morphology Transitions

Biphenyl-Induced Superhelix in <scp>l</scp> -Phenylalanine-Based Supramolecular Self-Assembly with Dynamic Morphology Transitions

Aggregation of Amphiphilic Carbocyanines: Fluorination Favors Cylindrical Micelles over Bilayered Tubes.

The synthesis of a new amphiphilic 5,5',6,6'-tetrachlorobenzimidacarbocyanine dye derivative with -(CH2)2-(CF2)5-CF3 chains attached to the nitrogen atoms in the 1,1'-position, CF8O3, is reported. Depending on the dye concentration and the addition of MeOH, CF8O3 forms J- and H-aggregates in aqueous solutions. The aggregation behavior was investigated using steady-state absorption, linear dichroism, and fluorescence spectroscopy, as well as by cryogenic transmission electron microscopy (cryo-TEM). The J-band of the MeOH-free solution is monomer-like, rather broad, and less red-shifted with respect to the monomer absorption, indicating weak excitonic coupling and disorder effects. Cryo-TEM reveals a diversity of supramolecular structures, wherein linear and branched cylindrical micelles dominate. It is concluded that the high stiffness of fluoroalkyl chains does not allow the chains to splay and completely fill up the hydrophobic gap between opposing chromophores. This destabilizes the bilayers and favors the micellar structure motifs instead. The aggregates appearing at 30% MeOH show a split absorption spectrum consisting of a broad blue-shifted H-band and an accompanying sharp red-shifted J-band with perpendicular polarizations. These HJ-type aggregates are also composed of micellar fibers, but these bundle into rope-like strands. For 10% MeOH, a narrow bilayered tube is the dominating morphology. The observed MeOH dependence of aggregation reveals a clear cosolvent effect.

DNA-Triggered Enhancement of Singlet Oxygen Production by Pyridinium Alkynylanthracenes.

There is an ongoing interest in 1 O2 sensitizers, whose activity is selectively controlled by their interaction with DNA. To this end, we synthesized three isomeric pyridinium alkynylanthracenes 2 o-p and a water-soluble trapping reagent for 1 O2 . In water and in the absence of DNA, these dyes show a poor efficiency to sensitize the photooxygenation of the trapping reagent as they decompose due to electron transfer processes. In contrast, in the presence of DNA 1 O2 is generated from the excited DNA-bound ligand. The interactions of 2 o-p with DNA were investigated by thermal DNA melting studies, UV/vis and fluorescence spectroscopy, and linear and circular dichroism spectroscopy. Our studies revealed an intercalative binding with an orientation of the long pyridyl-alkynyl axis parallel to the main axis of the DNA base pairs. In the presence of poly(dA : dT), all three isomers show an enhanced formation of singlet oxygen, as indicated by the reaction of the latter with the trapping reagent. With green light irradiation of isomer 2 o in poly(dA : dT), the conversion rate of the trapping reagent is enhanced by a factor >10. The formation of 1 O2 was confirmed by control experiments under anaerobic conditions, in deuterated solvents, or by addition of 1 O2 quenchers. When bound to poly(dG : dC), the opposite effect was observed only for isomers 2 o and 2 m, namely the trapping reagent reacted significantly slower. Overall, we showed that pyridinium alkynylanthracenes are very useful intercalators, that exhibit an enhanced photochemical 1 O2 generation in the DNA-bound state.

Shape-Dependent Linear Dichroism Spectra of Colloidal Semiconductor Nanocrystals.

Semiconductor nanocrystals are normally dispersed in the solvent for property studies as well as practical applications. However, rare attention has been paid to their orientation status in the colloidal solution. Herein, with the help of linear dichroism (LD) spectroscopy, we demonstrate that isotropic NCs of high symmetry (i.e., quantum dots, QDs) and anisotropic NCs (e.g., quantum rods, QRs and nanoplates, NPLs) but under diluted concentration are randomly dispersed without any preferential orientation. Meanwhile, anisotropic NCs under a high concentration can behave with some net orientation along a certain direction. For example, CdSe quantum rods (QRs) and nanoplatelets (NPLs) both show an obviously preferred orientation along the vertical direction in solution when their solution absorbances increase to certain values. An in-depth analysis of QRs' LD spectrum shows that the first excitonic transition of QRs is strongly quantumly confined while its higher-energy excitonic transitions are weakly quantumly confined. In contrast, the NPLs' LD spectrum indicates that their excitonic transitions are isotropic in the spatial space. This work provides a new viewpoint of the real status of anisotropic semiconductor NCs in solution.

Antiferromagnetism of CoO-NiO bilayers studied by XMLD spectroscopy

CoO-NiO epitaxial bilayer system grown on MgO(001) substrate is investigated using x-ray magnetic linear dichroism (XMLD) spectroscopy with varying CoO overlayer thickness. An analysis of the Ni L 2 edge XMLD spectra using anisotropic XMLD formulation within a two-domain model reveals that the Ni moments undergo a spin reorientation with increasing CoO thickness. Such a spin reorientation is attributed to the competing magnetic interactions at both the NiO film interfaces, suggesting the existence of a sharp horizontal domain wall separating the in-plane and out-of-plane NiO domains. Our study also demonstrates a possible way to investigate the spin-structure along the thickness within the same chemical structure using a model-based approach, in a noninvasive manner.