All-dielectric metasurface circular dichroism waveplate
Hu, Jingpei; Zhao, Xiaonan; Lin, Yu; Zhu, Aijiao; Zhu, Xiaojun; Guo, Peiji; Cao, Bing; Wang, Chinhua
2017-01-01
We propose and experimentally demonstrate a high efficient circularly polarizing dichroism waveplate (CPDW) using a Si-based all-dielectric 2Dchiral metasurface. We demonstrate that the CPDW exhibits a unique dichroism in that it functions as a transmissive quarter waveplate for one of either left-or right-handed circularly polarized incident lightand a reflective mirror for the opposite polarization. The circular polarization dichroism (CPD = IRCP − ILCP) in transmission at wavelength ~1.5 μm reaches 97% and the extinction ratio (ER = IRCP/ILCP) is as high as 345:1. Experimental fabrications and measurements of the proposed all-dielectric metasurface are implemented and found to be in excellent agreement with the simulations. The proposed all-dielectric chiral metasurface is of advantages of high-dichroism, easy-fabrication and standard semiconductor fabrication techniques compatible, which could lead to enhanced security in fiber and free-space communications, as well as imaging and sensing applications for circularly polarized light with a highly integrated photonic platform. PMID:28139753
All-dielectric metasurface circular dichroism waveplate.
Hu, Jingpei; Zhao, Xiaonan; Lin, Yu; Zhu, Aijiao; Zhu, Xiaojun; Guo, Peiji; Cao, Bing; Wang, Chinhua
2017-01-31
We propose and experimentally demonstrate a high efficient circularly polarizing dichroism waveplate (CPDW) using a Si-based all-dielectric 2Dchiral metasurface. We demonstrate that the CPDW exhibits a unique dichroism in that it functions as a transmissive quarter waveplate for one of either left-or right-handed circularly polarized incident lightand a reflective mirror for the opposite polarization. The circular polarization dichroism (CPD = I RCP - I LCP ) in transmission at wavelength ~1.5 μm reaches 97% and the extinction ratio (ER = I RCP /I LCP ) is as high as 345:1. Experimental fabrications and measurements of the proposed all-dielectric metasurface are implemented and found to be in excellent agreement with the simulations. The proposed all-dielectric chiral metasurface is of advantages of high-dichroism, easy-fabrication and standard semiconductor fabrication techniques compatible, which could lead to enhanced security in fiber and free-space communications, as well as imaging and sensing applications for circularly polarized light with a highly integrated photonic platform.
NASA Astrophysics Data System (ADS)
Wang, Zhi-Qiang; Wu, Cheng-Jun; Wang, Zhen-Hui; Huang, Chao; Huang, Jian; Wang, Jin-Hui; Sun, Tie-Min
2017-10-01
In this study, the stereochemistry of a new isopimarane-type diterpenoid isolated from the Callicarpa macrophylla Vahl, Callicapene M3, was studied by experimental electronic circular dichroism and vibrational circular dichroism with the aid of TDDFT theoretical calculations. The good consistence between the experimental and simulated circular dichroism has clearly confirmed the absolute configuration of the title compound as (4S, 5S, 9S, 10S, 13S, 14S)-14α-hydroxy-7,15-isopimaradien-18-oic acid.
Zhuo, G-Y; Lee, H; Hsu, K-J; Huttunen, M J; Kauranen, M; Lin, Y-Y; Chu, S-W
2014-03-01
Chirality is one of the most fundamental and essential structural properties of biological molecules. Many important biological molecules including amino acids and polysaccharides are intrinsically chiral. Conventionally, chiral species can be distinguished by interaction with circularly polarized light, and circular dichroism is one of the best-known approaches for chirality detection. As a linear optical process, circular dichroism suffers from very low signal contrast and lack of spatial resolution in the axial direction. It has been demonstrated that by incorporating nonlinear interaction with circularly polarized excitation, second-harmonic generation circular dichroism can provide much higher signal contrast. However, previous circular dichroism and second-harmonic generation circular dichroism studies are mostly limited to probe chiralities at surfaces and interfaces. It is known that second-harmonic generation, as a second-order nonlinear optical effect, provides excellent optical sectioning capability when combined with a laser-scanning microscope. In this work, we combine the axial resolving power of second-harmonic generation and chiral sensitivity of second-harmonic generation circular dichroism to realize three-dimensional chiral detection in biological tissues. Within the point spread function of a tight focus, second-harmonic generation circular dichroism could arise from the macroscopic supramolecular packing as well as the microscopic intramolecular chirality, so our aim is to clarify the origins of second-harmonic generation circular dichroism response in complicated three-dimensional biological systems. The sample we use is starch granules whose second-harmonic generation-active molecules are amylopectin with both microscopic chirality due to its helical structure and macroscopic chirality due to its crystallized packing. We found that in a starch granule, the second-harmonic generation for right-handed circularly polarized excitation is
Terahertz Absorption and Circular Dichroism Spectroscopy of Solvated Biopolymers
NASA Astrophysics Data System (ADS)
Xu, Jing; Plaxco, Kevin; Allen, S. James
2006-03-01
Biopolymers are expected to exhibit broad spectral features in the terahertz frequency range, corresponding to their functionally relevant, global and sub-global collective vibrational modes with ˜ picosecond timescale. Recent advances in terahertz technology have stimulated researchers to employ terahertz absorption spectroscopy to directly probe these postulated collective modes. However, these pioneering studies have been limited to dry and, at best, moist samples. Successful isolation of low frequency vibrational activities of solvated biopolymers in their natural water environment has remained elusive, due to the overwhelming attenuation of the terahertz radiation by water. Here we have developed a terahertz absorption and circular dichroism spectrometer suitable for studying biopolymers in biologically relevant water solutions. We have precisely isolated, for the first time, the terahertz absorption of solvated prototypical proteins, Bovine Serum Albumin and Lysozyme, and made important direct comparison to the existing molecular dynamic simulations and normal mode calculations. We have also successfully demonstrated the magnetic circular dichroism in semiconductors, and placed upper bounds on the terahertz circular dichroism signatures of prototypical proteins in water solution.
Photoexcitation circular dichroism in chiral molecules
NASA Astrophysics Data System (ADS)
Beaulieu, S.; Comby, A.; Descamps, D.; Fabre, B.; Garcia, G. A.; Géneaux, R.; Harvey, A. G.; Légaré, F.; Mašín, Z.; Nahon, L.; Ordonez, A. F.; Petit, S.; Pons, B.; Mairesse, Y.; Smirnova, O.; Blanchet, V.
2018-05-01
Chiral effects appear in a wide variety of natural phenomena and are of fundamental importance in science, from particle physics to metamaterials. The standard technique of chiral discrimination—photoabsorption circular dichroism—relies on the magnetic properties of a chiral medium and yields an extremely weak chiral response. Here, we propose and demonstrate an orders of magnitude more sensitive type of circular dichroism in neutral molecules: photoexcitation circular dichroism. This technique does not rely on weak magnetic effects, but takes advantage of the coherent helical motion of bound electrons excited by ultrashort circularly polarized light. It results in an ultrafast chiral response and the efficient excitation of a macroscopic chiral density in an initially isotropic ensemble of randomly oriented chiral molecules. We probe this excitation using linearly polarized laser pulses, without the aid of further chiral interactions. Our time-resolved study of vibronic chiral dynamics opens a way to the efficient initiation, control and monitoring of chiral chemical change in neutral molecules at the level of electrons.
Khanikaev, A. B.; Arju, N.; Fan, Z.; Purtseladze, D.; Lu, F.; Lee, J.; Sarriugarte, P.; Schnell, M.; Hillenbrand, R.; Belkin, M. A.; Shvets, G.
2016-01-01
Optical activity and circular dichroism are fascinating physical phenomena originating from the interaction of light with chiral molecules or other nano objects lacking mirror symmetries in three-dimensional (3D) space. While chiral optical properties are weak in most of naturally occurring materials, they can be engineered and significantly enhanced in synthetic optical media known as chiral metamaterials, where the spatial symmetry of their building blocks is broken on a nanoscale. Although originally discovered in 3D structures, circular dichroism can also emerge in a two-dimensional (2D) metasurface. The origin of the resulting circular dichroism is rather subtle, and is related to non-radiative (Ohmic) dissipation of the constituent metamolecules. Because such dissipation occurs on a nanoscale, this effect has never been experimentally probed and visualized. Using a suite of recently developed nanoscale-measurement tools, we establish that the circular dichroism in a nanostructured metasurface occurs due to handedness-dependent Ohmic heating. PMID:27329108
Terahertz circular dichroism spectroscopy of biomolecules
NASA Astrophysics Data System (ADS)
Xu, Jing; Galan, Jhenny; Ramian, Gerald; Savvidis, Pavlos; Scopatz, Anthony; Birge, Robert R.; Allen, S. James; Plaxco, Kevin
2004-02-01
Biopolymers such as proteins, DNA and RNA fold into large, macromolecular chiral structures. As charged macromolecules, they absorb strongly in the terahertz due to large-scale collective vibrational modes; as chiral objects, this absorption should be coupled with significant circular dichroism. Terahertz circular dichroism (TCD) is potentially important as a biospecific sensor, unobscured by spectral features related to abiological material. We have constructed atomistic simulations and elastic continuum models of TCD. These models estimate the magnitude of the TCD and the relation between TCD spectroscopic signatures (zero crossings) and the structure, charge distribution and mechanical properties of biomaterials. A broad band TCD spectrometer based on a polarizing interferometer is developed to explore TCD in biomolecules in aqueous solution. Preliminary results on TCD in lysozyme in water at several terahertz frequencies is presented.
Circular dichroism in photoelectron images from aligned nitric oxide molecules
Sen, Ananya; Pratt, S. T.; Reid, K. L.
2017-05-03
We have used velocity map photoelectron imaging to study circular dichroism of the photoelectron angular distributions (PADs) of nitric oxide following two-color resonanceenhanced two-photon ionization via selected rotational levels of the A 2Σ +, v' = 0 state. By using a circularly polarized pump beam and a counter-propagating, circularly polarized probe beam, cylindrical symmetry is preserved in the ionization process, and the images can be reconstructed using standard algorithms. The VMI set up enables individual ion rotational states to be resolved with excellent collection efficiency, rendering the measurements considerably simpler to perform than previous measurements conducted with a conventional photoelectronmore » spectrometer. The results demonstrate that circular dichroism is observed even when cylindrical symmetry is maintained, and serve as a reminder that dichroism is a general feature of the multiphoton ionization of atoms and molecules. Furthermore, the observed PADs are in good agreement with calculations based on parameters extracted from previous experimental results obtained by using a time-offlight electron spectrometer.« less
Circular dichroism in photoelectron images from aligned nitric oxide molecules
DOE Office of Scientific and Technical Information (OSTI.GOV)
Sen, Ananya; Pratt, S. T.; Reid, K. L.
We have used velocity map photoelectron imaging to study circular dichroism of the photoelectron angular distributions (PADs) of nitric oxide following two-color resonanceenhanced two-photon ionization via selected rotational levels of the A 2Σ +, v' = 0 state. By using a circularly polarized pump beam and a counter-propagating, circularly polarized probe beam, cylindrical symmetry is preserved in the ionization process, and the images can be reconstructed using standard algorithms. The VMI set up enables individual ion rotational states to be resolved with excellent collection efficiency, rendering the measurements considerably simpler to perform than previous measurements conducted with a conventional photoelectronmore » spectrometer. The results demonstrate that circular dichroism is observed even when cylindrical symmetry is maintained, and serve as a reminder that dichroism is a general feature of the multiphoton ionization of atoms and molecules. Furthermore, the observed PADs are in good agreement with calculations based on parameters extracted from previous experimental results obtained by using a time-offlight electron spectrometer.« less
Near shot-noise limited time-resolved circular dichroism pump-probe spectrometer
NASA Astrophysics Data System (ADS)
Stadnytskyi, Valentyn; Orf, Gregory S.; Blankenship, Robert E.; Savikhin, Sergei
2018-03-01
We describe an optical near shot-noise limited time-resolved circular dichroism (TRCD) pump-probe spectrometer capable of reliably measuring circular dichroism signals in the order of μdeg with nanosecond time resolution. Such sensitivity is achieved through a modification of existing TRCD designs and introduction of a new data processing protocol that eliminates approximations that have caused substantial nonlinearities in past measurements and allows the measurement of absorption and circular dichroism transients simultaneously with a single pump pulse. The exceptional signal-to-noise ratio of the described setup makes the TRCD technique applicable to a large range of non-biological and biological systems. The spectrometer was used to record, for the first time, weak TRCD kinetics associated with the triplet state energy transfer in the photosynthetic Fenna-Matthews-Olson antenna pigment-protein complex.
Bright circularly polarized soft X-ray high harmonics for X-ray magnetic circular dichroism.
Fan, Tingting; Grychtol, Patrik; Knut, Ronny; Hernández-García, Carlos; Hickstein, Daniel D; Zusin, Dmitriy; Gentry, Christian; Dollar, Franklin J; Mancuso, Christopher A; Hogle, Craig W; Kfir, Ofer; Legut, Dominik; Carva, Karel; Ellis, Jennifer L; Dorney, Kevin M; Chen, Cong; Shpyrko, Oleg G; Fullerton, Eric E; Cohen, Oren; Oppeneer, Peter M; Milošević, Dejan B; Becker, Andreas; Jaroń-Becker, Agnieszka A; Popmintchev, Tenio; Murnane, Margaret M; Kapteyn, Henry C
2015-11-17
We demonstrate, to our knowledge, the first bright circularly polarized high-harmonic beams in the soft X-ray region of the electromagnetic spectrum, and use them to implement X-ray magnetic circular dichroism measurements in a tabletop-scale setup. Using counterrotating circularly polarized laser fields at 1.3 and 0.79 µm, we generate circularly polarized harmonics with photon energies exceeding 160 eV. The harmonic spectra emerge as a sequence of closely spaced pairs of left and right circularly polarized peaks, with energies determined by conservation of energy and spin angular momentum. We explain the single-atom and macroscopic physics by identifying the dominant electron quantum trajectories and optimal phase-matching conditions. The first advanced phase-matched propagation simulations for circularly polarized harmonics reveal the influence of the finite phase-matching temporal window on the spectrum, as well as the unique polarization-shaped attosecond pulse train. Finally, we use, to our knowledge, the first tabletop X-ray magnetic circular dichroism measurements at the N4,5 absorption edges of Gd to validate the high degree of circularity, brightness, and stability of this light source. These results demonstrate the feasibility of manipulating the polarization, spectrum, and temporal shape of high harmonics in the soft X-ray region by manipulating the driving laser waveform.
Bright circularly polarized soft X-ray high harmonics for X-ray magnetic circular dichroism
Fan, Tingting; Grychtol, Patrik; Knut, Ronny; Hernández-García, Carlos; Hickstein, Daniel D.; Zusin, Dmitriy; Gentry, Christian; Dollar, Franklin J.; Mancuso, Christopher A.; Hogle, Craig W.; Kfir, Ofer; Legut, Dominik; Carva, Karel; Ellis, Jennifer L.; Dorney, Kevin M.; Chen, Cong; Shpyrko, Oleg G.; Fullerton, Eric E.; Cohen, Oren; Oppeneer, Peter M.; Milošević, Dejan B.; Becker, Andreas; Jaroń-Becker, Agnieszka A.; Popmintchev, Tenio; Murnane, Margaret M.; Kapteyn, Henry C.
2015-01-01
We demonstrate, to our knowledge, the first bright circularly polarized high-harmonic beams in the soft X-ray region of the electromagnetic spectrum, and use them to implement X-ray magnetic circular dichroism measurements in a tabletop-scale setup. Using counterrotating circularly polarized laser fields at 1.3 and 0.79 µm, we generate circularly polarized harmonics with photon energies exceeding 160 eV. The harmonic spectra emerge as a sequence of closely spaced pairs of left and right circularly polarized peaks, with energies determined by conservation of energy and spin angular momentum. We explain the single-atom and macroscopic physics by identifying the dominant electron quantum trajectories and optimal phase-matching conditions. The first advanced phase-matched propagation simulations for circularly polarized harmonics reveal the influence of the finite phase-matching temporal window on the spectrum, as well as the unique polarization-shaped attosecond pulse train. Finally, we use, to our knowledge, the first tabletop X-ray magnetic circular dichroism measurements at the N4,5 absorption edges of Gd to validate the high degree of circularity, brightness, and stability of this light source. These results demonstrate the feasibility of manipulating the polarization, spectrum, and temporal shape of high harmonics in the soft X-ray region by manipulating the driving laser waveform. PMID:26534992
Kamiński, Maciej; Cukras, Janusz; Pecul, Magdalena; Rizzo, Antonio; Coriani, Sonia
2015-07-15
We present a computational methodology to calculate the intensity of circular dichroism (CD) in spin-forbidden absorption and of circularly polarized phosphorescence (CPP) signals, a manifestation of the optical activity of the triplet-singlet transitions in chiral compounds. The protocol is based on the response function formalism and is implemented at the level of time-dependent density functional theory. It has been employed to calculate the spin-forbidden circular dichroism and circularly polarized phosphorescence signals of valence n → π* and n ← π* transitions, respectively, in several chiral enones and diketones. Basis set effects in the length and velocity gauge formulations have been explored, and the accuracy achieved when employing approximate (mean-field and effective nuclear charge) spin-orbit operators has been investigated. CPP is shown to be a sensitive probe of the triplet excited state structure. In many cases the sign of the spin-forbidden CD and CPP signals are opposite. For the β,γ-enones under investigation, where there are two minima on the lowest triplet excited state potential energy surface, each minimum exhibits a CPP signal of a different sign.
Natural circular dichroism in non-resonant x-ray emission
NASA Astrophysics Data System (ADS)
Vahtras, Olav; Ågren, Hans; Carravetta, Vincenzo
1997-03-01
The possibility of observing natural circular dichroism in non-resonant x-ray emission spectroscopy is investigated by means of simulations of the chiral molecules twisted ethylene, propylene oxide and trans-1, 2-dimethylcyclopropane, in a two-step model and at the SCF level, with or without relaxation of the core-hole states. We observe both a chemical and an element dependence of the phenomenon and also an effect of electron relaxation. However, the latter is much less crucial than for circular dichroism in x-ray absorption. The calculations indicate that, at least for the decay of the carbon core-hole states, the effect could be detectable with the present or soon to be available experimental equipment.
Bright circularly polarized soft X-ray high harmonics for X-ray magnetic circular dichroism
Fan, Tingting; Grychtol, Patrik; Knut, Ronny; ...
2015-11-03
Here, we demonstrate, to our knowledge, the first bright circularly polarized high-harmonic beams in the soft X-ray region of the electromagnetic spectrum, and use them to implement X-ray magnetic circular dichroism measurements in a tabletop-scale setup. Using counterrotating circularly polarized laser fields at 1.3 and 0.79 µm, we generate circularly polarized harmonics with photon energies exceeding 160 eV. The harmonic spectra emerge as a sequence of closely spaced pairs of left and right circularly polarized peaks, with energies determined by conservation of energy and spin angular momentum. We explain the single-atom and macroscopic physics by identifying the dominant electron quantummore » trajectories and optimal phase-matching conditions. The first advanced phase-matched propagation simulations for circularly polarized harmonics reveal the influence of the finite phase-matching temporal window on the spectrum, as well as the unique polarization-shaped attosecond pulse train. Finally, we use, to our knowledge, the first tabletop X-ray magnetic circular dichroism measurements at the N 4,5 absorption edges of Gd to validate the high degree of circularity, brightness, and stability of this light source. These results demonstrate the feasibility of manipulating the polarization, spectrum, and temporal shape of high harmonics in the soft X-ray region by manipulating the driving laser waveform.« less
Probing ultrafast spin dynamics with high-harmonic magnetic circular dichroism spectroscopy
NASA Astrophysics Data System (ADS)
Willems, F.; Smeenk, C. T. L.; Zhavoronkov, N.; Kornilov, O.; Radu, I.; Schmidbauer, M.; Hanke, M.; von Korff Schmising, C.; Vrakking, M. J. J.; Eisebitt, S.
2015-12-01
Magnetic circular dichroism in the extreme ultraviolet (XUV) spectral range is a powerful technique for element-specific probing of magnetization in multicomponent magnetic alloys and multilayers. We combine a high-harmonic generation source with a λ /4 phase shifter to obtain circularly polarized XUV femtosecond pulses for ultrafast magnetization studies. We report on simultaneously measured resonant magnetic circular dichroism (MCD) of Co and Ni at their respective M2 ,3 edges and of Pt at its O edge, originating from interface magnetism. We present a time-resolved MCD absorption measurement of a thin magnetic Pt/Co/Pt film, showing simultaneous demagnetization of Co and Pt on a femtosecond time scale.
Whitmore, Lee; Mavridis, Lazaros; Wallace, B A; Janes, Robert W
2018-01-01
Circular dichroism spectroscopy is a well-used, but simple method in structural biology for providing information on the secondary structure and folds of proteins. DichroMatch (DM@PCDDB) is an online tool that is newly available in the Protein Circular Dichroism Data Bank (PCDDB), which takes advantage of the wealth of spectral and metadata deposited therein, to enable identification of spectral nearest neighbors of a query protein based on four different methods of spectral matching. DM@PCDDB can potentially provide novel information about structural relationships between proteins and can be used in comparison studies of protein homologs and orthologs. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.
Liao, Wei-Chun; Liao, Shu-Wei; Chen, Kuo-Ju; Hsiao, Yu-Hao; Chang, Shu-Wei; Kuo, Hao-Chung; Shih, Min-Hsiung
2016-05-25
Circularly polarized laser sources with small footprints and high efficiencies can possess advanced functionalities in optical communication and biophotonic integrated systems. However, the conventional lasers with additional circular-polarization converters are bulky and hardly compatible with nanophotonic circuits, and most active chiral plasmonic nanostructures nowadays exhibit broadband emission and low circular dichroism. In this work, with spirals of gallium nitride (GaN) nanowires (NWRs) covered by a metal layer, we demonstrated an ultrasmall semiconductor laser capable of emitting circularly-polarized photons. The left- and right-hand spiral metal nanowire cavities with varied periods were designed at ultraviolet wavelengths to achieve the high quality factor circular dichroism metastructures. The dissymmetry factors characterizing the degrees of circular polarizations of the left- and right-hand chiral lasers were 1.4 and -1.6 (±2 if perfectly circular polarized), respectively. The results show that the chiral cavities with only 5 spiral periods can achieve lasing signals with the high degrees of circular polarizations.
Amide I vibrational circular dichroism of dipeptide: Conformation dependence and fragment analysis
NASA Astrophysics Data System (ADS)
Choi, Jun-Ho; Cho, Minhaeng
2004-03-01
The amide I vibrational circular dichroic response of alanine dipeptide analog (ADA) was theoretically investigated and the density functional theory calculation and fragment analysis results are presented. A variety of vibrational spectroscopic properties, local and normal mode frequencies, coupling constant, dipole, and rotational strengths, are calculated by varying two dihedral angles determining the three-dimensional ADA conformation. Considering two monopeptide fragments separately, we show that the amide I vibrational circular dichroism of the ADA can be quantitatively predicted. For several representative conformations of the model ADA, vibrational circular dichroism spectra are calculated by using both the density functional theory calculation and fragment analysis methods.
Quantized Rabi oscillations and circular dichroism in quantum Hall systems
NASA Astrophysics Data System (ADS)
Tran, D. T.; Cooper, N. R.; Goldman, N.
2018-06-01
The dissipative response of a quantum system upon periodic driving can be exploited as a probe of its topological properties. Here we explore the implications of such phenomena in two-dimensional gases subjected to a uniform magnetic field. It is shown that a filled Landau level exhibits a quantized circular dichroism, which can be traced back to its underlying nontrivial topology. Based on selection rules, we find that this quantized effect can be suitably described in terms of Rabi oscillations, whose frequencies satisfy simple quantization laws. We discuss how quantized dissipative responses can be probed locally, both in the bulk and at the boundaries of the system. This work suggests alternative forms of topological probes based on circular dichroism.
X-ray circular dichroism signals: a unique probe of local molecular chirality
Zhang, Yu; Rouxel, Jeremy R.; Autschbach, Jochen; ...
2017-06-26
Core-resonant circular dichroism (CD) signals are induced by molecular chirality and vanish for achiral molecules and racemic mixtures. The highly localized nature of core excitations makes them ideal probes of local chirality within molecules. Simulations of the circular dichroism spectra of several molecular families illustrate how these signals vary with the electronic coupling to substitution groups, the distance between the X-ray chromophore and the chiral center, geometry, and chemical structure. As a result, clear insight into the molecular structure is obtained through analysis of the X-ray CD spectra.
X-ray circular dichroism signals: a unique probe of local molecular chirality
DOE Office of Scientific and Technical Information (OSTI.GOV)
Zhang, Yu; Rouxel, Jeremy R.; Autschbach, Jochen
Core-resonant circular dichroism (CD) signals are induced by molecular chirality and vanish for achiral molecules and racemic mixtures. The highly localized nature of core excitations makes them ideal probes of local chirality within molecules. Simulations of the circular dichroism spectra of several molecular families illustrate how these signals vary with the electronic coupling to substitution groups, the distance between the X-ray chromophore and the chiral center, geometry, and chemical structure. As a result, clear insight into the molecular structure is obtained through analysis of the X-ray CD spectra.
Twisting dirac fermions: circular dichroism in bilayer graphene
NASA Astrophysics Data System (ADS)
Suárez Morell, E.; Chico, Leonor; Brey, Luis
2017-09-01
Twisted bilayer graphene is a chiral system which has been recently shown to present circular dichroism. In this work we show that the origin of this optical activity is the rotation of the Dirac fermions’ helicities in the top and bottom layer. Starting from the Kubo formula, we obtain a compact expression for the Hall conductivity that takes into account the dephasing of the electromagnetic field between the top and bottom layers and gathers all the symmetries of the system. Our results are based in both a continuum and a tight-binding model, and they can be generalized to any two-dimensional Dirac material with a chiral stacking between layers.
Conformational effects in photoelectron circular dichroism
NASA Astrophysics Data System (ADS)
Turchini, S.
2017-12-01
Photoelectron circular dichroism (PECD) is a novel type of spectroscopy, which presents surprising sensitivity to conformational effects in chiral systems. While classical photoelectron spectroscopy mainly responds to conformational effects in terms of energy level shifts, PECD provides a rich and detailed response to tiny changes in electronic and structural properties by means of the intensity dispersion of the circular dichroism as a function of photoelectron kinetic energy. In this work, the basics of PECD will be outlined, emphasizing the role of interference from the l,l+/- 1 outgoing partial wave of the photoelectron in the PECD transition matrix element, which is responsible for the extreme sensitivity to conformational effects. Examples using molecular systems and interfaces will shed light on the powerful application of PECD to classical conformational effects such as group substitution, isomerism, conformer population and clustering. Moreover, the PECD results will be reported in challenging new fields where conformations play a key role, such as vibrational effects, transient chirality and time- resolved experiments. To date, PECD has mostly been based on synchrotron radiation facilities, but it also has a future as a table-top lab experiment by means of multiphoton ionization. An important application of PECD as an analytical tool will be reported. The aim of this review is to illustrate that in PECD, the presence of conformational effects is essential for understanding a wide range of effects from a new perspective, making it different from classical spectroscopy.
Measurement of the Circular Dichroism of Electronic Transitions
DOE Office of Scientific and Technical Information (OSTI.GOV)
Sutherland, J.C.
2010-08-11
This chapter describes the measurement of circular dichroism (CD) for absorption due to transitions between two distinct electronic states. This is distinguished from absorption of lower energy photons, which are associated with changes of only the vibrational modes of the absorber and from the absorption of higher energy photons, which may result in ionizations. From the instrumental viewpoint, the chapter describes the measurement of CD that can be recorded using a photomultiplier or avalanche photodiode to quantify the intensity of a light beam, a photoelastic modulator to periodically alter the beam's polarization, and a monochromator located between the light sourcemore » and the modulator. Using either criterion, the focus is on the spectral domain spanning about a decade in wavelength (photon energy) from roughly 1.2 {micro}m (1 eV {approx} 160 zJ) in the near infrared to 120 nm (10 eV {approx} 1.6 aJ) in the vacuum ultraviolet (VUV). In the near infrared, there is overlap between the domain of electronic and purely vibrational transitions, the use of photomultipliers or avalanche photodiodes versus solid state detectors and dispersive versus Fourier-transform spectrometers. There is also some overlap in the VUV with synchrotron beamlines that use arrays of magnets called 'insertion devices' to cause the emitted synchrotron radiation to be elliptically polarized. To my knowledge, no single spectrometer spans this entire spectral domain discussed here, and the vast majority of laboratory instruments come nowhere close to either the upper or lower limit. However, similar analytical approaches and types of instrumentation are employed throughout this spectral domain and thus are logically treated together. The focus in this chapter is on the measurement of CD resulting from the inherent chirality of the absorbing system. Several spectroscopic methods that are closely related in terms of science or instrumentation are treated in other chapters. These include
Circular dichroism in photo-single-ionization of unoriented atoms.
Feagin, James M
2002-01-28
We predict circular dichroism in photo-single-ionization angular distributions from spherically symmetric atomic states if the ionized electron is detected using two-slit interferometry. We demonstrate that the resulting electron interference pattern captures phase information on quadrupole corrections to the photoionization amplitude lost in conventional angular distributions.
UV-CD12: synchrotron radiation circular dichroism beamline at ANKA
Bürck, Jochen; Roth, Siegmar; Windisch, Dirk; Wadhwani, Parvesh; Moss, David; Ulrich, Anne S.
2015-01-01
Synchrotron radiation circular dichroism (SRCD) is a rapidly growing technique for structure analysis of proteins and other chiral biomaterials. UV-CD12 is a high-flux SRCD beamline installed at the ANKA synchrotron, to which it had been transferred after the closure of the SRS Daresbury. The beamline covers an extended vacuum-UV to near-UV spectral range and has been open for users since October 2011. The current end-station allows for temperature-controlled steady-state SRCD spectroscopy, including routine automated thermal scans of microlitre volumes of water-soluble proteins down to 170 nm. It offers an excellent signal-to-noise ratio over the whole accessible spectral range. The technique of oriented circular dichroism (OCD) was recently implemented for determining the membrane alignment of α-helical peptides and proteins in macroscopically oriented lipid bilayers as mimics of cellular membranes. It offers improved spectral quality <200 nm compared with an OCD setup adapted to a bench-top instrument, and accelerated data collection by a factor of ∼3. In addition, it permits investigations of low hydrated protein films down to 130 nm using a rotatable sample cell that avoids linear dichroism artifacts. PMID:25931105
ERIC Educational Resources Information Center
Abriata, Luciano A.
2011-01-01
A simple algorithm was implemented in a spreadsheet program to simulate the circular dichroism spectra of proteins from their secondary structure content and to fit [alpha]-helix, [beta]-sheet, and random coil contents from experimental far-UV circular dichroism spectra. The physical basis of the method is briefly reviewed within the context of…
Conformational analysis and circular dichroism of bilirubin, the yellow pigment of jaundice
NASA Astrophysics Data System (ADS)
Lightner, David A.; Person, Richard; Peterson, Blake; Puzicha, Gisbert; Pu, Yu-Ming; Bojadziev, Stefan
1991-06-01
Conformational analysis of (4Z, 15Z)-bilirubin-IX(alpha) by molecular mechanics computations reveals a global energy minimum folded conformation. Powerful added stabilization is achieved through intramolecular hydrogen bonding. Theoretical treatment of bilirubin as a molecular exciton predicts an intense bisignate circular dichroism spectrum for the folded conformation: (Delta) (epsilon) is congruent to 270 L (DOT) mole-1 (DOT) cm-1 for the $OM450 nm electronic transition(s). Synthesis of bilirubin analogs with propionic acid groups methylated at the (alpha) or (beta) position introduces an allosteric effect that allows for an optical resolution of the pigments, with enantiomers exhibiting the theoretically predicted circular dichroism.
Lehmann, C Stefan; Ram, N Bhargava; Powis, Ivan; Janssen, Maurice H M
2013-12-21
Here, we provide a detailed account of novel experiments employing electron-ion coincidence imaging to discriminate chiral molecules. The full three-dimensional angular scattering distribution of electrons is measured after photoexcitation with either left or right circular polarized light. The experiment is performed using a simplified photoelectron-photoion coincidence imaging setup employing only a single particle imaging detector. Results are reported applying this technique to enantiomers of the chiral molecule camphor after three-photon ionization by circularly polarized femtosecond laser pulses at 400 nm and 380 nm. The electron-ion coincidence imaging provides the photoelectron spectrum of mass-selected ions that are observed in the time-of-flight mass spectra. The coincident photoelectron spectra of the parent camphor ion and the various fragment ions are the same, so it can be concluded that fragmentation of camphor happens after ionization. We discuss the forward-backward asymmetry in the photoelectron angular distribution which is expressed in Legendre polynomials with moments up to order six. Furthermore, we present a method, similar to one-photon electron circular dichroism, to quantify the strength of the chiral electron asymmetry in a single parameter. The circular dichroism in the photoelectron angular distribution of camphor is measured to be 8% at 400 nm. The electron circular dichroism using femtosecond multiphoton excitation is of opposite sign and about 60% larger than the electron dichroism observed before in near-threshold one-photon ionization with synchrotron excitation. We interpret our multiphoton ionization as being resonant at the two-photon level with the 3s and 3p Rydberg states of camphor. Theoretical calculations are presented that model the photoelectron angular distribution from a prealigned camphor molecule using density functional theory and continuum multiple scattering X alpha photoelectron scattering calculations
DOE Office of Scientific and Technical Information (OSTI.GOV)
Lehmann, C. Stefan; Ram, N. Bhargava; Janssen, Maurice H. M., E-mail: m.h.m.janssen@vu.nl
2013-12-21
Here, we provide a detailed account of novel experiments employing electron-ion coincidence imaging to discriminate chiral molecules. The full three-dimensional angular scattering distribution of electrons is measured after photoexcitation with either left or right circular polarized light. The experiment is performed using a simplified photoelectron-photoion coincidence imaging setup employing only a single particle imaging detector. Results are reported applying this technique to enantiomers of the chiral molecule camphor after three-photon ionization by circularly polarized femtosecond laser pulses at 400 nm and 380 nm. The electron-ion coincidence imaging provides the photoelectron spectrum of mass-selected ions that are observed in the time-of-flightmore » mass spectra. The coincident photoelectron spectra of the parent camphor ion and the various fragment ions are the same, so it can be concluded that fragmentation of camphor happens after ionization. We discuss the forward-backward asymmetry in the photoelectron angular distribution which is expressed in Legendre polynomials with moments up to order six. Furthermore, we present a method, similar to one-photon electron circular dichroism, to quantify the strength of the chiral electron asymmetry in a single parameter. The circular dichroism in the photoelectron angular distribution of camphor is measured to be 8% at 400 nm. The electron circular dichroism using femtosecond multiphoton excitation is of opposite sign and about 60% larger than the electron dichroism observed before in near-threshold one-photon ionization with synchrotron excitation. We interpret our multiphoton ionization as being resonant at the two-photon level with the 3s and 3p Rydberg states of camphor. Theoretical calculations are presented that model the photoelectron angular distribution from a prealigned camphor molecule using density functional theory and continuum multiple scattering X alpha photoelectron scattering calculations
PCDDB: new developments at the Protein Circular Dichroism Data Bank.
Whitmore, Lee; Miles, Andrew John; Mavridis, Lazaros; Janes, Robert W; Wallace, B A
2017-01-04
The Protein Circular Dichroism Data Bank (PCDDB) has been in operation for more than 5 years as a public repository for archiving circular dichroism spectroscopic data and associated bioinformatics and experimental metadata. Since its inception, many improvements and new developments have been made in data display, searching algorithms, data formats, data content, auxillary information, and validation techniques, as well as, of course, an increase in the number of holdings. It provides a site (http://pcddb.cryst.bbk.ac.uk) for authors to deposit experimental data as well as detailed information on methods and calculations associated with published work. It also includes links for each entry to bioinformatics databases. The data are freely available to accessors either as single files or as complete data bank downloads. The PCDDB has found broad usage by the structural biology, bioinformatics, analytical and pharmaceutical communities, and has formed the basis for new software and methods developments. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
Perfect Circular Dichroism in the Haldane Model
NASA Astrophysics Data System (ADS)
Ghalamkari, Kazu; Tatsumi, Yuki; Saito, Riichiro
2018-06-01
We theoretically show that perfect circular dichroism (CD) occurs in the Haldane model in which the two-dimensional (2D) material absorbs only either left-handed or right-handed circularly polarized light. Perfect CD occurs in the phase diagram of the Haldane model when the zero-field quantum Hall conductivity has a nonzero value. The coincidence of the occurrence of perfect CD and zero-field quantum Hall effect is attributed to the fact that the effect of broken time-reversal symmetry is larger than the effect of broken inversion symmetry. On the other hand, valley polarization and perfect CD occur exclusively in the phase diagram. Further, for the four regions of the phase diagram, pseudospin polarization occurs at the K and K' points in the hexagonal Brillouin zone with either the same sign or opposite sign for the K and K' points and for the valence and conduction bands. This theoretical prediction may have an impact on search for a new optical device that selects circularly polarized light controlled by the electric field.
Photoelectron circular dichroism in different ionization regimes
NASA Astrophysics Data System (ADS)
Wollenhaupt, Matthias
2016-12-01
Photoelectron circular dichroism (PECD) describes an asymmetry in the photoelectron angular distribution (PAD) from photoionization of randomly oriented enantiomers with circularly polarized light. Beaulieu et al present a comprehensive set of measured PADs from multiphoton ionization of limonene and fenchone in different ionization regimes (multiphoton and tunneling) and analyze the resulting PECD (Beaulieu et al 2016 New J. Phys. 18 102002). From their observations the authors conclude that the PECD is universal in the sense that the molecular chirality is encoded in the PAD independent of the ionization regime. The analysis is supplemented by a classical model based on electron scattering in a chiral potential. The paper presents beautiful data and is an important step towards a more complete physical picture of PECD. The results and their interpretation stimulate the ongoing vivid debate on the role of resonances in multiphoton PECD.
Muto, Shunsuke; Rusz, Ján; Tatsumi, Kazuyoshi; Adam, Roman; Arai, Shigeo; Kocevski, Vancho; Oppeneer, Peter M; Bürgler, Daniel E; Schneider, Claus M
2014-01-01
Electron magnetic circular dichroism (EMCD) allows the quantitative, element-selective determination of spin and orbital magnetic moments, similar to its well-established X-ray counterpart, X-ray magnetic circular dichroism (XMCD). As an advantage over XMCD, EMCD measurements are made using transmission electron microscopes, which are routinely operated at sub-nanometre resolution, thereby potentially allowing nanometre magnetic characterization. However, because of the low intensity of the EMCD signal, it has not yet been possible to obtain quantitative information from EMCD signals at the nanoscale. Here we demonstrate a new approach to EMCD measurements that considerably enhances the outreach of the technique. The statistical analysis introduced here yields robust quantitative EMCD signals. Moreover, we demonstrate that quantitative magnetic information can be routinely obtained using electron beams of only a few nanometres in diameter without imposing any restriction regarding the crystalline order of the specimen.
Chiral surface waves for enhanced circular dichroism
NASA Astrophysics Data System (ADS)
Pellegrini, Giovanni; Finazzi, Marco; Celebrano, Michele; Duò, Lamberto; Biagioni, Paolo
2017-06-01
We present a novel chiral sensing platform that combines a one-dimensional photonic crystal design with a birefringent surface defect. The platform sustains simultaneous transverse electric and transverse magnetic surface modes, which are exploited to generate chiral surface waves. The present design provides homogeneous and superchiral fields of both handednesses over arbitrarily large areas in a wide spectral range, resulting in the enhancement of the circular dichroism signal by more than two orders of magnitude, thus paving the road toward the successful combination of surface-enhanced spectroscopies and electromagnetic superchirality.
Isotope effect on the circular dichroism spectrum of methyl α-D-glucopyranoside in aqueous solution
Kanematsu, Yusuke; Kamiya, Yukiko; Matsuo, Koichi; Gekko, Kunihiko; Kato, Koichi; Tachikawa, Masanori
2015-01-01
H/D isotope effect on the circular dichroism spectrum of methyl α-D-glucopyranoside in aqueous solution has been analyzed by multicomponent density functional theory calculations using the polarizable continuum model. By comparing the computational spectra with the corresponding experimental spectrum obtained with a vacuum-ultraviolet circular dichroism spectrophotometer, it was demonstrated that the isotope effect provides insights not only into the isotopic difference of the intramolecular interactions of the solutes, but also into that of the solute–solvent intermolecular interaction. PMID:26658851
NASA Astrophysics Data System (ADS)
Shih, Min-Hsiung
2016-09-01
Circularly polarized light and chiroptical effect have received considerable attention in advanced photonic and electronic technologies including optical spintronics, quantum-based optical information processing and communication, and high-efficiency liquid crystal display backlights. Moreover, the development of circularly polarized photon sources has played a major role in circular dichroism (CD) spectroscopy, which is important for analyses of optically active molecules, chiral synthesis in biology and chemistry, and ultrafast magnetization control. However, the conventional collocation of light-emitting devices and additional circular-polarization converters that produce circularly polarized beams makes the setup bulky and hardly compatible with nanophotonic devices in ultrasmall scales. In fact, the direct generation of circularly polarized photons may simplify the system integration, compact the setup, lower the cost of external components, and perhaps enhance the power efficiency. In this work, with the spiral-type metal-gallium nitride (GaN) nanowire cavity, we demonstrated an ultrasmall semiconductor laser capable of emitting circularly-polarized photons. The left- and right-hand spiral metal nanowire cavities with varied periods were designed at ultraviolet wavelengths to achieve the high quality factor circular dichroism metastructures. The dissymmetry factors characterizing the degrees of circular polarizations of the left- and right-hand chiral lasers were 1.4 and -1.6 (2 if perfectly circular polarized), respectively. The results show that the chiral cavities with only 5 spiral periods can achieve lasing signals with decently high degrees of circular polarizations.
Magnetic circular dichroism of CdTe nanoparticles
NASA Astrophysics Data System (ADS)
Malakhovskii, A. V.; Sokolov, A. E.; Tsipotan, A. S.; Zharkov, S. M.; Zabluda, V. N.
2018-04-01
Magnetic circular dichroism (MCD) of water-soluble CdTe nanoparticles was observed in the visible spectral range for the first time. Diameter of nanoparticles varied from 2.3 to 4.5 nm. Absorption and photoluminescence spectra were also recorded. Absorption line at 19400 cm-1 and luminescent line at 18200 cm-1 were observed. Splitting of value 960 cm-1 was revealed in the MCD spectrum. Approximately the same splitting was extracted from the absorption spectrum. The MCD was identified as the temperature independent paramagnetic mixing effect. Nature of the absorption line and of its splitting are discussed.
Nuclear spin circular dichroism.
Vaara, Juha; Rizzo, Antonio; Kauczor, Joanna; Norman, Patrick; Coriani, Sonia
2014-04-07
Recent years have witnessed a growing interest in magneto-optic spectroscopy techniques that use nuclear magnetization as the source of the magnetic field. Here we present a formulation of magnetic circular dichroism (CD) due to magnetically polarized nuclei, nuclear spin-induced CD (NSCD), in molecules. The NSCD ellipticity and nuclear spin-induced optical rotation (NSOR) angle correspond to the real and imaginary parts, respectively, of (complex) quadratic response functions involving the dynamic second-order interaction of the electron system with the linearly polarized light beam, as well as the static magnetic hyperfine interaction. Using the complex polarization propagator framework, NSCD and NSOR signals are obtained at frequencies in the vicinity of optical excitations. Hartree-Fock and density-functional theory calculations on relatively small model systems, ethene, benzene, and 1,4-benzoquinone, demonstrate the feasibility of the method for obtaining relatively strong nuclear spin-induced ellipticity and optical rotation signals. Comparison of the proton and carbon-13 signals of ethanol reveals that these resonant phenomena facilitate chemical resolution between non-equivalent nuclei in magneto-optic spectra.
USDA-ARS?s Scientific Manuscript database
Time-dependent density functional theory (TDDFT) was employed for theoretical calculation of electronic circular dichroism (ECD) of a hexahydroxydiphenoyl (HHDP)-containing flavanone glycoside, mattucinol-7-O-[4'',6''-O-(aS)-hexahydroxydiphenoyl]-ß-d-glucopyranoside (2). It identified the roles of t...
Unboiling an Egg: An Introduction to Circular Dichroism and Protein Refolding
ERIC Educational Resources Information Center
Hoben, John P.; Wang, Jianing; Miller, Anne-Frances
2017-01-01
A signature of life is that biological molecules occur as a single stereoisomer with respect to each chiral center, and this is echoed in the structures of biological polymers. Thus, circular dichroism (CD) has emerged as a hallmark of biomolecular structures. The tangible and familiar phenomenon of raw egg white's conversion from transparent…
Mid-infrared Plasmonic Circular Dichroism Generated by Graphene Nanodisk Assemblies.
Kong, Xiang-Tian; Zhao, Runbo; Wang, Zhiming; Govorov, Alexander O
2017-08-09
It is very interesting to bring plasmonic circular dichroism spectroscopy to the mid-infrared spectral interval, and there are two reasons for this. This spectral interval is very important for thermal bioimaging, and simultaneously, this spectral range includes vibrational lines of many chiral biomolecules. Here we demonstrate that graphene plasmons indeed offer such opportunity. In particular, we show that chiral graphene assemblies consisting of a few graphene nanodisks can generate strong circular dichroism (CD) in the mid-infrared interval. The CD signal is generated due to the plasmon-plasmon coupling between adjacent nanodisks in the specially designed chiral graphene assemblies. Because of the large dimension mismatch between the thickness of a graphene layer and the incoming light's wavelength, three-dimensional configurations with a total height of a few hundred nanometers are necessary to obtain a strong CD signal in the mid-infrared range. The mid-infrared CD strength is mainly governed by the total dimensions (total height and helix scaffold radius) of the graphene nanodisk assembly and by the plasmon-plasmon interaction strength between its constitutive nanodisks. Both positive and negative CD bands can be observed in the graphene assembly array. The frequency interval of the plasmonic CD spectra overlaps with the vibrational modes of some important biomolecules, such as DNA and many different peptides, giving rise to the possibility of enhancing the vibrational optical activity of these molecular species by attaching them to the graphene assemblies. Simultaneously the spectral range of chiral mid-infrared plasmons in our structures appears near the typical wavelength of the human-body thermal radiation, and therefore, our chiral metastructures can be potentially utilized as optical components in thermal imaging devices.
Chiral detection in high-performance liquid chromatography by vibrational circular dichroism.
Tran, C D; Grishko, V I; Huang, G
1994-09-01
A novel chiral detector for high-performance liquid chromatography has been developed. This detector is based on the measurement of circular dichroism of chiral effluents in the infrared region, i.e., vibrational circular dichroism (VCD). In this instrument, a solid-state spectral tunable (from 2.4 to 3.5 microns) F-center laser was used as the light source. The linearly polarized laser beam was converted into left circularly polarized light (LCPL) and right circularly polarized light (RCPL) at 42 kHz by means of a photoelastic modulator. The intensity of the LCPL and RCPL transmitted through the sample was measured by a liquid nitrogen cooled indium antimonide detector. Double modulation was employed to reduce the noise associated with the laser beam. Specifically, the linearly polarized laser beam, prior to being converted to CPL, was modulated at 85 Hz by a mechanical chopper. Demodulation and amplification were accomplished with the use of two lock-in amplifiers. In its present configuration, the instrument can be used to measure the VCD of O-H groups. Its sensitivity is so high that it was able, for the first time, to detect chirally (with limits of detection of micrograms) (R)- and (S)-2,2,2-trifluoro-1-(9- anthryl)ethanol and (R)- and (S)-benzoin when these compounds were chromatographically separated from the corresponding racemic mixtures by a Chiralcel-OD column. The main advantage of this chiral detector is, however, its universality; i.e., it can be used to virtually detect any chiral compounds which has O-H group (e.g, aliphatic alcohols such as 2-octanol).
NASA Astrophysics Data System (ADS)
Kamiya, Mamoru
1980-11-01
The dynamic perturbation effects of polarizable monomer perturbers upon the circular dichroism intensity arising from absorption transitions of an arbitrary aggregate of dye chromophores bound to a large host polymer are formulated using the linear response theory in the decorrelation approximation, where the interchromophoric retardation phase factors are eliminated by a first-order Taylor expansion which is compatible with the use of the retarded helix selection rules in the long-wavelength approximation. A space-averaged and closed-form formulation of the non-conservative circular dichroism intensity which is perturbed by intensity with the outside perturber transitions is derived in the limit of the weak dynamic perturbation where perturber—perturber interactions are negligible. The relevant formulation is applied in order to investigate the intercalation model dependence of the non-conservative circular dichroism intensity induced at the visible absorption band of proflavine molecules intercalated in either poly(A—T) or poly(G—C).
Homonuclear 1H NMR and circular dichroism study of the HIV-1 Tat Eli variant.
Watkins, Jennifer D; Campbell, Grant R; Halimi, Hubert; Loret, Erwann P
2008-09-22
The HIV-1 Tat protein is a promising target to develop AIDS therapies, particularly vaccines, due to its extracellular role that protects HIV-1-infected cells from the immune system. Tat exists in two different lengths, 86 or 87 residues and 99 or 101 residues, with the long form being predominant in clinical isolates. We report here a structural study of the 99 residue Tat Eli variant using 2D liquid-state NMR, molecular modeling and circular dichroism. Tat Eli was obtained from solid-phase peptide synthesis and the purified protein was proven biologically active in a trans-activation assay. Circular dichroism spectra at different temperatures up to 70 degrees C showed that Tat Eli is not a random coil at 20 degrees C. Homonuclear 1H NMR spectra allowed us to identify 1639 NMR distance constraints out of which 264 were interresidual. Molecular modeling satisfying at least 1474 NMR constraints revealed the same folding for different model structures. The Tat Eli model has a core region composed of a part of the N-terminus including the highly conserved Trp 11. The extra residues in the Tat Eli C-terminus protrude from a groove between the basic region and the cysteine-rich region and are well exposed to the solvent. We show that active Tat variants share a similar folding pattern whatever their size, but mutations induce local structural changes.
Jasim, Sarah B; Li, Zhuo; Guest, Ellen E; Hirst, Jonathan D
2017-12-16
A fully quantitative theory connecting protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. The web server DichroCalc (http://comp.chem.nottingham.ac.uk/dichrocalc) allows one to compute from first principles the electronic circular dichroism spectrum of a (modeled or experimental) protein structure or ensemble of structures. The regular, repeating, chiral nature of secondary structure elements leads to intense bands in the far-ultraviolet (UV). The near-UV bands are much weaker and have been challenging to compute theoretically. We report some advances in the accuracy of calculations in the near-UV, realized through the consideration of the vibrational structure of the electronic transitions of aromatic side chains. The improvements have been assessed over a set of diverse proteins. We illustrate them using bovine pancreatic trypsin inhibitor and present a new, detailed analysis of the interactions which are most important in determining the near-UV circular dichroism spectrum. Copyright © 2018. Published by Elsevier Ltd.
A Circular Dichroism Reference Database for Membrane Proteins
DOE Office of Scientific and Technical Information (OSTI.GOV)
Wallace,B.; Wien, F.; Stone, T.
2006-01-01
Membrane proteins are a major product of most genomes and the target of a large number of current pharmaceuticals, yet little information exists on their structures because of the difficulty of crystallising them; hence for the most part they have been excluded from structural genomics programme targets. Furthermore, even methods such as circular dichroism (CD) spectroscopy which seek to define secondary structure have not been fully exploited because of technical limitations to their interpretation for membrane embedded proteins. Empirical analyses of circular dichroism (CD) spectra are valuable for providing information on secondary structures of proteins. However, the accuracy of themore » results depends on the appropriateness of the reference databases used in the analyses. Membrane proteins have different spectral characteristics than do soluble proteins as a result of the low dielectric constants of membrane bilayers relative to those of aqueous solutions (Chen & Wallace (1997) Biophys. Chem. 65:65-74). To date, no CD reference database exists exclusively for the analysis of membrane proteins, and hence empirical analyses based on current reference databases derived from soluble proteins are not adequate for accurate analyses of membrane protein secondary structures (Wallace et al (2003) Prot. Sci. 12:875-884). We have therefore created a new reference database of CD spectra of integral membrane proteins whose crystal structures have been determined. To date it contains more than 20 proteins, and spans the range of secondary structures from mostly helical to mostly sheet proteins. This reference database should enable more accurate secondary structure determinations of membrane embedded proteins and will become one of the reference database options in the CD calculation server DICHROWEB (Whitmore & Wallace (2004) NAR 32:W668-673).« less
Homonuclear 1H NMR and circular dichroism study of the HIV-1 Tat Eli variant
Watkins, Jennifer D; Campbell, Grant R; Halimi, Hubert; Loret, Erwann P
2008-01-01
Background The HIV-1 Tat protein is a promising target to develop AIDS therapies, particularly vaccines, due to its extracellular role that protects HIV-1-infected cells from the immune system. Tat exists in two different lengths, 86 or 87 residues and 99 or 101 residues, with the long form being predominant in clinical isolates. We report here a structural study of the 99 residue Tat Eli variant using 2D liquid-state NMR, molecular modeling and circular dichroism. Results Tat Eli was obtained from solid-phase peptide synthesis and the purified protein was proven biologically active in a trans-activation assay. Circular dichroism spectra at different temperatures up to 70°C showed that Tat Eli is not a random coil at 20°C. Homonuclear 1H NMR spectra allowed us to identify 1639 NMR distance constraints out of which 264 were interresidual. Molecular modeling satisfying at least 1474 NMR constraints revealed the same folding for different model structures. The Tat Eli model has a core region composed of a part of the N-terminus including the highly conserved Trp 11. The extra residues in the Tat Eli C-terminus protrude from a groove between the basic region and the cysteine-rich region and are well exposed to the solvent. Conclusion We show that active Tat variants share a similar folding pattern whatever their size, but mutations induce local structural changes. PMID:18808674
ERIC Educational Resources Information Center
Reed, Nicole A.; Rapp, Robert D.; Hamann, Christian S.; Artz, Pamela G.
2005-01-01
Dess-Martin periodinane oxidation is an experiment that provides an avenue to the introduction of Circular Dichroism (CD) spectroscopy in organic chemistry curriculum as a diagnostic tool for examination of the results of a familiar reaction, and absolute configuration. From the experiment, students increased their understanding of CD theory and…
Fourier transform vibrational circular dichroism of small pharmaceutical molecules
NASA Astrophysics Data System (ADS)
Long, Fujin; Freedman, Teresa B.; Nafie, Laurence A.
1998-06-01
Fourier transform vibrational circular dichroism (FT-VCD) spectra of the small pharmaceutical molecules propanolol, ibuprofen and naproxen have been measured in the hydrogen stretching and mid-infrared regions to obtain information on solution conformation and to identify markers for absolute configuration determination. Ab initio molecular orbital calculations of low energy conformations, vibrational frequencies and VCD intensities for fragments of the drugs were utilized in interpreting the spectra. Features characteristic of five conformers of propranolol were identified. The weak positive CH stretching VCD signal in ibuprofen and naproxen is characteristic of the S-configuration of the chiral center common to these two analgesics.
Determination of protein-dye association by near infrared fluorescence-detected circular dichroism.
Meadows, F; Narayanan, N; Patonay, G
2000-01-10
Near-infrared (NIR) squarylium dye spectral properties were evaluated by absorption, fluorescence, circular dichroism (CD), and fluorescence-detected circular dichroism (FDCD). Substituents of the two NN dyes differed at R(1) and R(2), located symmetrically on the chromophore. The side chains of NN525 are R(1)=hexanoic acid, R(2)=butyl sulfonate and R(1)=R(2)=ethyl for NN127. FDCD signals were first confirmed by denaturing BSA with 2-8 M urea showing a diminution of dye FDCD peaks, but no change occurred in spectral properties of the dyes in urea. This indicated that the observed cotton effects occurred by noncovalent interactions with the secondary structure of the protein. The average BSA-dye association constants found by fluorescence, absorbance, and FDCD were 1.27 x 10(6) (n=1) and 3.3 x 10(6) M(-1) (n=1) for NN127 and NN525 respectively. These values were in good agreement when calculated by the three spectroscopic methods validating the use of NIRFDCD for optical parameter calculations. These results are useful to describe NIR squarylium dye labeling of BSA.
Circular dichroism of magnetically induced transitions for D2 lines of alkali atoms
NASA Astrophysics Data System (ADS)
Tonoyan, A.; Sargsyan, A.; Klinger, E.; Hakhumyan, G.; Leroy, C.; Auzinsh, M.; Papoyan, A.; Sarkisyan, D.
2018-03-01
In this letter we study magnetic circular dichroism in alkali atoms exhibiting asymmetric behaviour of magnetically induced transitions. The magnetic field \\textbf{B}\\parallel\\textbf{k} induces transitions between Δ F = +/-2 hyperfine levels of alkali atoms and in the range of ∼0.1{\\text{--}}3 \\text{kG} magnetic field, the intensities of these transitions experience significant enhancement. We have inferred a general rule applicable for the D 2 lines of all alkali atoms, that is the transition intensity enhancement is around four times larger for the case of σ+ than for σ- excitation for Δ F = +2 , whereas it is several hundreds of thousand times larger in the case of σ- than that for σ+ polarization for Δ F = -2 . This asymmetric behaviour results in circular dichroism. For experimental verification we employed half-wavelength-thick atomic vapor nanocells using a derivative of the selective reflection technique, which provides a sub-Doppler spectroscopic linewidth (∼50 \\text{MHz} ). The presented theoretical curves well describe the experimental results. This effect can find applications particularly in parity violation experiments.
Shiraogawa, Takafumi; Ehara, Masahiro; Jurinovich, Sandro; Cupellini, Lorenzo; Mennucci, Benedetta
2018-06-15
Recently, a method to calculate the absorption and circular dichroism (CD) spectra based on the exciton coupling has been developed. In this work, the method was utilized for the decomposition of the CD and circularly polarized luminescence (CPL) spectra of a multichromophoric system into chromophore contributions for recently developed through-space conjugated oligomers. The method which has been implemented using rotatory strength in the velocity form and therefore it is gauge-invariant, enables us to evaluate the contribution from each chromophoric unit and locally excited state to the CD and CPL spectra of the total system. The excitonic calculations suitably reproduce the full calculations of the system, as well as the experimental results. We demonstrate that the interactions between electric transition dipole moments of adjacent chromophoric units are crucial in the CD and CPL spectra of the multichromophoric systems, while the interactions between electric and magnetic transition dipole moments are not negligible. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.
Understanding electron magnetic circular dichroism in a transition potential approach
NASA Astrophysics Data System (ADS)
Barthel, J.; Mayer, J.; Rusz, J.; Ho, P.-L.; Zhong, X. Y.; Lentzen, M.; Dunin-Borkowski, R. E.; Urban, K. W.; Brown, H. G.; Findlay, S. D.; Allen, L. J.
2018-04-01
This paper introduces an approach based on transition potentials for inelastic scattering to understand the underlying physics of electron magnetic circular dichroism (EMCD). The transition potentials are sufficiently localized to permit atomic-scale EMCD. Two-beam and three-beam systematic row cases are discussed in detail in terms of transition potentials for conventional transmission electron microscopy, and the basic symmetries which arise in the three-beam case are confirmed experimentally. Atomic-scale EMCD in scanning transmission electron microscopy (STEM), using both a standard STEM probe and vortex beams, is discussed.
DOE Office of Scientific and Technical Information (OSTI.GOV)
B Wallace; R Janes
CD (circular dichroism) spectroscopy is a well-established technique in structural biology. SRCD (synchrotron radiation circular dichroism) spectroscopy extends the utility and applications of conventional CD spectroscopy (using laboratory-based instruments) because the high flux of a synchrotron enables collection of data at lower wavelengths (resulting in higher information content), detection of spectra with higher signal-to-noise levels and measurements in the presence of absorbing components (buffers, salts, lipids and detergents). SRCD spectroscopy can provide important static and dynamic structural information on proteins in solution, including secondary structures of intact proteins and their domains, protein stability, the differences between wild-type and mutant proteins,more » the identification of natively disordered regions in proteins, and the dynamic processes of protein folding and membrane insertion and the kinetics of enzyme reactions. It has also been used to effectively study protein interactions, including protein-protein complex formation involving either induced-fit or rigid-body mechanisms, and protein-lipid complexes. A new web-based bioinformatics resource, the Protein Circular Dichroism Data Bank (PCDDB), has been created which enables archiving, access and analyses of CD and SRCD spectra and supporting metadata, now making this information publicly available. To summarize, the developing method of SRCD spectroscopy has the potential for playing an important role in new types of studies of protein conformations and their complexes.« less
Circular dichroism spectra of uridine derivatives: ChiraSac study.
Miyahara, Tomoo; Nakatsuji, Hiroshi; Wada, Takehiko
2014-04-24
The experimental circular dichroism (CD) spectra of uridine and NH2-uridine that were different in the intensity and shape were studied in the light of the ChiraSac method. The theoretical CD spectra at several different conformations using the symmetry-adapted-cluster configuration-interaction (SAC-CI) theory largely depended on the conformational angle, but those of the anti-conformers and the Boltzmann average reproduced the experimentally obtained CD spectra of both uridine and NH2-uridine. The differences in the CD spectra between the two uridine derivatives were analyzed by using the angle θ between the electric transition dipole moment (ETDM) and the magnetic transition dipole moment (MTDM).
Kumagai, Patricia S; DeMarco, Ricardo; Lopes, Jose L S
2017-10-01
The unordered secondary structural content of an intrinsically disordered protein (IDP) is susceptible to conformational changes induced by many different external factors, such as the presence of organic solvents, removal of water, changes in temperature, binding to partner molecules, and interaction with lipids and/or other ligands. In order to characterize the high-flexibility nature of an IDP, circular dichroism (CD) spectroscopy is a particularly useful method due to its capability of monitoring both subtle and remarkable changes in different environments, relative ease in obtaining measurements, the small amount of sample required, and the capability for sample recovery (sample not damaged) and others. Using synchrotron radiation as the light source for CD spectroscopy represents the state-of-the-art version of this technique with feasibility of accessing the lower wavelength UV region, and therefore presenting a series of advantages over conventional circular dichroism (cCD) to monitor a protein conformational behavior, check protein stability, detect ligand binding, and many others. In this paper, we have performed a comparative study using cCD and SRCD methods for investigating the secondary structure and the conformational behavior of natively unfolded proteins: MEG-14 and soybean trypsin inhibitor. We show that the SRCD technique greatly improves the analysis and accuracy of the studies on the conformations of IDPs.
Magnetic circular dichroism of chlorofullerenes: Experimental and computational study
NASA Astrophysics Data System (ADS)
Štěpánek, Petr; Straka, Michal; Šebestík, Jaroslav; Bouř, Petr
2016-03-01
Magnetic circular dichroism (MCD) spectra of C60Cl6, C70Cl10 and C60Cl24 were measured and interpreted using a sum-over-state (SOS) protocol exploiting time dependent density functional theory (TDDFT). Unlike for plain absorption, the MCD spectra exhibited easily recognizable features specific for each chlorinated molecule and appear as a useful tool for chlorofullerene identification. MCD spectrum of C60Cl24 was below 400 nm partially obscured due to scattering and low solubility. In all cases a finer vibrational structure of the electronic bands was observed at longer wavelengths. The TDDFT simulations provided a reasonable basis for interpretation of the most prominent spectral features.
Time-resolved circular dichroism: Application to the study of conformal changes in biomolecules
NASA Astrophysics Data System (ADS)
Hache, F.
2010-06-01
Circular dichroism (CD) is known to be a very sensitive probe of the conformation of molecules and biomolecules. It is therefore tempting to implement CD in a pump-probe experiment in order to measure ultrarapid conformational changes which occur in photochemical processes. We present two technical developments of such time-resolved CD experiments. The first one relies on the modulation of the probe polarization from left to right circular whereas the second one measures the pump-induced ellipticity of the probe with a Babinet-Soleil compensator. Some applications are described and extension of these techniques towards the study of elementary protein folding processes is discussed.
Gracheva, N K; Kharitonenkov, I G
1978-01-01
Circular dichroism was applied to the study of the structure of the insulin-transferrin complexes ("bound insulin") isolated from the blood sera of donors and patients suffering from diabetes mellitus of moderate severity. There proved to be a considerable (in comparison with the normal) reduction of the alpha-helix areas in the "bound insulin"molecule of the patients. A comparative study of the circular dichroism spectra in the area of absorption of aromatic amino acids permitted to suppose that the structural changes of the molecule of a complex isolated from the blood sera of patients could not be explained by alterations in the area of the aromatic amino acids.
Circular dichroism measurements at an x-ray free-electron laser with polarization control
NASA Astrophysics Data System (ADS)
Hartmann, G.; Lindahl, A. O.; Knie, A.; Hartmann, N.; Lutman, A. A.; MacArthur, J. P.; Shevchuk, I.; Buck, J.; Galler, A.; Glownia, J. M.; Helml, W.; Huang, Z.; Kabachnik, N. M.; Kazansky, A. K.; Liu, J.; Marinelli, A.; Mazza, T.; Nuhn, H.-D.; Walter, P.; Viefhaus, J.; Meyer, M.; Moeller, S.; Coffee, R. N.; Ilchen, M.
2016-08-01
A non-destructive diagnostic method for the characterization of circularly polarized, ultraintense, short wavelength free-electron laser (FEL) light is presented. The recently installed Delta undulator at the LCLS (Linac Coherent Light Source) at SLAC National Accelerator Laboratory (USA) was used as showcase for this diagnostic scheme. By applying a combined two-color, multi-photon experiment with polarization control, the degree of circular polarization of the Delta undulator has been determined. Towards this goal, an oriented electronic state in the continuum was created by non-resonant ionization of the O2 1s core shell with circularly polarized FEL pulses at hν ≃ 700 eV. An also circularly polarized, highly intense UV laser pulse with hν ≃ 3.1 eV was temporally and spatially overlapped, causing the photoelectrons to redistribute into so-called sidebands that are energetically separated by the photon energy of the UV laser. By determining the circular dichroism of these redistributed electrons using angle resolving electron spectroscopy and modeling the results with the strong-field approximation, this scheme allows to unambiguously determine the absolute degree of circular polarization of any pulsed, ultraintense XUV or X-ray laser source.
Dielectric tuned circular dichroism of L-shaped plasmonic metasurface
NASA Astrophysics Data System (ADS)
Qu, Yu; Zhang, Zhidong; Fu, Tong; Wang, Gang; Wang, Tiankun; Wang, Mingyan; Bai, Yu; Zhang, Zhongyue
2017-12-01
In this paper, a dielectric layer is introduced to tune circular dichroism (CD) of chiral plasmonic metasurfaces. The dielectric layer is used to control the optical phase of electric diploes in Born-Kuhn configurations. To prove our assumption, an L-shaped plasmonic metasurface consisting of two metallic slices is prepared by glancing angle deposition, and then an SiO2 slice is deposited on one arm of the L-shaped metasurface. Experimental results reveal that CD of the L-shaped plasmonic metasurface can be tuned by the thickness of the SiO2 slice. These findings not only contribute to a better understanding of the CD physical mechanism, but also can be used in nanophotonic metasurfaces because of the concise fabrication process.
NASA Astrophysics Data System (ADS)
Muhammad, Zahir; Wali, Faiz; Song, Li
2018-05-01
The authors regret
Atomic scale imaging of magnetic circular dichroism by achromatic electron microscopy.
Wang, Zechao; Tavabi, Amir H; Jin, Lei; Rusz, Ján; Tyutyunnikov, Dmitry; Jiang, Hanbo; Moritomo, Yutaka; Mayer, Joachim; Dunin-Borkowski, Rafal E; Yu, Rong; Zhu, Jing; Zhong, Xiaoyan
2018-03-01
In order to obtain a fundamental understanding of the interplay between charge, spin, orbital and lattice degrees of freedom in magnetic materials and to predict and control their physical properties 1-3 , experimental techniques are required that are capable of accessing local magnetic information with atomic-scale spatial resolution. Here, we show that a combination of electron energy-loss magnetic chiral dichroism 4 and chromatic-aberration-corrected transmission electron microscopy, which reduces the focal spread of inelastically scattered electrons by orders of magnitude when compared with the use of spherical aberration correction alone, can achieve atomic-scale imaging of magnetic circular dichroism and provide element-selective orbital and spin magnetic moments atomic plane by atomic plane. This unique capability, which we demonstrate for Sr 2 FeMoO 6 , opens the door to local atomic-level studies of spin configurations in a multitude of materials that exhibit different types of magnetic coupling, thereby contributing to a detailed understanding of the physical origins of magnetic properties of materials at the highest spatial resolution.
A circular dichroism and structural study of the inclusion complex artemisinin-β-cyclodextrin
NASA Astrophysics Data System (ADS)
Marconi, Giancarlo; Monti, Sandra; Manoli, Francesco; Degli Esposti, Alessandra; Mayer, Bernd
2004-01-01
The inclusion complex between the powerful antimalarial agent Artemisinin and β-cyclodextrin has been studied by means of Circular Dichroism and elucidated by Density Functional Theory calculations on the isolated molecule combined to a statistical Monte Carlo search of the most stable geometry of the complex. The results evidence a host-guest structure in full agreement with the almost unaffected functionality of the drug, which is found to experience a significant hydrophilic environment when complexed.
NASA Astrophysics Data System (ADS)
Kim, Jinhyeok; Mizuguchi, Masaki; Inami, Nobuhito; Ueno, Tetsuro; Ueda, Shigenori; Takanashi, Koki
2018-04-01
An epitaxially grown Mn72Ge28 film with a tetragonal crystal structure was fabricated. It was clarified that the film had a perpendicular magnetization and a high perpendicular magnetic anisotropy energy of 14.3 Merg/cm3. The electronic structure was investigated by X-ray magnetic circular dichroism and hard X-ray photoelectron spectroscopy. The obtained X-ray magnetic circular dichroism spectrum revealed that the Mn orbital magnetic moment governed the magnetocrystalline anisotropy of the Mn72Ge28 film. A doublet structure was observed for the Mn 2p3/2 peak of hard X-ray photoelectron spectrum, indicating the spin exchange interaction between the 2p core-hole and 3d valence electrons.
USDA-ARS?s Scientific Manuscript database
Density functional theory/B3LYP has been employed to optimize the conformations of selected 4-arylflavan-3-ols and their phenolic methyl ether 3-O-acetates. The electronic circular dichroism spectra of the major conformers have been calculated using time-dependent density functional theory to valida...
Electrically controlled magnetic circular dichroism and Faraday rotation in graphene
NASA Astrophysics Data System (ADS)
Kuzmenko, Alexey; Poumirol, Jean-Marie; Liu, Peter Q. Liu; Slipchenko, Tetiana; Nikitin, Alexey; Martin-Moreno, Luis; Faist, Jerome
Magnetic circular dichroism (MCD) and Faraday rotation (FR) are the fundamental phenomena of great practical importance arising from the breaking of the time reversal symmetry by a magnetic field. In most materials the strength and the sign of these effects can be only controlled by the field value and its orientation. Using broadband terahertz magneto-electro-optical spectroscopy, we demonstrate that in graphene both the MCD and the FR can be modulated in intensity, tuned in frequency and, importantly, inverted using only electrostatic doping at a fixed magnetic field due to the unique properties of the Dirac fermions. Our results indicate the fundamental possibility of compact, efficient, electrically invertible and wavelength-tunable non-reciprocal passive terahertz elements based on graphene operating at ambient temperature.
ERIC Educational Resources Information Center
Carvalho, Josue´; Queiroz, João A.; Cruz, Carla
2017-01-01
Circular dichroism (CD) has emerged as one of the standard biophysical techniques for the study of guaninequadruplex (G4) folding, cation effect, and ligand binding. The utility of this technique is based on its robustness, ease of use, and requirement of only small quantities of nucleic acid. This experiment is also extendable to the classroom…
Larrabee, James A; Schenk, Gerhard; Mitić, Nataša; Riley, Mark J
2015-09-01
Magnetic circular dichroism (MCD) is a convenient technique for providing structural and mechanistic insight into enzymatic systems in solution. The focus of this review is on aspects of geometric and electronic structure that can be determined by MCD, and how this method can further our understanding of enzymatic mechanisms. Dinuclear Co(II) systems that catalyse hydrolytic reactions were selected to illustrate the approach. These systems all contain active sites with similar structures consisting of two Co(II) ions bridged by one or two carboxylates and a water or hydroxide. In most of these active sites one Co(II) is five-coordinate and one is six-coordinate, with differing binding affinities. It is shown how MCD can be used to determine which binding site--five or six-coordinate--has the greater affinity. Importantly, zero-field-splitting data and magnetic exchange coupling constants may be determined from the temperature and field dependence of MCD data. The relevance of these data to the function of the enzymatic systems is discussed.
Keiderling, Timothy A
2017-12-01
Isotope labeling has a long history in chemistry as a tool for probing structure, offering enhanced sensitivity, or enabling site selection with a wide range of spectroscopic tools. Chirality sensitive methods such as electronic circular dichroism are global structural tools and have intrinsically low resolution. Consequently, they are generally insensitive to modifications to enhance site selectivity. The use of isotope labeling to modify vibrational spectra with unique resolvable frequency shifts can provide useful site-specific sensitivity, and these methods have been recently more widely expanded in biopolymer studies. While the spectral shifts resulting from changes in isotopic mass can provide resolution of modes from specific parts of the molecule and can allow detection of local change in structure with perturbation, these shifts alone do not directly indicate structure or chirality. With vibrational circular dichroism (VCD), the shifted bands and their resultant sign patterns can be used to indicate local conformations in labeled biopolymers, particularly if multiple labels are used and if their coupling is theoretically modeled. This mini-review discusses selected examples of the use of labeling specific amides in peptides to develop local structural insight with VCD spectra. © 2017 Wiley Periodicals, Inc.
Enhanced Circular Dichroism via Symmetry Breaking in a Chiral Plasmonic Nanoparticle Oligomer
NASA Astrophysics Data System (ADS)
Le, Khai Q.
2018-02-01
A chiral plasmonic nanoparticle oligomer, consisting of four symmetrically arranged nanodisks of different heights and having different optical absorption responses to left and right-handed circularly polarized light illumination, has been experimentally reported in the literature. The resulting circular dichroism (CD) signal was detectable with state of the art CD spectrometers but was much weaker than those of existing chiral nanostructures, i.e., three-dimensional (3-D) chiral metamaterials. In this letter, via symmetry breaking in such an oligomer, the author demonstrates that the CD can be enhanced up to six times compared to that of a symmetric oligomer, and is in the range of a relevant 3-D chiral metamolecule. Through investigation of geometrical parameters including particle size, asymmetric and symmetric gaps, the CD evolution was reported, which provides a useful guideline for design of two-dimensional chiral oligomers adopted as efficient probes for CD spectroscopic applications.
Longo, Edoardo; Hussain, Rohanah; Siligardi, Giuliano
2015-03-01
Synchrotron radiation circular dichroism (SRCD) is a powerful tool for photo-stability assessment of proteins. Recently our research has been interested in applying SRCD to develop screening methodologies for accelerated photo-stability assessment of monoclonal antibody formulations. Despite it was proven to be reliable and applicable within a wide range of salts and excipients containing solutions, the presence of far-UV (<260nm) strong absorbing species (e.g., sodium chloride, histidine, arginine) in common formulations completely prevent the analysis. Herein, we propose a new method based on CD coupled with magnetic CD (MCD) to address the problem and offer an additional versatile tool for monitoring the photo-stability. This is done by assessing the stability of the samples by looking at the near-UV band, as well as giving insights in the denaturation mechanism. We applied this method to four mAbs formulations and correlated the results with dynamic light scattering data. Finally, we applied MCD in ligand interaction to key proteins such as lysozyme, comparing the human with the hen enzyme in the binding of N,N',N''-triacetylchitotriose. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.
Circular Dichroism studies on the interactions of antimicrobial peptides with bacterial cells
NASA Astrophysics Data System (ADS)
Avitabile, Concetta; D'Andrea, Luca Domenico; Romanelli, Alessandra
2014-03-01
Studying how antimicrobial peptides interact with bacterial cells is pivotal to understand their mechanism of action. In this paper we explored the use of Circular Dichroism to detect the secondary structure of two antimicrobial peptides, magainin 2 and cecropin A, with E. coli bacterial cells. The results of our studies allow us to gain two important information in the context of antimicrobial peptides- bacterial cells interactions: peptides fold mainly due to interaction with LPS, which is the main component of the Gram negative bacteria outer membrane and the time required for the folding on the bacterial cells depends on the peptide analyzed.
Probing topology by "heating": Quantized circular dichroism in ultracold atoms.
Tran, Duc Thanh; Dauphin, Alexandre; Grushin, Adolfo G; Zoller, Peter; Goldman, Nathan
2017-08-01
We reveal an intriguing manifestation of topology, which appears in the depletion rate of topological states of matter in response to an external drive. This phenomenon is presented by analyzing the response of a generic two-dimensional (2D) Chern insulator subjected to a circular time-periodic perturbation. Because of the system's chiral nature, the depletion rate is shown to depend on the orientation of the circular shake; taking the difference between the rates obtained from two opposite orientations of the drive, and integrating over a proper drive-frequency range, provides a direct measure of the topological Chern number (ν) of the populated band: This "differential integrated rate" is directly related to the strength of the driving field through the quantized coefficient η 0 = ν/ ℏ 2 , where h = 2π ℏ is Planck's constant. Contrary to the integer quantum Hall effect, this quantized response is found to be nonlinear with respect to the strength of the driving field, and it explicitly involves interband transitions. We investigate the possibility of probing this phenomenon in ultracold gases and highlight the crucial role played by edge states in this effect. We extend our results to 3D lattices, establishing a link between depletion rates and the nonlinear photogalvanic effect predicted for Weyl semimetals. The quantized circular dichroism revealed in this work designates depletion rate measurements as a universal probe for topological order in quantum matter.
Albetel, Angela-Nadia; Outten, Caryn E
2018-01-01
Monothiol glutaredoxins (Grxs) with a conserved Cys-Gly-Phe-Ser (CGFS) active site are iron-sulfur (Fe-S) cluster-binding proteins that interact with a variety of partner proteins and perform crucial roles in iron metabolism including Fe-S cluster transfer, Fe-S cluster repair, and iron signaling. Various analytical and spectroscopic methods are currently being used to monitor and characterize glutaredoxin Fe-S cluster-dependent interactions at the molecular level. The electronic, magnetic, and vibrational properties of the protein-bound Fe-S cluster provide a convenient handle to probe the structure, function, and coordination chemistry of Grx complexes. However, some limitations arise from sample preparation requirements, complexity of individual techniques, or the necessity for combining multiple methods in order to achieve a complete investigation. In this chapter, we focus on the use of UV-visible circular dichroism spectroscopy as a fast and simple initial approach for investigating glutaredoxin Fe-S cluster-dependent interactions. © 2018 Elsevier Inc. All rights reserved.
Circular Dichroism Control of Tungsten Diselenide (WSe2) Atomic Layers with Plasmonic Metamolecules.
Lin, Hsiang-Ting; Chang, Chiao-Yun; Cheng, Pi-Ju; Li, Ming-Yang; Cheng, Chia-Chin; Chang, Shu-Wei; Li, Lance L J; Chu, Chih-Wei; Wei, Pei-Kuen; Shih, Min-Hsiung
2018-05-09
Controlling circularly polarized (CP) states of light is critical to the development of functional devices for key and emerging applications such as display technology and quantum communication, and the compact circular polarization-tunable photon source is one critical element to realize the applications in the chip-scale integrated system. The atomic layers of transition metal dichalcogenides (TMDCs) exhibit intrinsic CP emissions and are potential chiroptical materials for ultrathin CP photon sources. In this work, we demonstrated CP photon sources of TMDCs with device thicknesses approximately 50 nm. CP photoluminescence from the atomic layers of tungsten diselenide (WSe 2 ) was precisely controlled with chiral metamolecules (MMs), and the optical chirality of WSe 2 was enhanced more than 4 times by integrating with the MMs. Both the enhanced and reversed circular dichroisms had been achieved. Through integrations of the novel gain material and plasmonic structure which are both low-dimensional, a compact device capable of efficiently manipulating emissions of CP photon was realized. These ultrathin devices are suitable for important applications such as the optical information technology and chip-scale biosensing.
Sono, M; Bracete, A M; Huff, A M; Ikeda-Saito, M; Dawson, J H
1991-01-01
To probe the identity of the active site heme-type prosthetic group of myeloperoxidase, whose structure has not been established unambiguously [proposed structures are (i) a chlorin (dihydroporphyrin) or (ii) a formyl-substituted porphyrin such as present in heme a], Spirographis heme (2-formyl-4-vinyldeuteroheme IX) has been incorporated into apo-myoglobin as a possible iron porphyrin model. Comparison of parallel derivatives of these two green proteins with magnetic circular dichroism spectroscopy reveals considerable similarities between several derivatives of these proteins, including the pyridine hemochromogen, the native ferric, ferrous-oxy, and ferrous-CO forms. In contrast, the magnetic circular dichroism spectra of available iron chlorin (octaethylchlorin) model complexes in analogous ligation and oxidation states do not show any significant spectral similarities to myeloperoxidase. This finding provides important evidence in favor of a formyl-substituted porphyrin as the structure of the prosthetic group macrocycle of myeloperoxidase. PMID:1662385
Emitter-site-selective photoelectron circular dichroism of trifluoromethyloxirane
Ilchen, M.; Hartmann, G.; Rupprecht, P.; ...
2017-05-30
The angle-resolved inner-shell photoionization of R-trifluoromethyloxirane, C 3H 3F 3O, is studied experimentally and theoretically. Thereby, we investigate the photoelectron circular dichroism (PECD) for nearly symmetric O 1s and F 1s electronic orbitals, which are localized on different molecular sites. The respective dichroic β 1 and angular distribution β 2 parameters are measured at the photoelectron kinetic energies from 1 to 16 eV by using variably polarized synchrotron radiation and velocity map imaging spectroscopy. The present experimental results are in good agreement with the outcome of ab initio electronic structure calculations. We report a sizable chiral asymmetry β 1 ofmore » up to about 9% for the K -shell photoionization of oxygen atom. For the individual fluorine atoms, the present calculations predict asymmetries of similar size. However, being averaged over all fluorine atoms, it drops down to about 2%, as also observed in the present experiment. Our study demonstrates a strong emitter and site sensitivity of PECD in the one-photon inner-shell ionization of this chiral molecule.« less
Circular dichroism study of the carbohydrate-modified opioid peptides
NASA Astrophysics Data System (ADS)
Horvat, Štefica; Otvos, Laszlo; Urge, Laszlo; Horvat, Jaroslav; Čudić, Mare; Varga-Defterdarović, Lidija
1999-09-01
The conformational preferences of enkephalins and the related glycoconjugates in which free or protected carbohydrate moieties were linked to the opioid peptides through an ether, ester or amide bond were investigated by circular dichroism spectroscopy in water, trifluoroethanol and water-trifluoroethanol mixtures. The analysis of the spectra revealed that the conformation of the enkephalin molecule is very sensitive to slight changes in the peptide structure around the C-terminal region. It was found that the type II β-turn structures are populated in N-terminal tetrapeptide enkephalin fragment, while leucine-enkephalin amide feature a type I (III) β-turn structure in solution. Incorporation of the sugar moiety into opioid peptide compound did not significantly influence the overall conformation of the peptide backbone, although minor intensity changes may reflect shifts in the population of the different turn systems. These small structural alterations can be responsible for the receptor-subtype selectivity of the various carbohydrate-modified enkephalin analogs.
Enhanced Circular Dichroism of Gold Bilayered Slit Arrays Embedded with Rectangular Holes.
Zhang, Hao; Wang, Yongkai; Luo, Lina; Wang, Haiqing; Zhang, Zhongyue
2017-01-01
Gold bilayered slit arrays with rectangular holes embedded into the metal surface are designed to enhance the circular dichroism (CD) effect of gold bilayered slit arrays. The rectangular holes in these arrays block electric currents and generate localized surface plasmons around these holes, thereby strengthening the CD effect. The CD enhancement factor depends strongly on the rotational angle and the structural parameters of the rectangular holes; this factor can be enhanced further by drilling two additional rectangular holes into the metal surfaces of the arrays. These results help facilitate the design of chiral structures to produce a strong CD effect and large electric fields.
Goodman, Thomas C.; Hardies, Stephen C.; Cortez, Carlos; Hillen, Wolfgang
1981-01-01
Computer programs are described that direct the collection, processing, and graphical display of numerical data obtained from high resolution thermal denaturation (1-3) and circular dichroism (4) studies. Besides these specific applications, the programs may also be useful, either directly or as programming models, in other types of spectrophotometric studies employing computers, programming languages, or instruments similar to those described here (see Materials and Methods). PMID:7335498
NASA Astrophysics Data System (ADS)
Bettinger, J. S.; Piamonteze, C.; Chopdekar, R. V.; Liberati, M.; Arenholz, E.; Suzuki, Y.
2009-10-01
We have used x-ray magnetic circular dichroism (XMCD) in conjunction with multiplet simulations to directly probe the origin of photomagnetism in nanocrystalline (Mn,Zn,Fe)3O4 . A photomagnetic effect at room temperature has been observed in these films with HeNe illumination. We have verified an intervalence charge transfer among octahedral Fe cations to account for the increase in magnetization observed at and above room temperature in small magnetic fields. Using XMCD, we demonstrate that the dichroism of Fe in octahedral sites increases by 18% at room temperature, while the dichroism of Fe in tetrahedral sites does not change.
Magnetic properties of Co/Rh (001) multilayers studied by x-ray magnetic-circular dichroism
NASA Astrophysics Data System (ADS)
Tomaz, M. A.; Mayo, E.; Lederman, D.; Hallin, E.; Sham, T. K.; O'brien, W. L.; Harp, G. R.
1998-11-01
The layer-averaged magnetic moments of Co and Rh have been measured in sputter deposited Co/Rh (001) multilayer thin films using the x-ray magnetic circular dichroism. The Rh moments were measured at both the L and M absorption edges, where we find that the Rh moment decreases as a function of increasing Rh layer thickness (tRh). The decline of the layer-averaged Rh moment is well described in terms of a simple dilution, implying that the Rh moment is confined to the interfacial region. We find that the Co moment remains largely unaffected, maintaining a bulklike value of 1.7μB in the region preceding the first antiferromagnetic coupling peak where tRh ranges from 0 to 4 Å. We also find, via application of the dichroism sum rules, that the ratio
Dai, Peng; Jiang, Nan; Tan, Ren-Xiang
2016-01-01
Elucidation of absolute configuration of chiral molecules including structurally complex natural products remains a challenging problem in organic chemistry. A reliable method for assigning the absolute stereostructure is to combine the experimental circular dichroism (CD) techniques such as electronic and vibrational CD (ECD and VCD), with quantum mechanics (QM) ECD and VCD calculations. The traditional QM methods as well as their continuing developments make them more applicable with accuracy. Taking some chiral natural products with diverse conformations as examples, this review describes the basic concepts and new developments of QM approaches for ECD and VCD calculations in solution and solid states.
Probing topology by “heating”: Quantized circular dichroism in ultracold atoms
Tran, Duc Thanh; Dauphin, Alexandre; Grushin, Adolfo G.; Zoller, Peter; Goldman, Nathan
2017-01-01
We reveal an intriguing manifestation of topology, which appears in the depletion rate of topological states of matter in response to an external drive. This phenomenon is presented by analyzing the response of a generic two-dimensional (2D) Chern insulator subjected to a circular time-periodic perturbation. Because of the system’s chiral nature, the depletion rate is shown to depend on the orientation of the circular shake; taking the difference between the rates obtained from two opposite orientations of the drive, and integrating over a proper drive-frequency range, provides a direct measure of the topological Chern number (ν) of the populated band: This “differential integrated rate” is directly related to the strength of the driving field through the quantized coefficient η0 = ν/ℏ2, where h = 2π ℏ is Planck’s constant. Contrary to the integer quantum Hall effect, this quantized response is found to be nonlinear with respect to the strength of the driving field, and it explicitly involves interband transitions. We investigate the possibility of probing this phenomenon in ultracold gases and highlight the crucial role played by edge states in this effect. We extend our results to 3D lattices, establishing a link between depletion rates and the nonlinear photogalvanic effect predicted for Weyl semimetals. The quantized circular dichroism revealed in this work designates depletion rate measurements as a universal probe for topological order in quantum matter. PMID:28835930
NASA Astrophysics Data System (ADS)
Kuzmenko, Alexey B.
We measure broadband far-infrared magneto-optical conductivity spectra of pure bismuth separately for left- and right-handed circular polarizations in magnetic fields up to 7 T that allows us to obtain the magnetic circular dichroism (MCD). Thanks to a high spectral resolution we distinguish the Landau level (LL) transitions in the Dirac-like electron and the parabolic hole bands. The hole transitions exhibit a full (100%) MCD as is indeed expected for a circular cyclotron orbit. However, the MCD for electron-pocket transitions is reduced to only 13 +/-1%. This strong suppression can be attributed to the huge effective-mass anisotropy ( 200) in the electron pockets and can be generally interpreted as a signature of the mismatch between the spatial metric experienced by the photons and the electrons. An important consequence of this observation is that the magneto-absorption in bismuth is highly valley sensitive, which paves the way to future valleytronic applications in materials with a strong effective-mass anisotropy.
Enhancement of magnetic circular dichroism in bi-layered ZnO-Bi:YIG thin films
NASA Astrophysics Data System (ADS)
Mito, Shinichiro; Shiotsu, Yusaku; Sasano, Junji; Takagi, Hiroyuki; Inoue, Mitsuteru
2017-05-01
Bi-layered zinc oxide (ZnO) and bismuth substituted yttrium iron garnet (Bi:YIG) was fabricated and magneto-optically investigated. Enhancement of Faraday rotation and magnetic circular dichroism (MCD) was observed. The wavelength of MCD enhancement was in good agreement with exciton wavelength of ZnO. This enhancement was only observed in the bi-layer, and implies that the exciton generated in ZnO interacted with Bi:YIG. Because the exciton wavelength of ZnO can be controlled by electro-optic effect, this result has the potential for realizing voltage control of magneto-optic effect.
NASA Astrophysics Data System (ADS)
Matsui, Fumihiko; Matsushita, Tomohiro; Daimon, Hiroshi
2018-06-01
The local atomic structure around a specific element atom can be recorded as a photoelectron diffraction pattern. Forward focusing peaks and diffraction rings around them indicate the directions and distances from the photoelectron emitting atom to the surrounding atoms. The state-of-the-art holography reconstruction algorithm enables us to image the local atomic arrangement around the excited atom in a real space. By using circularly polarized light as an excitation source, the angular momentum transfer from the light to the photoelectron induces parallax shifts in these diffraction patterns. As a result, stereographic images of atomic arrangements are obtained. These diffraction patterns can be used as atomic-site-resolved probes for local electronic structure investigation in combination with spectroscopy techniques. Direct three-dimensional atomic structure visualization and site-specific electronic property analysis methods are reviewed. Furthermore, circular dichroism was also found in valence photoelectron and Auger electron diffraction patterns. The investigation of these new phenomena provides hints for the development of new techniques for local structure probing.
Intrinsic transmission magnetic circular dichroism spectra of GaMnAs
NASA Astrophysics Data System (ADS)
Terada, Hiroshi; Ohya, Shinobu; Tanaka, Masaaki
2018-03-01
Transmission magnetic circular dichroism (MCD) spectroscopy has been widely used to reveal the spin-dependent band structure of ferromagnetic semiconductors. In these previous studies, some band pictures have been proposed from the spectral shapes observed in transmission MCD; however, extrinsic signals originating from optical interference have not been appropriately considered. In this study, we calculate the MCD spectra taking into account the optical interference of the layered structure of samples and show that the spectral shape of MCD is strongly influenced by optical interference. To correctly understand the transmission MCD, we also calculate the intrinsic MCD spectra of GaMnAs that are not influenced by the optical interference. The spectral shape of the intrinsic MCD can be explained by the characteristic band structure of GaMnAs, that is, the spin-polarized valence band and the impurity band existing above the valence band top.
Stephens, P J; McCann, D M; Devlin, F J; Smith, A B
2006-07-01
The determination of the absolute configurations (ACs) of chiral molecules using the chiroptical techniques of optical rotation (OR), electronic circular dichroism (ECD), and vibrational circular dichroism (VCD) has been revolutionized by the development of density functional theory (DFT) methods for the prediction of these properties. Here, we demonstrate the significance of these advances for the stereochemical characterization of natural products. Time-dependent DFT (TDDFT) calculations of the specific rotations, [alpha](D), of four cytotoxic natural products, quadrone (1), suberosenone (2), suberosanone (3), and suberosenol A acetate (4), are used to assign their ACs. TDDFT calculations of the ECD of 1 are used to assign its AC. The VCD spectrum of 1 is reported and also used, together with DFT calculations, to assign its AC. The ACs of 1 derived from its [alpha](D), ECD, and VCD are identical and in agreement with the AC previously determined via total synthesis. The previously undetermined ACs of 2-4, derived from their [alpha](D) values, have absolute configurations of their tricyclic cores identical to that of 1. Further studies of the ACs of these molecules using ECD and, especially, VCD are recommended to establish more definitively this finding. Our studies of the OR, ECD, and VCD of quadrone are the first to utilize DFT calculations of all three properties for the determination of the AC of a chiral natural product molecule.
NASA Astrophysics Data System (ADS)
Valencia, Israel; Ávila-Torres, Yenny; Barba-Behrens, Norah; Garzón, Ignacio L.
2015-04-01
Studies on the physicochemical properties of biomimetic compounds of multicopper oxidases are fundamental to understand their reaction mechanisms and catalytic behavior. In this work, electronic, optical, and chiroptical properties of copper(II) complexes with amino-alcohol chiral ligands are theoretically studied by means of time-dependent density functional theory. The calculated absorption and circular dichroism spectra are compared with experimental measurements of these spectra for an uncoordinated pseudoephedrine derivative, as well as for the corresponding mononuclear and trinuclear copper(II)-coordinated complexes. This comparison is useful to gain insights into their electronic structure, optical absorption and optical activity. The optical absorption and circular dichroism bands of the pseudoephedrine derivative are located in the UV-region. They are mainly due to transitions originated from n to π anti-bonding orbitals of the alcohol and amino groups, as well as from π bonding to π anti-bonding orbitals of carboxyl and phenyl groups. In the case of the mononuclear and trinuclear compounds, additional signals in the visible spectral region are present. In both systems, the origin of these bands is due to charge transfer from ligand to metal and d-d transitions.
Fe/Rh (100) multilayer magnetism probed by x-ray magnetic circular dichroism
NASA Astrophysics Data System (ADS)
Tomaz, M. A.; Ingram, D. C.; Harp, G. R.; Lederman, D.; Mayo, E.; O'brien, W. L.
1997-09-01
We report the layer-averaged magnetic moments of both Fe and Rh in sputtered Fe/Rh (100) multilayer thin films as measured by x-ray magnetic circular dichroism. We observe two distinct regimes in these films. The first is characterized by Rh moments of at least 1μB, Fe moments enhanced as much as 30% above bulk, and a bct crystal structure. The second regime is distinguished by sharp declines of both Fe and Rh moments accompanied by a transition to an fct crystal lattice. The demarcation between the two regions is identified as the layer thickness for which both bct and fct phases first coexist, which we term the critical thickness tcrit. We attribute the change in magnetic behavior to the structural transformation.
Relativistic effects on magnetic circular dichroism studied by GUHF/SECI method
NASA Astrophysics Data System (ADS)
Honda, Y.; Hada, M.; Ehara, M.; Nakatsuji, H.; Downing, J.; Michl, J.
2002-04-01
Quasi-relativistic formulation of the Magnetic circular dichroism (MCD) Faraday terms are presented using the generalized unrestricted Hartree-Fock (GUHF)/single excitation configuration interaction (SECI) method combined with the finite perturbation method and applied to the MCD of the three n-σ ∗ states ( 3Q1, 3Q0, 1Q1) of CH 3I. The Faraday B term for the 1Q1 state was 0.1976( Debye) 2( Bohr magneton )/(10 3 cm-1) in the non-relativistic theory, but was dramatically improved by the relativistic effect and became 0.0184 in agreement with the experimental values, 0.014 and 0.0257. This change was mainly due to the one-electron spin-orbit (SO1) term rather than the spin-free relativistic (SFR) and the two-electron spin-orbit (SO2) terms.
NASA Astrophysics Data System (ADS)
Liu, Wei-Chun; Lo, Yu-Lung; Phan, Quoc-Hung
2018-03-01
A method is proposed for extracting the circular birefringence (CB), circular dichroism (CD) and depolarization (Dep) properties of optical scattering samples using an amplitude-modulation polarimetry technique. The validity of the proposed method is demonstrated by extracting the CB property of pure glucose aqueous samples, the CB/Dep properties of glucose solutions containing 0.02% lipofundin particles, and the CD/Dep properties of chlorophyllin solutions containing suspended polystyrene microspheres. The results show that the proposed technique has the ability to detect pure glucose with a resolution of 66 mg/dL over a concentration range of 0-500 mg/dL. Moreover, the glucose concentration of the CB/Dep samples can be detected over the same range with a resolution of 168 mg/dL. Finally, the chlorophyllin concentration of the CD/Dep sample can be detected over the range of 0-200 μg/dL with a resolution of 6.5 × 10-5. In general, the results show that the proposed technique provides a reliable and accurate means of measuring the CB/CD properties of optical samples with scattering effects, and thus has significant potential for biological sensing applications.
NASA Astrophysics Data System (ADS)
Baǧda, Efkan; Baǧda, Esra; Yabaş, Ebru
2017-01-01
In the present study, interaction of a double-decker phthalocyanine with two G-quadruplex DNA, Tel 21 and cMYC, was investigated. To the best of our knowledge, this is the first study about G-quadruplex-double decker phthalocyanine interaction. The spectrophotometric titration method was used for binding constant calculations. From the binding constants, it can be said that double-decker phthalocyanine more likely to bind Tel 21 rather than cMYC. The conformational changes upon binding were monitored via circular dichroism spectroscopy. The ethidium bromide replacement assay was investigated spectrofluorometrically.
Theoretical Investigation of Single-Molecule Sensing Using Nanotube-Enhanced Circular Dichroism.
Silva, Jaime; Milne, Bruce F; Nogueira, Fernando
2018-06-19
First-principles calculations have been used to investigate the potential use of circular dichroism (CD) spectroscopy in single-molecule sensing. Using a real-space implementation of time-dependent density functional theory (TDDFT), several systems involving single-walled carbon nanotubes (SWCNT) and small molecules have been studied to evaluate their CD response. Large induced CD (ICD) effects, differing for each test molecule, were observed in all SWCNT-molecule complexes. As the SWCNT used in this study shows no intrinsic CD response, the ICD spectra are the result of interaction with the small molecules. This finding is general and independent of the (a)chiral nature of the adsorbed molecule. Our results indicate that it is possible to design a system that uses SWCNT for detection of molecules using the change in CD spectrum of the system induced by adsorption of the molecule onto the SWCNT surface.
Hu, Li; Tian, Xiaorui; Huang, Yingzhou; Fang, Liang; Fang, Yurui
2016-02-14
Plasmonic chirality has drawn much attention because of tunable circular dichroism (CD) and the enhancement for chiral molecule signals. Although various mechanisms have been proposed to explain the plasmonic CD, a quantitative explanation like the ab initio mechanism for chiral molecules, is still unavailable. In this study, a mechanism similar to the mechanisms associated with chiral molecules was analyzed. The giant extrinsic circular dichroism of a plasmonic splitting rectangle ring was quantitatively investigated from a theoretical standpoint. The interplay of the electric and magnetic modes of the meta-structure is proposed to explain the giant CD. We analyzed the interplay using both an analytical coupled electric-magnetic dipole model and a finite element method model. The surface charge distributions showed that the circular current yielded by the splitting rectangle ring causes the ring to behave like a magneton at some resonant modes, which then interact with the electric modes, resulting in a mixing of the two types of modes. The strong interplay of the two mode types is primarily responsible for the giant CD. The analysis of the chiral near-field of the structure shows potential applications for chiral molecule sensing.
Xi, Jia-Fu; Tang, Lei; Zhang, Jian-Hua; Zhang, Hong-Jian; Chen, Xu-Sheng; Mao, Zhong-Gui
2014-11-01
Circular dichroism (CD) is a special absorption spectrum. The secondary structure of protein such as α-helix, β-sheet and β-turn in the far ultraviolet region (190-250 nm) has a characteristic CD spectrum. In order to understand the activity and structural changes of ascorbate peroxidase from Chinese kale (BaAPX) during denaturation, specific activity and percentage of secondary structure of BaAPX under different time, temperature and concentration were analyzed by CD dynamically. In addition, the percentage of four secondary structures in BaAPX was calculated by CD analysis software Dichroweb. The results show that BaAPX is a full α-type enzyme whose specific activity is positively related to the percentage of α-helix. During denaturation of BaAPX, three kinds of structural changes were proposed: the one-step structural change from initial state (N state) to minimum state of α-helix (R state) under low concentration and low temperature; the one-step structural change from N state to equilibrium state (T state) under high concentration and low temperature; the two-step structural changes from N state through R state to final T state under heat treatment and low temperature renaturation.
NASA Astrophysics Data System (ADS)
Hu, Li; Huang, Yingzhou; Fang, Liang; Chen, Guo; Wei, Hua; Fang, Yurui
2015-11-01
In this work, the circular dichroisms (CD) of nanorice heterodimers consisting of two parallel arranged nanorices with the same size but different materials are investigated theoretically. Symmetry-breaking is introduced by using different materials and oblique incidence to achieve strong CD at the vicinity of Fano resonance peaks. We demonstrate that all Au-Ag heterodimers exhibit multipolar Fano resonances and strong CD effect. A simple quantitative analysis shows that the structure with larger Fano asymmetry factor has stronger CD. The intensity and peak positions of the CD effect can be flexibly tuned in a large range by changing particle size, shape, the inter-particle distance and surroundings. Furthermore, CD spectra exhibit high sensitivity to ambient medium in visible and near infrared regions. Our results here are beneficial for the design and application of high sensitive CD sensors and other related fields.
Chirality sensing of bioactive compounds with amino alcohol unit via circular dichroism.
Górecki, Marcin; Groszek, Grażyna; Frelek, Jadwiga
2017-10-01
The aim of the present work was to test various chiroptical techniques, including in particular the in situ dirhodium methodology, to assign the absolute configuration of 1,2- and 1,3-amino alcohols. As models, we selected mainly compounds that have both an additional strongly absorbing and interfering chromophoric system and application in medicinal chemistry. Determination of the absolute configuration (AC) of the tested molecules such as cinchona alkaloids, Tamiflu, and others was carried out using a combination of electronic and vibrational circular dichroism (ECD, VCD) spectroscopy. It has been demonstrated that both 1,2- and 1,3-aminol moieties are subject to the same sector rule correlating stereostructure of formed Rh 2 -complex with chiroptical properties, and that the changes in the position of the stereogenic center do not affect its proper use. © 2017 Wiley Periodicals, Inc.
Hebenstreit, D; Ferreira, F
2005-09-01
Several studies showed that calcium-binding proteins have a fixed place in the spectrum of allergenic substances. Often the binding of a calcium ion induces conformational changes and affects immunoglobulin E-binding to the allergen. Hence, the quantitative characterization of the binding to calcium is of importance to understand both the biologic and allergenic activity of these proteins. In the present study we describe a procedure for determining the stoichiometry and dissociation constant (K(D)) of calcium-binding allergens using circular dichroism (CD) techniques. For the experiments, we used recombinant Bet v 4, a two EF-hand allergen from birch pollen. Solutions of Bet v 4 were titrated with calcium and the change in molar ellipticity at 222 nm was monitored with a CD spectropolarimeter. The determination of the binding stoichiometry as well as of the K(D) for one EF-hand (4 microM) demonstrated the applicability of the method. CD-monitored calcium-titration of protein solutions represents a fast and easy method for determining the binding characteristics of calcium-binding allergens.
NASA Astrophysics Data System (ADS)
Lee, Kyung-Koo; Joo, Cheonik; Yang, Seongeun; Han, Hogyu; Cho, Minhaeng
2007-06-01
The phosphorylation effect on the small peptide conformation in water has not been clearly understood yet, despite the widely acknowledged notion that control of protein activity by phosphorylation works mainly by inducing conformational change. To elucidate the detailed mechanism, we performed infrared (IR) absorption and vibrational and electronic circular dichroism studies of both unphosphorylated and phosphorylated tetrapeptides, GSSS 1 and GSSpS 2. The solution structure of the tetrapeptide is found to be little dependent on the presence of the neutral or negatively charged phosphoryl group, and to be a mixture of extended structures including polyproline II (PII) and β-sheet conformations. The additional band at 1598cm-1 in the amide I IR spectrum of the phosphorylated peptide GSSpS at neutral pD appears to be clear spectroscopic evidence for direct intramolecular hydrogen-bonding interaction between the side chain dianionic phosphoryl group and the backbone amide proton. On the basis of amide I IR band analyses, the authors found that the probability of finding the phosphoryl group strongly H bonded to the backbone proton in GSSpS is about 43% at pD 7.0 and 37°C. Such a H-bonding interaction in GSSpS has the biological standard enthalpy and entropy of -15.1kJ /mol and -51.2J/Kmol, respectively. Comparisons between the experimentally measured IR and VCD spectra and the numerically simulated ones suggested that the currently available force field parameters need to be properly modified. The results in this paper may shed light on an unknown mechanism of controlling the peptide conformation by phosphorylation.
NASA Astrophysics Data System (ADS)
Shen, Jian; Magesh, Sadagopan; Chen, Lin; Hu, Longqin; He, Yanan
2018-03-01
LH601A is a novel non-reactive chiral molecule inhibiting Keap1-Nrf2 protein-protein interaction. The absolute configuration (AC) was independently determined in this study using vibrational circular dichroism (VCD) spectroscopy. Because of band overlapping and broadening in the IR spectrum, a direct VCD spectrum comparison method is devised without the conventional IR band alignment. Being an unbiased AC inquiry, all possible chiralities are evaluated based on the statistical analysis of VCD similarity, Sv. The AC of three-center stereoisomer LH601A is unambiguously assigned to (S,R,S). A comparative study was also carried out to investigate the structural and energy differences of calculated conformers using the polarized continuum model of dimethyl sulfoxide.
Direct surface magnetometry with photoemission magnetic x-ray dichroism
DOE Office of Scientific and Technical Information (OSTI.GOV)
Tobin, J.G.; Goodman, K.W.; Schumann, F.O.
1997-04-01
Element specific surface magnetometry remains a central goal of synchrotron radiation based studies of nanomagnetic structures. One appealing possibility is the combination of x-ray absorption dichroism measurements and the theoretical framework provided by the {open_quotes}sum rules.{close_quotes} Unfortunately, sum rule analysis are hampered by several limitations including delocalization of the final state, multi-electronic phenomena and the presence of surface dipoles. An alternative experiment, Magnetic X-Ray Dichroism in Photoelectron Spectroscopy, holds out promise based upon its elemental specificity, surface sensitivity and high resolution. Computational simulations by Tamura et al. demonstrated the relationship between exchange and spin orbit splittings and experimental data ofmore » linear and circular dichroisms. Now the authors have developed an analytical framework which allows for the direct extraction of core level exchange splittings from circular and linear dichroic photoemission data. By extending a model initially proposed by Venus, it is possible to show a linear relation between normalized dichroism peaks in the experimental data and the underlying exchange splitting. Since it is reasonable to expect that exchange splittings and magnetic moments track together, this measurement thus becomes a powerful new tool for direct surface magnetometry, without recourse to time consuming and difficult spectral simulations. The theoretical derivation will be supported by high resolution linear and circular dichroism data collected at the Spectromicroscopy Facility of the Advanced Light Source.« less
Goyal, Megha; Chaudhuri, Tapan K; Kuwajima, Kunihiro
2014-01-01
Thermal denaturation of Escherichia coli maltodextrin glucosidase was studied by differential scanning calorimetry, circular dichroism (230 nm), and UV-absorption measurements (340 nm), which were respectively used to monitor heat absorption, conformational unfolding, and the production of solution turbidity. The denaturation was irreversible, and the thermal transition recorded at scan rates of 0.5-1.5 K/min was significantly scan-rate dependent, indicating that the thermal denaturation was kinetically controlled. The absence of a protein-concentration effect on the thermal transition indicated that the denaturation was rate-limited by a mono-molecular process. From the analysis of the calorimetric thermograms, a one-step irreversible model well represented the thermal denaturation of the protein. The calorimetrically observed thermal transitions showed excellent coincidence with the turbidity transitions monitored by UV-absorption as well as with the unfolding transitions monitored by circular dichroism. The thermal denaturation of the protein was thus rate-limited by conformational unfolding, which was followed by a rapid irreversible formation of aggregates that produced the solution turbidity. It is thus important to note that the absence of the protein-concentration effect on the irreversible thermal denaturation does not necessarily means the absence of protein aggregation itself. The turbidity measurements together with differential scanning calorimetry in the irreversible thermal denaturation of the protein provided a very effective approach for understanding the mechanisms of the irreversible denaturation. The Arrhenius-equation parameters obtained from analysis of the thermal denaturation were compared with those of other proteins that have been reported to show the one-step irreversible thermal denaturation. Maltodextrin glucosidase had sufficiently high kinetic stability with a half-life of 68 days at a physiological temperature (37°C).
ERIC Educational Resources Information Center
Yakubu, Abdallah; Suzuki, Takayoshi; Kita, Masakazu
2017-01-01
This paper describes the development of a simple magnetic circular dichroism (MCD) apparatus from a wood base and neodymium magnets and its configuration in the Faraday alignment. The applicability and effectiveness of the apparatus for MCD spectra measurements have been examined. The apparatus was used by undergraduate students to conduct MCD…
DOE Office of Scientific and Technical Information (OSTI.GOV)
Zsila, Ferenc; Gedeon, Gabor
2006-08-11
The polyanionic glycosaminoglycans (GAGs) are intimately involved in the pathogenesis of protein conformational disorders such as amyloidosis and prion diseases. Several cationic agents are known to exhibit anti-prion activity but their mechanism of action is poorly understood. In this study, UV absorption and circular dichroism (CD) spectroscopic techniques were used to investigate the interaction between heparin and chondroitin-6-sulfate and anti-prion drugs including acridine, quinoline, and phenothiazine derivatives. UV band hypochromism of ({+-})-quinacrine, ({+-})-primaquine, tacrine, quinidine, chlorpromazine, and induced CD spectra of ({+-})-quinacrine upon addition of GAGs provided evidence for the GAG binding of these compounds. The association constants ({approx}10{sup 6}-10{supmore » 7} M{sup -1}) estimated from the UV titration curves show high-affinity drug-heparin interactions. Ionic strength-dependence of the absorption spectra suggested that the interaction between GAGs and the cationic drugs is principally electrostatic in nature. Drug binding differences of heparin and chondroitin-6-sulfate were attributed to their different negative charge density. These results call the attention to the alteration of GAG-prion/GAG-amyloid interactions by which these compounds might exert their anti-prion/anti-amyloidogenic activities.« less
Atomic moments in Mn 2CoAl thin films analyzed by X-ray magnetic circular dichroism
Jamer, M. E.; Assaf, B. A.; Sterbinsky, G. E.; ...
2014-12-05
Spin gapless semiconductors are known to be strongly affected by structural disorder when grown epitaxially as thin films. The magnetic properties of Mn 2CoAl thin films grown on GaAs (001) substrates are investigated here as a function of annealing. This study investigates the atomic-specific magnetic moments of Mn and Co atoms measured through X-ray magnetic circular dichroism as a function of annealing and the consequent structural ordering. Results indicate that the structural distortion mainly affects the Mn atoms as seen by the reduction of the magnetic moment from its predicted value.
Daidone, Isabella; Magliano, Alessandro; Di Nola, Alfredo; Mignogna, Giuseppina; Clarkson, Matilda Manuela; Lizzi, Anna Rita; Oratore, Arduino; Mazza, Fernando
2011-04-01
Lactoferricins are potent antimicrobial peptides released by pepsin cleavage of Lactoferrins. Bovine Lactoferricin (LfcinB) has higher activity than the intact bovine Lactoferrin, and is the most active among the other Lactoferricins of human, murine and caprine origin. In the intact protein the fragment corresponding to LfcinB is in an helical conformation, while in water LfcinB adopts an amphipathic β-hairpin structure. However, whether any of these structural motifs is the antibacterial active conformation, i.e., the one interacting with bacterial membrane components, remains to be seen. Here we present Circular Dichroism (CD) spectra and Molecular Dynamics (MD) simulations indicating that in membrane-mimicking solvents the LfcinB adopts an amphipathic β-hairpin structure similar to that observed in water, but differing in the dynamic behavior of the side-chains of the two tryptophan residues. In the membrane-mimicking solvent these side-chains show a high propensity to point towards the hydrophobic environment, rather than being in the hydrophobic core as seen in water, while the backbone preserves the hairpin conformation as found in water. These results suggest that the tryptophans might act as anchors pulling the stable, solvent-invariant hairpin structure into the membrane.
Cukras, Janusz; Kauczor, Joanna; Norman, Patrick; Rizzo, Antonio; Rikken, Geert L J A; Coriani, Sonia
2016-05-21
A computational protocol for magneto-chiral dichroism and magneto-chiral birefringence dispersion is presented within the framework of damped response theory, also known as complex polarization propagator theory, at the level of time-dependent Hartree-Fock and time-dependent density functional theory. Magneto-chiral dichroism and magneto-chiral birefringence spectra in the (resonant) frequency region below the first ionization threshold of R-methyloxirane and l-alanine are presented and compared with the corresponding results obtained for both the electronic circular dichroism and the magnetic circular dichroism. The additional information content yielded by the magneto-chiral phenomena, as well as their potential experimental detectability for the selected species, is discussed.
Phan, Quoc-Hung; Lo, Yu-Lung
2017-04-01
A surface plasmon resonance (SPR)-enhanced method is proposed for measuring the circular dichroism (CD), circular birefringence (CB), and degree of polarization (DOP) of turbid media using a Stokes–Mueller matrix polarimetry technique. The validity of the analytical model is confirmed by means of numerical simulations. The simulation results show that the proposed detection method enables the CD and CB properties to be measured with a resolution of 10 ? 4 refractive index unit (RIU) and 10 ? 5 ?? RIU , respectively, for refractive indices in the range of 1.3 to 1.4. The practical feasibility of the proposed method is demonstrated by detecting the CB/CD/DOP properties of glucose–chlorophyllin compound samples containing polystyrene microspheres. It is shown that the extracted CB value decreases linearly with the glucose concentration, while the extracted CD value increases linearly with the chlorophyllin concentration. However, the DOP is insensitive to both the glucose concentration and the chlorophyllin concentration. Consequently, the potential of the proposed SPR-enhanced Stokes–Mueller matrix polarimetry method for high-resolution CB/CD/DOP detection is confirmed. Notably, in contrast to conventional SPR techniques designed to detect relative refractive index changes, the SPR technique proposed in the present study allows absolute measurements of the optical properties (CB/CD/DOP) to be obtained.
On the magnetic circular dichroism of benzene. A density-functional study
NASA Astrophysics Data System (ADS)
Kaminský, Jakub; Kříž, Jan; Bouř, Petr
2017-04-01
Spectroscopy of magnetic circular dichroism (MCD) provides enhanced information on molecular structure and a more reliable assignment of spectral bands than absorption alone. Theoretical modeling can significantly enhance the information obtained from experimental spectra. In the present study, the time dependent density functional theory is employed to model the lowest-energy benzene transitions, in particular to investigate the role of the Rydberg states and vibrational interference in spectral intensities. The effect of solvent is explored on model benzene-methane clusters. For the lowest-energy excitation, the vibrational sub-structure of absorption and MCD spectra is modeled within the harmonic approximation, providing a very good agreement with the experiment. The simulations demonstrate that the Rydberg states have a much stronger effect on the MCD intensities than on the absorption, and a very diffuse basis set must be used to obtain reliable results. The modeling also indicates that the Rydberg-like states and associated transitions may persist in solutions. Continuum-like solvent models are thus not suitable for their modeling; solvent-solute clusters appear to be more appropriate, providing they are large enough.
Goyal, Megha; Chaudhuri, Tapan K.; Kuwajima, Kunihiro
2014-01-01
Thermal denaturation of Escherichia coli maltodextrin glucosidase was studied by differential scanning calorimetry, circular dichroism (230 nm), and UV-absorption measurements (340 nm), which were respectively used to monitor heat absorption, conformational unfolding, and the production of solution turbidity. The denaturation was irreversible, and the thermal transition recorded at scan rates of 0.5–1.5 K/min was significantly scan-rate dependent, indicating that the thermal denaturation was kinetically controlled. The absence of a protein-concentration effect on the thermal transition indicated that the denaturation was rate-limited by a mono-molecular process. From the analysis of the calorimetric thermograms, a one-step irreversible model well represented the thermal denaturation of the protein. The calorimetrically observed thermal transitions showed excellent coincidence with the turbidity transitions monitored by UV-absorption as well as with the unfolding transitions monitored by circular dichroism. The thermal denaturation of the protein was thus rate-limited by conformational unfolding, which was followed by a rapid irreversible formation of aggregates that produced the solution turbidity. It is thus important to note that the absence of the protein-concentration effect on the irreversible thermal denaturation does not necessarily means the absence of protein aggregation itself. The turbidity measurements together with differential scanning calorimetry in the irreversible thermal denaturation of the protein provided a very effective approach for understanding the mechanisms of the irreversible denaturation. The Arrhenius-equation parameters obtained from analysis of the thermal denaturation were compared with those of other proteins that have been reported to show the one-step irreversible thermal denaturation. Maltodextrin glucosidase had sufficiently high kinetic stability with a half-life of 68 days at a physiological temperature (37°C). PMID
Zhekova, Hristina R; Seth, Michael; Ziegler, Tom
2010-06-03
The excitation, circular dichroism, magnetic circular dichroism (MCD) and electron paramagnetic resonance (EPR) spectra of small models of four blue copper proteins are simulated on the TDDFT/BP86 level. X-Ray diffraction geometries are used for the modeling of the blue copper sites in azurin, plastocyanin, cucumber basic protein, and nitrite reductase. Comparison with experimental data reveals that the calculations reproduce most of the qualitative trends of the observed experimental spectra with some discrepancies in the orbital decompositions and the values of the excitation energies, the g( parallel) components of the g tensor, and the components of the A tensor. These discrepancies are discussed relative to deficiencies in the time-dependent density functional theory (TDDFT) methodology, as opposed to previous studies which address them as a result of insufficient model size or poor performance of the BP86 functional. In addition, attempts are made to elucidate the correlation between the MCD and EPR signals.
Titze, Katharina; Zollitsch, Tilo; Heiz, Ulrich; Boesl, Ulrich
2014-09-15
An experiment on chiral molecules that combines circular dichroism (CD) spectroscopy, mass-selective detection by laser mass spectrometry (MS), and cooling of molecules by using a supersonic beam is presented. The combination of the former two techniques (CD-laser-MS) is a new method to investigate chiral molecules and is now used by several research groups. Cooling in a supersonic beam supplies a substantial increase in spectroscopic resolution, a feature that has not yet been used in CD spectroscopy. In the experiments reported herein, a large variation in the electronic CD of carbonyl 3-methylcyclopentanone was observed depending on the excited vibrational modes in the n → π* transition. This finding should be of interest for the detection of chiral molecules and for the theoretical understanding of the CD of vibronic bands. It is expected that this effect will show up in other chiral carbonyls because the n → π* transition is typical for the carbonyl group. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
NASA Astrophysics Data System (ADS)
Kadhane, Umesh; Holm, Anne I. S.; Hoffmann, Søren Vrønning; Nielsen, Steen Brøndsted
2008-02-01
Circular dichroism (CD) experiments on DNA single strands (dAn) at the ASTRID synchrotron radiation facility reveal that eight adenine (A) bases electronically couple upon 190nm excitation. After n=8 , the CD signal increases linearly with n with a slope equal to the sum of the coupling terms. Nearest neighbor interactions account for only 24% of the CD signal whereas electronic communication is limited to nearest neighbors for two other exciton bands observed at 218 and 251nm (i.e., dimer excited states). Electronic coupling between bases in DNA is important for nonradiative deexcitation of electronically excited states since the hazardous energy is spread over a larger spatial region.
Krief, Alain; Dunkle, Melissa; Bahar, Masoud; Bultinck, Patrick; Herrebout, Wouter; Sandra, Pat
2015-07-01
The absolute configuration of rhizopine, an opine-like natural product present in nitrogen-fixing nodules of alfalfa infected by rhizobia, is elucidated using a combination of state-of-the-art analytical and semi-preparative supercritical fluid chromatography and vibrational circular dichroism spectroscopy. A synthetic peracetylated racemate was fractionated into its enantiomers and subjected to absolute configuration analysis revealing that natural rhizopine exists as a single enantiomer. The stereochemistry of non-derivatized natural rhizopine corresponds to (1R,2S,3R,4R,5S,6R)-4-amino-6-methoxycyclohexane-1,2,3,5-tetraol. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Local X-ray magnetic circular dichroism study of Fe/Cu(111) using a tunneling smart tip
DiLullo, Andrew; Shirato, Nozomi; Cummings, Marvin; Kersell, Heath; Chang, Hao; Rosenmann, Daniel; Miller, Dean; Freeland, John W.; Hla, Saw-Wai; Rose, Volker
2016-01-01
Localized spectroscopy with simultaneous topographic, elemental and magnetic information is presented. A synchrotron X-ray scanning tunneling microscope has been employed for the local study of the X-ray magnetic circular dichroism at the Fe L 2,3-edges of a thin iron film grown on Cu(111). Polarization-dependent X-ray absorption spectra have been obtained through a tunneling smart tip that serves as a photoelectron detector. In contrast to conventional spin-polarized scanning tunneling microscopy, X-ray excitations provide magnetic contrast even with a non-magnetic tip. Intensity variations in the photoexcited tip current point to chemical variations within a single magnetic Fe domain. PMID:26917146
Local X-ray magnetic circular dichroism study of Fe/Cu(111) using a tunneling smart tip
DiLullo, Andrew; Shirato, Nozomi; Cummings, Marvin; ...
2016-01-28
Localized spectroscopy with simultaneous topographic, elemental and magnetic information is presented. A synchrotron X-ray scanning tunneling microscope has been employed for the local study of the X-ray magnetic circular dichroism at the FeL 2,3-edges of a thin iron film grown on Cu(111). Polarization-dependent X-ray absorption spectra have been obtained through a tunneling smart tip that serves as a photoelectron detector. In contrast to conventional spin-polarized scanning tunneling microscopy, X-ray excitations provide magnetic contrast even with a non-magnetic tip. Intensity variations in the photoexcited tip current point to chemical variations within a single magnetic Fe domain.
Local X-ray magnetic circular dichroism study of Fe/Cu(111) using a tunneling smart tip.
DiLullo, Andrew; Shirato, Nozomi; Cummings, Marvin; Kersell, Heath; Chang, Hao; Rosenmann, Daniel; Miller, Dean; Freeland, John W; Hla, Saw-Wai; Rose, Volker
2016-03-01
Localized spectroscopy with simultaneous topographic, elemental and magnetic information is presented. A synchrotron X-ray scanning tunneling microscope has been employed for the local study of the X-ray magnetic circular dichroism at the Fe L2,3-edges of a thin iron film grown on Cu(111). Polarization-dependent X-ray absorption spectra have been obtained through a tunneling smart tip that serves as a photoelectron detector. In contrast to conventional spin-polarized scanning tunneling microscopy, X-ray excitations provide magnetic contrast even with a non-magnetic tip. Intensity variations in the photoexcited tip current point to chemical variations within a single magnetic Fe domain.
Soft X-ray magnetic circular dichroism of Heusler-type alloy Co 2MnGe
NASA Astrophysics Data System (ADS)
Miyamoto, K.; Iori, K.; Kimura, A.; Xie, T.; Taniguchi, M.; Qiao, S.; Tsuchiya, K.
2003-10-01
Co and Mn 2p core absorption (XAS) and X-ray magnetic circular dichroism (XMCD) spectra have been measured for the ferromagnetic ternary alloy Co 2MnGe. The observed Co 2p XAS spectrum can be understood on the basis of the unoccupied Co 3d partial density of states, whereas the overall features of the Mn 2p XAS and XMCD spectra have been partly reproduced by the Mn 2p 53d 6 final state multiplets. We have found that the orbital polarization of the Co 3d and even the Mn 3d states are recognizable, which suggests that a spin-orbit coupling should be taken into account in the energy band structure in order to reproduce the half metallic nature of this alloy.
Gorinstein, S; Zemser, M; Vargas-Albores, F; Ochoa, J L; Paredes-Lopez, O; Scheler, C; Aksu, S; Salnikow, J
1999-02-01
Characterization of three cactus proteins (native and denatured) from Machaerocereus gummosus (Pitahaya agria), Lophocereu schottii (Garambullo), and Cholla opuntia (Cholla), was based on electrophoretic, fluorescence, CD (circular dichroism), DSC (differential scanning calorimetry), and FT-IR (Fourier transform infrared) measurements. The obtained results of intrinsic fluorescence, DSC, and CD were dissimilar for the three species of cactus, providing evidence of differences in secondary and tertiary structures. Cactus proteins may be situated in the following order corresponding to their relative stability: Machaerocereus gummosus (Pitahaya agria) > Cholla opuntia (Cholla) > Lophocereu schottii (Garambullo). Thermodynamic properties of proteins and their changes upon denaturation (temperature of denaturation, enthalphy, and the number of ruptured hydrogen bonds) were correlated with the secondary structure of proteins and disappearance of alpha-helix.
Gigantic transverse x-ray magnetic circular dichroism in ultrathin Co in Au/Co/Au(001)
NASA Astrophysics Data System (ADS)
Koide, T.; Mamiya, K.; Asakura, D.; Osatune, Y.; Fujimori, A.; Suzuki, Y.; Katayama, T.; Yuasa, S.
2014-04-01
Transverse-geometry x-ray magnetic circular dichroism (TXMCD) measurements on Au/Co-staircase/Au(001) reveal the orbital origin of intrinsic in-plane magnetic anisotropy A gigantic TXMCD was successfully observed at the Co L3,2 edges for Co thickness (tC0) in the 2-monolayer regime. A TXMCD-sum-rule analysis shows a remarkable enhancement of an orbital-moment anisotropy (Δmorb) and of an in-plane magnetic dipole moment (m||T). Both Δmorb and m||T exhibit close similarity in tCo dependence, reflecting the in-plane magnetic anisotropy These observations evidence that extremely strong, intrinsic, in-plane magnetic anisotropy originates from the anisotropic orbital part of the wave function, dominating the dipole-dipole-interaction-derived, extrinsic, in-plane magnetic anisotropy.
NASA Astrophysics Data System (ADS)
Ueno, Tetsuro; Hino, Hideitsu; Hashimoto, Ai; Takeichi, Yasuo; Sawada, Masahiro; Ono, Kanta
2018-01-01
Spectroscopy is a widely used experimental technique, and enhancing its efficiency can have a strong impact on materials research. We propose an adaptive design for spectroscopy experiments that uses a machine learning technique to improve efficiency. We examined X-ray magnetic circular dichroism (XMCD) spectroscopy for the applicability of a machine learning technique to spectroscopy. An XMCD spectrum was predicted by Gaussian process modelling with learning of an experimental spectrum using a limited number of observed data points. Adaptive sampling of data points with maximum variance of the predicted spectrum successfully reduced the total data points for the evaluation of magnetic moments while providing the required accuracy. The present method reduces the time and cost for XMCD spectroscopy and has potential applicability to various spectroscopies.
Padula, Daniele; Pescitelli, Gennaro
2018-01-09
Chiroptical spectra such as electronic circular dichroism (ECD) are said to be much more sensitive to conformation than their non-chiroptical counterparts, however, it is difficult to demonstrate such a common notion in a clear-cut way. We run DFT and TDDFT calculations on two closely related 1,1-diarylmethanols which show mirror-image ECD spectra for the same absolute configuration. We demonstrate that the main reason for the different chiroptical response of the two compounds lies in different conformational ensembles, caused by a single hydrogen-to-methyl substitution. We conclude that two compounds, having the same configuration but different conformation, may exhibit mirror-image ECD signals, stressing the importance and impact of conformational factors on ECD spectra.
Lux, Christian; Wollenhaupt, Matthias; Sarpe, Cristian; Baumert, Thomas
2015-01-12
Photoelectron circular dichroism (PECD) is a CD effect up to the ten-percent regime and shows contributions from higher-order Legendre polynomials when multiphoton ionization is compared to single-photon ionization. We give a full account of our experimental methodology for measuring the multiphoton PECD and derive quantitative measures that we apply on camphor, fenchone and norcamphor. Different modulations and amplitudes of the contributing Legendre polynomials are observed despite the similarity in chemical structure. In addition, we study PECD for elliptically polarized light employing tomographic reconstruction methods. Intensity studies reveal dissociative ionization as the origin of the observed PECD effect, whereas ionization of the intermediate resonance is dominating the signal. As a perspective, we suggest to make use of our tomographic data as an experimental basis for a complete photoionization experiment and give a prospect of PECD as an analytic tool. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
NASA Astrophysics Data System (ADS)
Shiratsu, Taisuke; Yao, Hiroshi
2016-10-01
Magneto-optical activity is demonstrated in thiolate-protected Au nanoparticles with magnetic circular dichroism (MCD) spectroscopy. The samples examined are decanethiolate-protected Au nanoparticles with the mean diameters ranging from 2.0 to 4.7 nm. The nanoparticles larger than 2.4 nm in diameter exhibit a derivative-like MCD signal, indicating the presence of two circular modes of surface magnetoplasmon, but the spectral shape is so asymmetric that its identification is rather difficult. This is due to the contribution of interband transitions occurring at around the localized surface plasmon resonance (LSPR) frequency. We then develop an efficient method to phenomenologically separate the effects of magnetoplasmonic intraband (= Drude) and interband transitions in the measured MCD spectra using an approximation that the optical response of the Au nanoparticle with a critical size (˜2.0 nm) for the disappearance of LSPR, which is also experimentally obtainable, is substantially dominated by the interband transitions. The consistency of the method is ensured for tiopronin-protected Au nanoparticles, and a very small bisignate magnetoplasmonic response hidden in the total MCD spectrum can be extracted. The practical advantage of the proposed method is that we can intuitively and effectively evaluate the characteristic features of the surface magnetoplasmon of thiolate-protected Au nanoparticles without performing complicated Mie or quasielectrostatic calculations.
Lewis, Russell L; Seal, Erin L; Lorts, Aimee R; Stewart, Amanda L
2017-11-01
The undergraduate biochemistry laboratory curriculum is designed to provide students with experience in protein isolation and purification protocols as well as various data analysis techniques, which enhance the biochemistry lecture course and give students a broad range of tools upon which to build in graduate level laboratories or once they begin their careers. One of the most common biochemistry protein purification experiments is the isolation and characterization of cytochrome c. Students across the country purify cytochrome c, lysozyme, or some other well-known protein to learn these common purification techniques. What this series of experiments lacks is the use of sophisticated instrumentation that is rarely available to undergraduate students. To give students a broader background in biochemical spectroscopy techniques, a new circular dichroism (CD) laboratory experiment was introduced into the biochemistry laboratory curriculum. This CD experiment provides students with a means of conceptualizing the secondary structure of their purified protein, and assessments indicate that students' understanding of the technique increased significantly. Students conducted this experiment with ease and in a short time frame, so this laboratory is conducive to merging with other data analysis techniques within a single laboratory period. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(6):515-520, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.
Chen, Yihui; Miclea, Razvan; Srikrishnan, Thamarapu; Balasubramanian, Sathyamangalam; Dougherty, Thomas J; Pandey, Ravindra K
2005-07-01
A series of pyropheophorbide-a and bacteriopurpurinimides were investigated to understand the correlation between HSA (site II) binding affinity and in vivo photosensitizing activity. In our study, photosensitizers that bound to site II of HSA produced a significant difference in the circular dichroism spectra of the corresponding complexes, especially at Soret band region of the photosensitizers. Our results suggest that CD spectroscopy of the photosensitizer-HSA complexes could be a valuable tool in screening new photosensitizers before evaluating them for in vivo efficacy.
NASA Astrophysics Data System (ADS)
Rafiee Fanood, Mohammad M.; Janssen, Maurice H. M.; Powis, Ivan
2016-09-01
Enantiomers of the monoterpene limonene have been investigated by (2 + 1) resonance enhanced multiphoton ionization and photoelectron circular dichroism employing tuneable, circularly polarized femtosecond laser pulses. Electron imaging detection provides 3D momentum measurement while electron-ion coincidence detection can be used to mass-tag individual electrons. Additional filtering, by accepting only parent ion tagged electrons, can be then used to provide discrimination against higher energy dissociative ionization mechanisms where more than three photons are absorbed to better delineate the two photon resonant, one photon ionization pathway. The promotion of different vibrational levels and, tentatively, different electronic ion core configurations in the intermediate Rydberg states can be achieved with different laser excitation wavelengths (420 nm, 412 nm, and 392 nm), in turn producing different state distributions in the resulting cations. Strong chiral asymmetries in the lab frame photoelectron angular distributions are quantified, and a comparison made with a single photon (synchrotron radiation) measurement at an equivalent photon energy.
NASA Astrophysics Data System (ADS)
Ardakani, Abbas Ghasempour; Moradi, Khatereh
2018-02-01
In this paper, an extrinsic chiral metasurface based on a silver thin film containing a periodic array of V-shaped nanostructures is proposed. The proposed structure is normally and obliquely illuminated by right- and left-handed circularly polarized plane waves and the transmission through the structure is calculated using the frequency domain finite-integration technique. Our simulation results show that the designed metasurface exhibits strong circular dichroism (CD) in the transmission Δ = T_{RCP}- T_{LCP}=0.98 in the near-infrared region under oblique incidence. To our knowledge, this is one of highest CD effects that have been achieved so far in the single-layer metasurface based on metallic nanostructures. The physical mechanism for this strong CD effect is explained in terms of the current density distribution. Furthermore, the effects of change of the incident angle, the refractive index of surrounding medium and structure parameters, such as film thickness and lattice constants on CD spectrum, are investigated. In addition, the CD phenomenon in the structure is analyzed in other frequency regions.
NASA Astrophysics Data System (ADS)
Orlov, Sergey; Goncharova, Iryna; Urbanová, Marie
Although recent investigations have shown that bilirubin not only has a negative role in the organism but also exhibits significant antimutagenic properties, the mechanisms of interactions between bilirubin and mutagens are not clear. In this study, interaction between bilirubin bound to different binding sites of mammalian serum albumins with structural analogues of the mutagens 2-aminofluorene, 2,7-diaminofluorene and mutagen 2,4,7-trinitrofluorenone were investigated by circular dichroism and absorption spectroscopy. Homological human and bovine serum albumins were used as chiral matrices, which preferentially bind different conformers of bilirubin in the primary binding sites and make it observable by circular dichroism. These molecular systems approximated a real system for the study of mutagens in blood serum. Differences between the interaction of bilirubin bound to primary and to secondary binding sites of serum albumins with mutagens were shown. For bilirubin bound to secondary binding sites with low affinity, partial displacement and the formation of self-associates were observed in all studied mutagens. The associates of bilirubin bound to primary binding sites of serum albumins are formed with 2-aminofluorene and 2,4,7-trinitrofluorenone. It was proposed that 2,7-diaminofluorene does not interact with bilirubin bound to primary sites of human and bovine serum albumins due to the spatial hindrance of the albumins binding domains. The spatial arrangement of the bilirubin bound to serum albumin along with the studied mutagens was modelled using ligand docking, which revealed a possibility of an arrangement of the both bilirubin and 2-aminofluorene and 2,4,7-trinitrofluorenone in the primary binding site of human serum albumin.
Mavridis, Lazaros; Janes, Robert W
2017-01-01
Circular dichroism (CD) spectroscopy is extensively utilized for determining the percentages of secondary structure content present in proteins. However, although a large contributor, secondary structure is not the only factor that influences the shape and magnitude of the CD spectrum produced. Other structural features can make contributions so an entire protein structural conformation can give rise to a CD spectrum. There is a need for an application capable of generating protein CD spectra from atomic coordinates. However, no empirically derived method to do this currently exists. PDB2CD has been created as an empirical-based approach to the generation of protein CD spectra from atomic coordinates. The method utilizes a combination of structural features within the conformation of a protein; not only its percentage secondary structure content, but also the juxtaposition of these structural components relative to one another, and the overall structure similarity of the query protein to proteins in our dataset, the SP175 dataset, the 'gold standard' set obtained from the Protein Circular Dichroism Data Bank (PCDDB). A significant number of the CD spectra associated with the 71 proteins in this dataset have been produced with excellent accuracy using a leave-one-out cross-validation process. The method also creates spectra in good agreement with those of a test set of 14 proteins from the PCDDB. The PDB2CD package provides a web-based, user friendly approach to enable researchers to produce CD spectra from protein atomic coordinates. http://pdb2cd.cryst.bbk.ac.uk CONTACT: r.w.janes@qmul.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.
Magnetic x-ray dichroism in ultrathin epitaxial films
DOE Office of Scientific and Technical Information (OSTI.GOV)
Tobin, J.G.; Goodman, K.W.; Cummins, T.R.
1997-04-01
The authors have used Magnetic X-ray Linear Dichroism (MXLD) and Magnetic X-ray Circular Dichroism (MXCD) to study the magnetic properties of epitaxial overlayers in an elementally specific fashion. Both MXLD and MXCD Photoelectron Spectroscopy were performed in a high resolution mode at the Spectromicroscopy Facility of the ALS. Circular Polarization was obtained via the utilization of a novel phase retarder (soft x-ray quarter wave plate) based upon transmission through a multilayer film. The samples were low temperature Fe overlayers, magnetic alloy films of NiFe and CoNi, and Gd grown on Y. The authors results include a direct comparison of highmore » resolution angle resolved Photoelectron Spectroscopy performed in MXLD and MXCD modes as well as structural studies with photoelectron diffraction.« less
Arroyo-Reyna, A; Hernandez-Arana, A; Arreguin-Espinosa, R
1994-01-01
Two forms of stem bromelain (EC 3.4.22.4) were isolated from commercial, crude and chromatographically purified preparations of the enzyme by means of gel-filtration and cation-exchange liquid chromatography. These forms possess nearly identical secondary and tertiary structures, as judged from their circular dichroism (c.d.) spectra. The spectral characteristics of stem bromelain suggest that this enzyme belongs to the alpha + beta protein class, as other cysteine proteinases do. In agreement with these results, quantitative estimation of secondary structures yielded amounts similar to those for papain and proteinase omega. However, the bromelain c.d. curve is clearly distinguishable from those reported for papain and proteinase omega, on one hand, and that of chymopapain, on the other. Thus, it is apparent that there are at least three types of c.d. spectra associated with the family of cysteine proteinases. PMID:8198520
NASA Astrophysics Data System (ADS)
Haider, Shahid A.; Tran, Megan Y.; Wong, Alexander
2018-02-01
Observing the circular dichroism (CD) caused by organic molecules in biological fluids can provide powerful indicators of patient health and provide diagnostic clues for treatment. Methods for this kind of analysis involve tabletop devices that weigh tens of kilograms with costs on the order of tens of thousands of dollars, making them prohibitive in point-of-care diagnostic applications. In an e ort to reduce the size, cost, and complexity of CD estimation systems for point-of-care diagnostics, we propose a novel method for CD estimation that leverages a vortex half-wave retarder in between two linear polarizers and a two-dimensional photodetector array to provide an overall complexity reduction in the system. This enables the measurement of polarization variations across multiple polarizations after they interact with a biological sample, simultaneously, without the need for mechanical actuation. We further discuss design considerations of this methodology in the context of practical applications to point-of-care diagnostics.
Harada, Takunori; Hayakawa, Hiroshi; Kuroda, Reiko
2008-07-01
We have designed and built a novel universal chiroptical spectrophotometer (UCS-2: J-800KCMF), which can carry out in situ chirality measurement of solid samples without any pretreatment, in the UV-vis region and with high relative efficiency. The instrument was designed to carry out transmittance and diffuse reflectance (DR) circular dichroism (CD) measurements simultaneously, thus housing two photomultipliers. It has a unique feature that light impinges on samples vertically so that loose powders can be measured by placing them on a flat sample holder in an integrating sphere. As is our first universal chiroptical spectrophotometer, UCS-1, two lock-in amplifiers are installed to remove artifact signals arising from macroscopic anisotropies which are unique to solid samples. High performance was achieved by theoretically analyzing and experimentally proven the effect of the photoelastic modulator position on the CD base line shifts, and by selecting high-quality optical and electric components. Measurement of microcrystallines of both enantiomers of ammonium camphorsulfonate by the DRCD mode gave reasonable results.
Compton, L A; Johnson, W C
1986-05-15
Inverse circular dichroism (CD) spectra are presented for each of the five major secondary structures of proteins: alpha-helix, antiparallel and parallel beta-sheet, beta-turn, and other (random) structures. The fraction of the each secondary structure in a protein is predicted by forming the dot product of the corresponding inverse CD spectrum, expressed as a vector, with the CD spectrum of the protein digitized in the same way. We show how this method is based on the construction of the generalized inverse from the singular value decomposition of a set of CD spectra corresponding to proteins whose secondary structures are known from X-ray crystallography. These inverse spectra compute secondary structure directly from protein CD spectra without resorting to least-squares fitting and standard matrix inversion techniques. In addition, spectra corresponding to the individual secondary structures, analogous to the CD spectra of synthetic polypeptides, are generated from the five most significant CD eigenvectors.
NASA Astrophysics Data System (ADS)
Gevorgyan, A. H.
2017-01-01
The specific features of the circular dichroism (CD) spectra of a cholesteric liquid crystal (CLC) layer with a defect layer inside in the presence of gain have been investigated. The features of the dependence of CD on the parameter characterizing the gain on the defect mode are analyzed for two cases: (i) gain is present in the defect layer and is absent in the CLC sublayers and (ii) gain is absent in the defect layer but is present in the CLC sublayers. It is shown that these dependences significantly differ in the two aforementioned cases. The dependences of the reflection, transmission, and absorption on the defect mode on the gain parameter have been investigated for incident light with both circular polarizations.
Kanazawa, Hideko; Tsubayashi, Akane; Nagata, Yoshiko; Matsushima, Yoshikazu; Mori, Chiharu; Kizu, Junko; Higaki, Megumu
2002-03-01
The chiral separation of loxoprofen was achieved on a chiral column with UV and circular dichroism (CD) detection. The good resolution of four loxoprofen stereoisomers was obtained. The column used for the chiral separation was Chiralcel OJ column (250 x 4.6 mm) using hexane-2-propanol-trifluoroacetic acid (95:5:0.1), as an eluent. The flow-rate was 1.0 ml/min and the detection was at 225 nm. In addition, CD and UV spectra were obtained by stopped flow scanning. The method allows the determination of the stereoisomers of loxoprofen in human plasma after the administration of therapeutic dose of the racemic drug, thus HPLC with CD detector is useful for the stereospecific determination of loxoprofen products in biological samples.
Müller, Anne D; Artemyev, Anton N; Demekhin, Philipp V
2018-06-07
Angle-resolved multiphoton ionization of fenchone and camphor by short intense laser pulses is computed by the time-dependent single center method. Thereby, the photoelectron circular dichroism (PECD) in the three-photon resonance enhanced ionization and four-photon above-threshold ionization of these molecules is investigated in detail. The computational results are in satisfactory agreement with the available experimental data, measured for randomly oriented fenchone and camphor molecules at different wavelengths of the exciting pulses. We predict a significant enhancement of the multiphoton PECD for uniaxially oriented fenchone and camphor.
NASA Astrophysics Data System (ADS)
Müller, Anne D.; Artemyev, Anton N.; Demekhin, Philipp V.
2018-06-01
Angle-resolved multiphoton ionization of fenchone and camphor by short intense laser pulses is computed by the time-dependent single center method. Thereby, the photoelectron circular dichroism (PECD) in the three-photon resonance enhanced ionization and four-photon above-threshold ionization of these molecules is investigated in detail. The computational results are in satisfactory agreement with the available experimental data, measured for randomly oriented fenchone and camphor molecules at different wavelengths of the exciting pulses. We predict a significant enhancement of the multiphoton PECD for uniaxially oriented fenchone and camphor.
Linear and circular dichroism characterization of thionine binding mode with DNA polynucleotides
NASA Astrophysics Data System (ADS)
Tuite, Eimer Mary; Nordén, Bengt
2018-01-01
The binding mode of thionine (3,7-diamino-5-phenothiazinium) with alternating and non-alternating DNA polynucleotides at low binding ratios was conclusively determined using linear and circular dichroism spectroscopies. The binding to [poly(dG-dC)]2 and poly(dG)·poly(dC) was purely intercalative and was insensitive to ionic strength. Intercalative binding to [poly(dA-dT)]2 is observed at low ionic strength, but a shift of some dye to an non-intercalative mode is observed as the background salt concentration increases. With poly(dA)·poly(dT), intercalative binding is unfavourable, although some dye molecules may intercalate at low ionic strength, and groove binding is strongly promoted with increasing concentration of background salt. However, stacking with bases is observed with single-stranded poly(dA) and with triplex poly(dT)*poly(dA)·poly(dT) which suggests that the unusual structure of poly(dA)·poly(dT) precludes intercalation. Thionine behaves similarly to the related dye methylene blue, and small differences may be attributed either to the ability of thionine to form H-bonds that stabilize intercalation or to its improved stacking interactions in the basepair pocket on steric grounds.
pH titration monitored by quantum cascade laser-based vibrational circular dichroism.
Rüther, Anja; Pfeifer, Marcel; Lórenz-Fonfría, Víctor A; Lüdeke, Steffen
2014-04-10
Vibrational circular dichroism (VCD) spectra of aqueous solutions of proline were recorded in the course of titrations from basic to acidic pH using a spectrometer equipped with a quantum cascade laser (QCL) as an infrared light source in the spectral range from 1320 to 1220 cm(-1). The pH-dependent spectra were analyzed by singular value decomposition and global fitting of a two-pK Henderson-Hasselbalch model. The analysis delivered relative fractions of the three different protonation species. Their agreement with the relative fractions obtained from performing the same analysis on pH-dependent Fourier transform infrared (FT-IR) and QCL-IR spectra validates the quantitative results from QCL-VCD. Global fitting of the pH-dependent VCD spectra of L-proline allowed for extraction of pure spectra corresponding to anionic, zwitterionic, and cationic L-proline. From a static experiment, only pure spectra of the zwitterion would be accessible in a straightforward way. A comparison to VCD spectra calculated for all three species led to assignment of vibrational modes that are characteristic for the respective protonation states. The study demonstrates the applicability of QCL-VCD both for quantitative evaluation and for qualitative interpretation of dynamic processes in aqueous solutions.
NASA Astrophysics Data System (ADS)
Ding, Fei; Liu, Wei; Sun, Ye; Yang, Xin-Ling; Sun, Ying; Zhang, Li
2012-01-01
Chloramphenicol is a low cost, broad spectrum, highly active antibiotic, and widely used in the treatment of serious infections, including typhoid fever and other life-threatening infections of the central nervous system and respiratory tract. The purpose of the present study was to examine the conjugation of chloramphenicol with hemoglobin (Hb) and compared with albumin at molecular level, utilizing fluorescence, UV/vis absorption, circular dichroism (CD) as well as molecular modeling. Fluorescence data indicate that drug bind Hb generate quenching via static mechanism, this corroborates UV/vis absorption measurements that the ground state complex formation with an affinity of 10 4 M -1, and the driving forces in the Hb-drug complex are hydrophilic interactions and hydrogen bonds, as derived from computational model. The accurate binding site of drug has been identified from the analysis of fluorescence and molecular modeling, α1β2 interface of Hb was assigned to possess high-affinity for drug, which located at the β-37 Trp nearby. The structural investigation of the complexed Hb by synchronous fluorescence, UV/vis absorption, and CD observations revealed some degree of Hb structure unfolding upon complexation. Based on molecular modeling, we can draw the conclusion that the binding affinity of drug with albumin is superior, compared with Hb. These phenomena can provide salient information on the absorption, distribution, pharmacology, and toxicity of chloramphenicol and other drugs which have analogous configuration with chloramphenicol.
NASA Astrophysics Data System (ADS)
Chen, Shaojin; Liu, Wei; Ge, Zhaohai; Zhang, Wenxuan; Wang, Kunpeng; Hu, Zhiqiang
2018-03-01
Axial chiral bisbenzocoumarins were synthesized for the first time by converting naphthanol units in 1,1‧-binaphthol (BINOL) molecule to the benzocoumarin rings. The substitute groups on 3,3‧-positions of bisbenzocoumarins showed significant influence on their aggregation-induced emission enhancement (AEE) properties. It was also found that BBzC1 with ester groups on 3,3‧-positions exhibit an abnormal aggregation-annihilation circular dichroism (AACD) phenomenon, which could be caused by the decrease of the dihedral angle between adjacent benzocoumarin rings in the aggregation state. The single crystal structure of BBzC1 showed that the large dihedral angle in molecule prohibited the strong π-π stacking interactions, which could be main factors for its AEE properties.
Diaz, Carlos; Lin, Na; Toro, Carlos; Passier, Remy; Rizzo, Antonio; Hernández, Florencio E
2012-07-05
Herein we report on the theoretical-experimental study of the effect of curvature of the π-electron delocalization on the two-photon circular dichroism (TPCD) of a family of optically active biaryl derivatives (S-BINOL, S-VANOL, and S-VAPOL). The comparative analysis of the influence of the different transition moments to their corresponding TPCD rotatory strength reveals an enhanced contribution of the magnetic transition dipole moment on VAPOL. This effect is hereby attributed to the additional twist in the π-electron delocalization on this compound. TPCD measurements were done using the double L-scan technique in the picosecond regime. Theoretical calculations were completed using modern analytical response theory, within a time-dependent density functional theory (TD-DFT) approach, at both, B3LYP and CAM-B3LYP levels, with the aug-cc-pVDZ basis set for S-BINOL and S-VANOL, and 6-31G* for S-VAPOL. Solvent effects were included by means of the polarizable continuum model (PCM) in CH2Cl2.
NASA Astrophysics Data System (ADS)
Kitagawa, Yuya; Akinaga, Yoshinobu; Kawashima, Yukio; Jung, Jaewoon; Ten-no, Seiichiro
2012-06-01
A QM/MM (quantum-mechanical/molecular-mechanical) molecular-dynamics approach based on the generalized hybrid-orbital (GHO) method, in conjunction with the second-order perturbation (MP2) theory and the second-order approximate coupled-cluster (CC2) model, is employed to calculate electronic property accounting for a protein environment. Circular dichroism (CD) spectra originating from chiral disulfide bridges of oxytocin and insulin at room temperature are computed. It is shown that the sampling of thermal fluctuation of molecular geometries facilitated by the GHO-MD method plays an important role in the obtained spectra. It is demonstrated that, while the protein environments in an oxytocin molecule have significant electrostatic influence on its chiral center, it is compensated by solvent induced charges. This gives a reasonable explanation to experimental observations. GHO-MD simulations starting from different experimental structures of insulin indicate that existence of the disulfide bridges with negative dihedral angles is crucial.
Miclet, Emeric; Bourgoin-Voillard, Sandrine; Byrne, Cillian; Jacquot, Yves
2016-01-01
The estrogen receptor α ligand-binding domain (ERα-LBD) binds the natural hormone 17β-estradiol (E2) to induce transcription and cell proliferation. This process occurs with the contribution of protein and peptide partners (also called coactivators) that can modulate the structure of ERα, and therefore its specificity of action. As with most transcription factors, ERα exhibits a high content of α helix, making it difficult to routinely run spectroscopic studies capable of deciphering the secondary structure of the different partners under binding conditions. Ca(2+)-calmodulin, a protein also highly structured in α-helix, is a key coactivator for ERα activity. Here, we show how circular dichroism can be used to study the interaction of ERα with Ca(2+)-calmodulin. Our approach allows the determination not only of the conformational changes induced upon complex formation but also the dissociation constant (K d) of this interaction.
Circularly polarized luminescence of syndiotactic polystyrene
NASA Astrophysics Data System (ADS)
Rizzo, Paola; Abbate, Sergio; Longhi, Giovanna; Guerra, Gaetano
2017-11-01
Syndiotactic polystyrene (s-PS) films, when crystallized from the amorphous state by temporary sorption of non-racemic guest molecules (like carvone) not only exhibit unusually high optical activity, both in the UV-Visible and Infrared ranges, but also present circularly polarized luminescence (CPL) with high dissymmetry ratios (g = ΔI/I values in the range 0.02-0.03). Experimental evidences provide support, rather than to the usual molecular circular dichroism, to a supramolecular chiral optical response being extrinsic to the site of photon absorption and emission, possibly associated with a helical morphology of s-PS crystallites.
Advanced Applications of Vibrational Circular Dichroism: from Small Chiral Molecules to Fibrils
NASA Astrophysics Data System (ADS)
Dukor, Rina K.
2017-06-01
Vibrational Circular Dichroism (VCD), first discovered in the early 1970s, and commercialized in the late 1990's, is finally coming of age! No longer a curiosity of the few selected academic groups, it is now used by all major pharmaceutical companies, regulatory agencies, government labs and academic institutions. The main application for the technology has been determination of absolute configuration of small pharmaceutical molecules. In more recent years, this has extended to more complicated molecules such as natural products with many chiral centers and conformational flexibility. Other applications include determination of enantiomeric purity, chiral polymers, and characterization of other biological molecules such as proteins, carohydrates and nucleic acids. One of the most fascinating discoveries in the VCD field has been been unusual enhancement in intensity for proteins that form fibrils. We have demonstrated sensitivity of VCD to in situ solution-phase probe of the process of fibrillogenesis and subsequent development that currently can only be studied in detail with dried samples by such techniques as scanning electron microscopy or atomic force microscopy. We have further shown that several different proteins, that in their native state have different secondary structures, have a very similar unique signature of mature fibrils. In this presentation, we will discuss fundamentals of VCD, demonstrate a few examples of different applications and showcase the sensitivity to structure of fibrils, including new results on micro-sampling.
Sato, Hisako; Yajima, Tomoko; Yamagishi, Akihiko
2016-05-01
Vibrational circular dichroism (VCD) spectroscopy was applied to gelation by a chiral low-molecular mass weight gelator, N,N'-diperfluoroalkanoyl-1,2-trans-diaminocyclohexane. Attention was focused on the winding effects of (-CF2 )n chains on the gelating ability. For this purpose, a series of gelators were synthesized with perfluoroalkyl chains of different length (n = 6-8). When gelation was studied using acetonitrile as a solvent, the fibrils took different morphologies, depending on the chain length: twisted saddle-like ribbon or helical ribbon from fibril (n = 6) and a helical ribbon from platelet (n = 8). The signs of VCD peaks assigned to the couplet of C=O stretching and to the C-F stretching were also dependent on n, indicating that a gelator molecule changed conformation on elongating perfluoroalkyl chains. A model is proposed for the aggregation modes in fibrils. Chirality 28:361-364, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
Ke, Yaling; Zhao, Yi
2017-05-07
A theoretically solid and numerically exact method is presented for the calculation of absorption and circular dichroism (CD) spectra of molecular aggregates immersed in a harmonic bath constituted as the combination of some prominent quantized vibrational modes and continuous overdamped Brownian oscillators. The feasibility and the validity of newly proposed method are affirmed in the analytical monomer spectra. To go beyond the independent local bath approximation, all the correlations of site energy fluctuations and excitonic coupling fluctuations are included in our strategy, and their influence on the absorption and CD spectra is investigated based on the Frenkel exciton model of homodimer. In the end, a good fit of the absorption and part of CD spectra for the entire B800-B850 ring in the light-harvesting complexes 2 of purple bacteria to the experimental data is given, and the simulation results suggest that the asymmetry in the 800 nm region of CD spectra is actually an indication of B800-B850 inter-ring coupling.
NASA Astrophysics Data System (ADS)
Ke, Yaling; Zhao, Yi
2017-05-01
A theoretically solid and numerically exact method is presented for the calculation of absorption and circular dichroism (CD) spectra of molecular aggregates immersed in a harmonic bath constituted as the combination of some prominent quantized vibrational modes and continuous overdamped Brownian oscillators. The feasibility and the validity of newly proposed method are affirmed in the analytical monomer spectra. To go beyond the independent local bath approximation, all the correlations of site energy fluctuations and excitonic coupling fluctuations are included in our strategy, and their influence on the absorption and CD spectra is investigated based on the Frenkel exciton model of homodimer. In the end, a good fit of the absorption and part of CD spectra for the entire B800-B850 ring in the light-harvesting complexes 2 of purple bacteria to the experimental data is given, and the simulation results suggest that the asymmetry in the 800 nm region of CD spectra is actually an indication of B800-B850 inter-ring coupling.
Lin, J.; Zhong, X. Y.; Song, C.; ...
2017-12-27
Physicists are fascinated with topological defects in solid-state materials, because by breaking the translational symmetry they offer emerging properties that are not present in their parental phases. For example, edge dislocations—the 2π phase-winding topological defects—in antiferromagnetic NiO crystals can exhibit ferromagnetic behaviors. Herein, we study how these defects could give rise to exotic topological orders when they interact with a high energy electron beam. To probe this interaction, we formed a coherent electron nanobeam in a scanning transmission electron microscope and recorded the far-field transmitted patterns as the beam steps through the edge dislocation core in [001] NiO. Surprisingly, wemore » found the amplitude patterns of the <020> Bragg disks evolve in a similar manner to the evolution of an annular solar eclipse. Using the ptychographic technique, we recovered the missing phase information in the diffraction plane and revealed the topological phase vortices in the diffracted beams. Through atomic topological defects, the wave function of electrons can be converted from plane wave to electron vortex. This approach provides a new perspective for boosting the collection efficiency of magnetic circular dichroism spectra with high spatial resolution and understanding the relationship between symmetry breaking and exotic property of individual topological defect at atomic level.« less
DOE Office of Scientific and Technical Information (OSTI.GOV)
Lin, J.; Zhong, X. Y.; Song, C.
Physicists are fascinated with topological defects in solid-state materials, because by breaking the translational symmetry they offer emerging properties that are not present in their parental phases. For example, edge dislocations—the 2π phase-winding topological defects—in antiferromagnetic NiO crystals can exhibit ferromagnetic behaviors. Herein, we study how these defects could give rise to exotic topological orders when they interact with a high energy electron beam. To probe this interaction, we formed a coherent electron nanobeam in a scanning transmission electron microscope and recorded the far-field transmitted patterns as the beam steps through the edge dislocation core in [001] NiO. Surprisingly, wemore » found the amplitude patterns of the <020> Bragg disks evolve in a similar manner to the evolution of an annular solar eclipse. Using the ptychographic technique, we recovered the missing phase information in the diffraction plane and revealed the topological phase vortices in the diffracted beams. Through atomic topological defects, the wave function of electrons can be converted from plane wave to electron vortex. This approach provides a new perspective for boosting the collection efficiency of magnetic circular dichroism spectra with high spatial resolution and understanding the relationship between symmetry breaking and exotic property of individual topological defect at atomic level.« less
Avilés, Edward; Rodríguez, Abimael D; Vicente, Jan
2013-11-15
Two new natural products, 3 and 4, and their predecessor 7-isocyanoisoneoamphilecta-1(14),15-diene (2), of the rare isoneoamphilectane class of marine diterpenes, along with the known amphilectane diterpenes 6-8, were isolated from the n-hexane extract of the marine sponge Svenzea flava collected at Great Inagua Island, Bahamas. The molecular structures of compounds 3 and 4 were established by spectroscopic (1D/2D NMR, IR, UV, HRMS) methods and confirmed by a series of chemical correlation studies. In a first ever case study of the assignment of the absolute configuration of a molecule based on the isoneoamphilectane carbon skeleton, the absolute configuration of compound 5 was established as 3S,4R,7S,8S,11R,12S,13R by application of vibrational circular dichroism (VCD). In vitro anti-TB screenings revealed that metabolites 2-4 and, in particular, semisynthetic analogue 5, are strong growth inhibitors of Mycobacterium tuberculosis H37Rv.
Strohm, Cornelius; Perrin, Florian; Dominguez, Marie-Christine; Headspith, Jon; van der Linden, Peter; Mathon, Olivier
2011-01-01
Using a fast silicon strip detector, a multi-frame acquisition scheme was implemented to perform energy-dispersive X-ray magnetic circular dichroism at the iron K-edge in pulsed high magnetic fields. The acquisition scheme makes use of the entire field pulse. The quality of the signal obtained from samples of ferrimagnetic erbium iron garnet allows for quantitative evaluation of the signal amplitude. Below the compensation point, two successive field-induced phase transitions and the reversal of the net magnetization of the iron sublattices in the intermediate phase were observed. PMID:21335909
Kosaka, Tomoyo; Inoue, Yoshihisa; Mori, Tadashi
2016-03-03
Hexaarylbenzenes (HABs) have greatly attracted much attention due to their unique propeller-shaped structure and potential application in materials science, such as liquid crystals, molecular capsules/rotors, redox materials, nonlinear optical materials, as well as molecular wires. Less attention has however been paid to their propeller chirality. By introducing small point-chiral group(s) at the periphery of HABs, propeller chirality was effectively induced, provoking strong Cotton effects in the circular dichroism (CD) spectrum. Temperature and solvent polarity manipulate the dynamics of propeller inversion in solution. As such, whizzing toroids become more substantial in polar solvents and at an elevated temperature, where radial aromatic rings (propeller blades) prefer orthogonal alignment against the central benzene ring (C6 core), maximizing toroidal interactions.
Simulation of Electronic Circular Dichroism of Nucleic Acids: From the Structure to the Spectrum.
Padula, Daniele; Jurinovich, Sandro; Di Bari, Lorenzo; Mennucci, Benedetta
2016-11-14
We present a quantum mechanical (QM) simulation of the electronic circular dichroism (ECD) of nucleic acids (NAs). The simulation combines classical molecular dynamics, to obtain the structure and its temperature-dependent fluctuations, with a QM excitonic model to determine the ECD. The excitonic model takes into account environmental effects through a polarizable embedding and uses a refined approach to calculate the electronic couplings in terms of full transition densities. Three NAs with either similar conformations but different base sequences or similar base sequences but different conformations have been investigated and the results were compared with experimental observations; a good agreement was seen in all cases. A detailed analysis of the nature of the ECD bands in terms of their excitonic composition was also carried out. Finally, a comparison between the QM and the DeVoe models clearly revealed the importance of including fluctuations of the excitonic parameters and of accurately determining the electronic couplings. This study demonstrates the feasibility of the ab initio simulation of the ECD spectra of NAs, that is, without the need of experimental structural or electronic data. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
NASA Astrophysics Data System (ADS)
Combier, Tristan; Palacio-Morales, Alexandra; Sanchez, Jean-Pierre; Wilhelm, Fabrice; Pourret, Alexandre; Brison, Jean-Pascal; Aoki, Dai; Rogalev, Andrei
2017-02-01
The itinerant metamagnet UCoAl has been investigated by high field X-ray magnetic circular dichroism (XMCD) at the U M4,5 and Co K edges. The orbital and spin moments of U at 2.1 K for H || c applied below and above the first order metamagnetic transition field (HM) have been determined. The magnetism of UCoAl is dominated by the U moment. There is no evidence for any change of the orbital to spin moment ratio (˜-2.05) across HM and within the ferromagnetic phase up to 17 T. The possibility of a Fermi surface reconstruction at HM remains an open option. XMCD at the Co K-edge reveals the presence of a small Co 4p-orbital moment parallel to the macroscopic magnetization. In addition, the Co 3d-moment is estimated to be at most 0.1 μB at 17 T. The similar field dependence of the U and Co magnetizations indicates that the Co moment is induced by the U moment.
Cang-Rong, Jason Teng; Pastorin, Giorgia
2009-06-24
In the last decade, many environmental organizations have devoted their efforts to identifying renewable biosystems, which could provide sustainable fuels and thus enhance energy security. Amidst the myriad of possibilities, some biofuels make use of different types of waste biomasses, and enzymes are often employed to hydrolyze these biomasses and produce sugars that will be subsequently converted into ethanol. In this project, we aimed to bridge nanotechnology and biofuel production: here we report on the activity and structure of the enzyme amyloglucosidase (AMG), physically adsorbed or covalently immobilized onto single-walled carbon nanotubes (SWNTs) and multi-walled carbon nanotubes (MWNTs). In fact, carbon nanotubes (CNTs) present several properties that render them ideal support systems, without the diffusion limitations displayed by porous material and with the advantage of being further functionalizable at their surface. Chemical ligation was achieved both on oxidized nanotubes (via carbodiimide chemistry), as well as on amino-functionalized nanotubes (via periodate-oxidized AMG). Results showed that AMG retained a certain percentage of its specific activity for all enzyme-carbon nanotubes complexes prepared, with the physically adsorbed samples displaying better catalytic efficiency than the covalently immobilized samples. Analysis of the enzyme's structure through circular dichroism (CD) spectroscopy revealed significant structural changes in all samples, the degree of change being consistent with the activity profiles. This study proves that AMG interacts differently with carbon nanotubes depending on the method employed. Due to the higher activity reported by the enzyme physically adsorbed onto CNTs, these samples demonstrated a vast potential for further development. At the same time, the possibility of inducing magnetic properties into CNTs offers the opportunity to easily separate them from the original solution. Hence, substances to which they
NASA Astrophysics Data System (ADS)
Cang-Rong, Jason Teng; Pastorin, Giorgia
2009-06-01
In the last decade, many environmental organizations have devoted their efforts to identifying renewable biosystems, which could provide sustainable fuels and thus enhance energy security. Amidst the myriad of possibilities, some biofuels make use of different types of waste biomasses, and enzymes are often employed to hydrolyze these biomasses and produce sugars that will be subsequently converted into ethanol. In this project, we aimed to bridge nanotechnology and biofuel production: here we report on the activity and structure of the enzyme amyloglucosidase (AMG), physically adsorbed or covalently immobilized onto single-walled carbon nanotubes (SWNTs) and multi-walled carbon nanotubes (MWNTs). In fact, carbon nanotubes (CNTs) present several properties that render them ideal support systems, without the diffusion limitations displayed by porous material and with the advantage of being further functionalizable at their surface. Chemical ligation was achieved both on oxidized nanotubes (via carbodiimide chemistry), as well as on amino-functionalized nanotubes (via periodate-oxidized AMG). Results showed that AMG retained a certain percentage of its specific activity for all enzyme-carbon nanotubes complexes prepared, with the physically adsorbed samples displaying better catalytic efficiency than the covalently immobilized samples. Analysis of the enzyme's structure through circular dichroism (CD) spectroscopy revealed significant structural changes in all samples, the degree of change being consistent with the activity profiles. This study proves that AMG interacts differently with carbon nanotubes depending on the method employed. Due to the higher activity reported by the enzyme physically adsorbed onto CNTs, these samples demonstrated a vast potential for further development. At the same time, the possibility of inducing magnetic properties into CNTs offers the opportunity to easily separate them from the original solution. Hence, substances to which they
Rode, Joanna E; Jamróz, Michał H; Dobrowolski, Jan Cz; Sadlej, Joanna
2012-08-02
Vibrational circular dichroism (VCD) chirality transfer occurs when an achiral molecule interacts with a chiral one and becomes VCD-active. Unlike for H-bonds, for organic electron donor-acceptor (EDA) complexes this phenomenon remains almost unknown. Here, the VCD chirality transfer from chiral quinine to achiral BF3 is studied at the B3LYP/aug-cc-pVDZ level. Accessibility of four quinine electron donor sites changes with conformation. Therefore, the quinine conformational landscape was explored and a considerable agreement between X-ray and the most stable conformer geometries was achieved. The BF3 complex through the aliphatic quinuclidine N atom is definitely dominating and is predicted to be easily recognizable in the VCD spectrum. Out of several VCD chirality transfer modes, the ν(s)(BF3) mode, the most intense in the entire VCD spectrum, satisfies the VCD mode robustness criterion and can be used for monitoring the chirality transfer phenomenon in quinine···BF3 system.
Yang, Guochun; Tran, Ha; Fan, Eric; Shi, Wei; Lowary, Todd L; Xu, Yunjie
2010-08-01
The absolute configurations of three synthesized anthracycline analogues have been determined using vibrational circular dichroism (VCD) spectroscopy and the density functional theory (DFT) calculations. The experimental VCD spectra of the three compounds have been measured for the first time in the film state, prepared from their CDCl(3) solutions. Conformational searches for the monomers and some dimers of the three compounds have been performed at the DFT level using the B3LYP functional and the 6-311G** and 6-311++G** basis sets. The corresponding vibrational absorption and VCD spectra have been calculated. The good agreement between the experimental and the calculated spectra allows one to assign the absolute configurations of the three compounds with high confidence. In addition, the dominant conformers of the three compounds have also been identified. Copyright 2010 Wiley-Liss, Inc.
Norman, Patrick; Linares, Mathieu
2014-09-01
The chirality of stacked weakly interacting π-systems was interpreted in terms of Frenkel exciton states and the formation of excitonic circular dichroism (CD) bands was monitored for ethylene stacks of varying sizes. Convergence of CD bands with respect to the system size was observed for stacks involving around 10 molecules. By means of rotation around the C-C double bond in ethylene, chirality was induced in the monomeric system and which was shown to dominate the spectral responses, even for polymer aggregates. In helical assemblies of chiral entities, there will always be a mix of excitonic and monomeric contributions to the CD signal and it is demonstrated that the complex polarization propagator approach in combination with Density Functional Theory is a suitable method to address this situation. © 2014 Wiley Periodicals, Inc.
Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy
Micsonai, András; Wien, Frank; Kernya, Linda; Lee, Young-Ho; Goto, Yuji; Réfrégiers, Matthieu; Kardos, József
2015-01-01
Circular dichroism (CD) spectroscopy is a widely used technique for the study of protein structure. Numerous algorithms have been developed for the estimation of the secondary structure composition from the CD spectra. These methods often fail to provide acceptable results on α/β-mixed or β-structure–rich proteins. The problem arises from the spectral diversity of β-structures, which has hitherto been considered as an intrinsic limitation of the technique. The predictions are less reliable for proteins of unusual β-structures such as membrane proteins, protein aggregates, and amyloid fibrils. Here, we show that the parallel/antiparallel orientation and the twisting of the β-sheets account for the observed spectral diversity. We have developed a method called β-structure selection (BeStSel) for the secondary structure estimation that takes into account the twist of β-structures. This method can reliably distinguish parallel and antiparallel β-sheets and accurately estimates the secondary structure for a broad range of proteins. Moreover, the secondary structure components applied by the method are characteristic to the protein fold, and thus the fold can be predicted to the level of topology in the CATH classification from a single CD spectrum. By constructing a web server, we offer a general tool for a quick and reliable structure analysis using conventional CD or synchrotron radiation CD (SRCD) spectroscopy for the protein science research community. The method is especially useful when X-ray or NMR techniques fail. Using BeStSel on data collected by SRCD spectroscopy, we investigated the structure of amyloid fibrils of various disease-related proteins and peptides. PMID:26038575
Uranium 5f shell in UPd2Al3 and URu2Si2 studied by x-ray magnetic circular dichroism
NASA Astrophysics Data System (ADS)
Yaouanc, A.; Dalmas de Réotier, P.; van der Laan, G.; Hiess, A.; Goulon, J.; Neumann, C.; Lejay, P.; Sato, N.
1998-10-01
We report x-ray magnetic circular dichroism (XMCD) measurements performed at the uranium M4,5 edges in the paramagnetic phase of the heavy fermion superconductors UPd2Al3 and URu2Si2. The analysis of the spectra with the first sum rule yields the orbital moment of the 5f shell for both compounds. The shape of the dichroic spectrum at the M5 edge for the two compounds is qualitatively different: a single lobe is observed for URu2Si2 and two lobes are detected for UPd2Al3. This two lobe structure reflects the strong effect of the interaction of the uranium 5f electrons with their environment in the latter compound.
High Field Magnetic Circular Dichroism in Ferromagnetic InMnSb and InMnAs
NASA Astrophysics Data System (ADS)
Meeker, M. A.; Magill, B. A.; Khodaparast, G. A.; Saha, D.; Stanton, C. J.; McGill, S.; Wessels, B. W.
An understanding of the fundamental interactions in narrow gap ferromagnetic semiconductors such as InMnAs and InMnSb has been developed primarily from static magnetization and electrical transport measurements. In this study, to provide a better understanding of the coupling of the Mn impurities to the conduction and valence bands through the sp-d exchange interactions, we have performed magnetic circular dichroism measurements (MCD) on MOVPE grown InMnAs and InMnSb. In our samples, the Mn content varies from 2% to 10.7% and all the samples have Curie temperatures above 300 K. The samples were photo-excited using a Quartz Tungsten Halogen lamp with energies ranging between 0.92-1.45 eV, and in magnetic fields up to 31 T. The temperatures ranged from 15-190 K. Comparison of the observed MCD with theoretical calculations provides a direct method to probe the band structure including the temperature dependence of the spin-orbit split-off bandgap and g-factors, as well as a means to estimate the sp-d coupling constants. Supported by the AFOSR through grant FA9550-14-1-0376, NSF-Career Award DMR-0846834 , NSF-DMR-60035274 , NSF-DMR-1305666, NSF MRI program (DMR-1229217).
NASA Astrophysics Data System (ADS)
Evangelisti, Luca; Holdren, Martin S.; Mayer, Kevin J.; Smart, Taylor; West, Channing; Pate, Brooks
2017-06-01
The absolute configuration of 3-methylcyclohexanone was established by chiral tag rotational spectroscopy measurements using 3-butyn-2-ol as the tag partner. This molecule was chosen because it is a benchmark measurement for vibrational circular dichroism (VCD). A comparison of the analysis approaches of chiral tag rotational spectroscopy and VCD will be presented. One important issue in chiral analysis by both methods is the conformational flexibility of the molecule being analyzed. The analysis of conformational composition of samples will be illustrated. In this case, the high spectral resolution of molecular rotational spectroscopy and potential for spectral simplification by conformational cooling in the pulsed jet expansion are advantages for chiral tag spectroscopy. The computational chemistry requirements for the two methods will also be discussed. In this case, the need to perform conformer searches for weakly bound complexes and to perform reasonably high level quantum chemistry geometry optimizations on these complexes makes the computational time requirements less favorable for chiral tag rotational spectroscopy. Finally, the issue of reliability of the determination of the absolute configuration will be considered. In this case, rotational spectroscopy offers a "gold standard" analysis method through the determination of the ^{13}C-subsitution structure of the complex between 3-methylcyclohexanone and an enantiopure sample of the 3-butyn-2-ol tag.
Local structure and X-ray magnetic circular dichroism of Au in Au-Co nanoalloys
NASA Astrophysics Data System (ADS)
Maurizio, C.; Michieli, N.; Kalinic, B.; Mattarello, V.; Bello, V.; Wilhelm, F.; Ollefs, K.; Mattei, G.
2018-03-01
Coupling a plasmonic metal with a magnetic one in thin films and nanostructures is very interesting for the emerging field of magnetoplasmonics. In particular, coupling through alloying is a promising strategy to induce a magnetic moment on the plasmonic metal atoms, in a way that is intimately related to the local structure of the (metastable) alloy material. In this framework, Au:Co bimetallic films have been produced via magnetron co-sputtering deposition. X-ray absorption spectroscopy (XAS) at both Au- and Co-edges clearly indicates the formation of a full-metallic layer composed for the major part of a binary AuxCo1-x alloy, with x = 0.7-0.8. XAS and transmission electron microscopy analyses suggest the presence of a minor fraction of segregated metals. X-ray magnetic circular dichroism (XMCD) analysis at Au L2,3 edges detected a net magnetic moment of Au atoms (μ = 0.06 μB), significantly larger (≈3.5 times) that the one for Au-capped Co nanoclusters and comparable to the one for a Co-rich Au/Co multilayer, despite the 4 times larger concentration of Co with respect to the present case. This Au-Co magnetic coupling is favored by a high degree of mixing of the two metals in the alloy.
Synchrotron radiation circular dichroism spectroscopy study of recombinant T β4 folding
NASA Astrophysics Data System (ADS)
Huang, Yung-Chin; Chu, Hsueh-Liang; Chen, Peng-Jen; Chang, Chia-Ching
Thymosin beta 4 (T β4) is a 43-amino acid small peptide, has been demonstrated that it can promote cardiac repair, wound repair, tissue protection, and involve in the proliferation of blood cell precursor stem cells of bone marrow. Moreover, T β4 has been identified as a multifunction intrinsically disordered protein, which is lacking the stable tertiary structure. Owing to the small size and disordered character, the T β4 protein degrades rapidly and the storage condition is critical. Therefore, it is not easy to reveal its folding mechanism of native T β4. However, recombinant T β4 protein (rT β4), which fused with a 5-kDa peptide in its amino-terminal, is stable and possesses identical function of T β4. Therefore, rT β4 can be used to study its folding mechanism. By using over-critical folding process, stable folding intermediates of rT β4 can be obtained. Structure analysis of folding intermediates by synchrotron radiation circular dichroism (SRCD) and fluorescence spectroscopies indicate that rT β4 is a random coli major protein and its hydrophobic region becomes compact gradually. Moreover, the rT β4 folding is a two state transition. Thermal denaturation analysis indicates that rT β4 lacks stable tertiary structure. These results indicated that rT β4, similar to T β4, is an intrinsically disordered protein. Research is supported by MOST, Taiwan. MOST 103-2112-M-009-011-MY3. Corresponding author: Chia-Ching Chang; ccchang01@faculty.nctu.edu.tw.
NASA Astrophysics Data System (ADS)
Fujimoto, Kazuhiro J.; Balashov, Sergei P.
2017-03-01
The role of vibronic coupling of antenna carotenoid and retinal in xanthorhodopsin (XR) in its circular dichroism (CD) spectrum is examined computationally. A vibronic exciton model combined with a transition-density-fragment interaction (TDFI) method is developed, and applied to absorption and CD spectral calculations of XR. The TDFI method is based on the electronic Coulomb and exchange interactions between transition densities for individual chromophores [K. J. Fujimoto, J. Chem. Phys. 137, 034101 (2012)], which provides a quantitative description of electronic coupling energy. The TDFI calculation reveals a dominant contribution of the Coulomb interaction to the electronic coupling energy and a negligible contribution of the exchange interaction, indicating that the antenna function of carotenoid results from the Förster type of excitation-energy transfer, not from the Dexter one. The calculated absorption and CD spectra successfully reproduce the main features of the experimental results, which allow us to investigate the mechanism of biphasic CD spectrum observed in XR. The results indicate that vibronic coupling between carotenoid and retinal plays a significant role in the shape of the CD spectrum. Further analysis reveals that the negative value of electronic coupling directly contributes to the biphasic shape of CD spectrum. This study also reveals that the C6—C7 bond rotation of salinixanthin is not the main factor for the biphasic CD spectrum although it gives a non-negligible contribution to the spectral shift. The present method is useful for analyzing the molecular mechanisms underlying the chromophore-chromophore interactions in biological systems.
Bose, Debosreeta; Sarkar, Deboleena; Chattopadhyay, Nitin
2010-01-01
In the present investigation, an attempt has been made to study the interaction of phenosafranin (PSF), a cationic phenazinium dye with the transport proteins, bovine serum albumin (BSA) and human serum albumin (HSA), employing steady-state and time-resolved fluorometric and circular dichroism (CD) techniques. The photophysical properties of the dye are altered on binding with the serum proteins. An explicit study with respect to the modification of the fluorescence and fluorescence anisotropy upon binding, effect of denaturant, fluorescence lifetime and CD measurements reveal that the dye binds to both BSA and HSA with almost the same affinity. Far-UV CD spectra indicate a decrease in the percentage of alpha-helicity only for BSA upon binding with the probe. Near-UV CD responses indicate an alteration in the tertiary structure of both the transport proteins because of binding.
Wesolowski, Steven S; Pivonka, Don E
2013-07-15
The absolute stereochemistry of chiral drugs is usually established via X-ray crystallography. However, vibrational circular dichroism (VCD) spectroscopy coupled with quantum mechanics simulations offers a rapid alternative to crystallography and is readily applied to both crystalline and non-crystalline samples. VCD is an effective complement to X-ray analysis of drug candidates, and it can be used as a high-throughput means of assessing absolute stereochemistry at all phases of the discovery process (hundreds of assignments per year). The practical implementation (or fee-for-service outsourcing) of VCD and selected case studies are illustrated with an emphasis on providing utility and impact to pharmaceutical discovery programs. Copyright © 2013 Elsevier Ltd. All rights reserved.
Jones, Robert M.; Inscore, Frank E.; Hille, Russ; Kirk, Martin L.
1999-11-01
Freeze-quench magnetic circular dichroism spectroscopy (MCD) has been used to trap and study the excited-state electronic structure of the Mo(V) active site in a xanthine oxidase intermediate generated with substoichiometric concentrations of the slow substrate 2-hydroxy-6-methylpurine. EPR spectroscopy has shown that the intermediate observed in the MCD experiment is the "very rapid" intermediate, which lies on the main catalytic pathway. The low-energy (< approximately 30 000 cm(-1)) C-term MCD of this intermediate is remarkably similar to that of the model compound LMoO(bdt) (L = hydrotris(3,5-dimethyl-1-pyrazolyl)borate; bdt = 1,2-benzenedithiolate), and the MCD bands have been assigned as dithiolate S(ip) --> Mo d(xy) and S(op) --> Mo d(xz,yz) LMCT transitions. These transitions result from a coordination geometry of the intermediate where the Mo=O bond is oriented cis to the ene-1,2-dithiolate of the pyranopterin. Since X-ray crystallography has indicated that a terminal sulfido ligand is oriented cis to the ene-1,2-dithiolate in oxidized xanthine oxidase related Desulfovibrio gigas aldehyde oxidoreductase, we have suggested that a conformational change occurs upon substrate binding. The substrate-mediated conformational change is extremely significant with respect to electron-transfer regeneration of the active site, as covalent interactions between the redox-active Mo d(xy) orbital and the S(ip) orbitals of the ene-1,2-dithiolate are maximized when the oxo ligand is oriented cis to the dithiolate plane. This underlies the importance of the ene-1,2-dithiolate portion of the pyranopterin in providing an efficient superexchange pathway for electron transfer. The results of this study indicate that electron-transfer regeneration of the active site may be gated by the orientation of the Mo=O bond relative to the ene-1,2-dithiolate chelate. Poor overlap between the Mo d(xy) orbital and the S(ip) orbitals of the dithiolate in the oxidized enzyme geometry may
DOE Office of Scientific and Technical Information (OSTI.GOV)
Goings, Joshua J.; Li, Xiaosong, E-mail: xsli@uw.edu
2016-06-21
One of the challenges of interpreting electronic circular dichroism (ECD) band spectra is that different states may have different rotatory strength signs, determined by their absolute configuration. If the states are closely spaced and opposite in sign, observed transitions may be washed out by nearby states, unlike absorption spectra where transitions are always positive additive. To accurately compute ECD bands, it is necessary to compute a large number of excited states, which may be prohibitively costly if one uses the linear-response time-dependent density functional theory (TDDFT) framework. Here we implement a real-time, atomic-orbital based TDDFT method for computing the entiremore » ECD spectrum simultaneously. The method is advantageous for large systems with a high density of states. In contrast to previous implementations based on real-space grids, the method is variational, independent of nuclear orientation, and does not rely on pseudopotential approximations, making it suitable for computation of chiroptical properties well into the X-ray regime.« less
First-principles analysis of X-ray magnetic circular dichroism for transition metal complex oxides
DOE Office of Scientific and Technical Information (OSTI.GOV)
Ikeno, Hidekazu, E-mail: h-ikeno@21c.osakafu-u.ac.jp
2016-10-14
X-ray magnetic circular dichroism (XMCD) is widely used for the characterization of magnetism of materials. However, information from XMCD related to the atomic, electronic, and magnetic structures is not fully utilized due to the lack of reliable theoretical tools for spectral analysis. In this work, the first-principles configuration interaction (CI) calculations for X-ray absorption spectra developed by the author were extended for the calculation of XMCD, where the Zeeman energy was taken into the Hamiltonian of the CI to mimic magnetic polarization in the solid state. This technique was applied to interpret the L{sub 2,3} XMCD from 3d transition metalmore » complex oxides, such as NiFe{sub 2}O{sub 4} and FeTiO{sub 3}. The experimental XMCD spectra were quantitatively reproduced using this method. The oxidation states as well as the magnetic ordering between transition metal ions on crystallographically different sites in NiFe{sub 2}O{sub 4} can be unambiguously determined. A first-principles analysis of XMCD in FeTiO{sub 3} revealed the presence of Fe{sup 3+} and Ti{sup 3+} ions, which indicates that the charge transfer from Fe to Ti ions occurs. The origin of magnetic polarization of Ti ions in FeTiO{sub 3} was also discussed.« less
NASA Astrophysics Data System (ADS)
Shibata, Goro; Kitamura, Miho; Minohara, Makoto; Yoshimatsu, Kohei; Kadono, Toshiharu; Ishigami, Keisuke; Harano, Takayuki; Takahashi, Yukio; Sakamoto, Shoya; Nonaka, Yosuke; Ikeda, Keisuke; Chi, Zhendong; Furuse, Mitsuho; Fuchino, Shuichiro; Okano, Makoto; Fujihira, Jun-ichi; Uchida, Akira; Watanabe, Kazunori; Fujihira, Hideyuki; Fujihira, Seiichi; Tanaka, Arata; Kumigashira, Hiroshi; Koide, Tsuneharu; Fujimori, Atsushi
2018-01-01
Magnetic anisotropies of ferromagnetic thin films are induced by epitaxial strain from the substrate via strain-induced anisotropy in the orbital magnetic moment and that in the spatial distribution of spin-polarized electrons. However, the preferential orbital occupation in ferromagnetic metallic La1-xSrxMnO3 (LSMO) thin films studied by x-ray linear dichroism (XLD) has always been found out-of-plane for both tensile and compressive epitaxial strain and hence irrespective of the magnetic anisotropy. In order to resolve this mystery, we directly probed the preferential orbital occupation of spin-polarized electrons in LSMO thin films under strain by angle-dependent x-ray magnetic circular dichroism (XMCD). Anisotropy of the spin-density distribution was found to be in-plane for the tensile strain and out-of-plane for the compressive strain, consistent with the observed magnetic anisotropy. The ubiquitous out-of-plane preferential orbital occupation seen by XLD is attributed to the occupation of both spin-up and spin-down out-of-plane orbitals in the surface magnetic dead layer.
Ground-state wave function of plutonium in PuSb as determined via x-ray magnetic circular dichroism
Janoschek, M.; Haskel, D.; Fernandez-Rodriguez, J.; ...
2015-01-14
Measurements of x-ray magnetic circular dichroism (XMCD) and x-ray absorption near-edge structure (XANES) spectroscopy at the Pu M₄,₅ edges of the ferromagnet PuSb are reported. Using bulk magnetization measurements and a sum rule analysis of the XMCD spectra, we determine the individual orbital [μ L = 2.8(1)μ B/Pu] and spin moments [μ S = –2.0(1)μ B/Pu] of the Pu 5f electrons for the first time. Atomic multiplet calculations of the XMCD and XANES spectra reproduce well the experimental data and are consistent with the experimental value of the spin moment. These measurements of L z and S z are inmore » excellent agreement with the values that have been extracted from neutron magnetic form factor measurements, and confirm the local character of the 5f electrons in PuSb. We demonstrate that a split M₅ as well as a narrow M₄ XMCD signal may serve as a signature of 5f electron localization in actinide compounds.« less
Greenfield, Norma J.
2009-01-01
Circular dichroism (CD) is an excellent spectroscopic technique for following the unfolding and folding of proteins as a function of temperature. One of its principal applications is to determine the effects of mutations and ligands on protein and polypeptide stability If the change in CD as a function of temperature is reversible, analysis of the data may be used to determined the van't Hoff enthalpy (ΔH) and entropy (ΔS) of unfolding, the midpoint of the unfolding transition (TM) and the free energy (ΔG) of unfolding. Binding constants of protein-protein and protein-ligand interactions may also be estimated from the unfolding curves. Analysis of CD spectra obtained as a function of temperature is also useful to determine whether a protein has unfolding intermediates. Measurement of the spectra of five folded proteins and their unfolding curves at a single wavelength takes approximately eight hours. PMID:17406506
Nový, Jakub; Urbanová, Marie
2007-03-01
The interactions of two different porphyrins, without axial ligands-5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin-Cu(II) tetrachloride (Cu(II)TMPyP) and with bulky meso substituents-5,10,15,20-tetrakis(N,N,N-trimethylanilinium-4-yl)porphyrin tetrachloride (TMAP), with (dG-dC)10 and (dA-dT)10 were studied by combination of vibrational circular dichroism (VCD) and electronic circular dichroism (ECD) spectroscopy at different [oligonucleotide]/[porphyrin] ratios, where [oligonucleotide] and [porphyrin] are the concentrations of oligonucleotide per base-pair and porphyrin, respectively. The combination of VCD and ECD spectroscopy enables us to identify the types of interactions, and to specify the sites of interactions: The intercalative binding mode of Cu(II)TMPyP with (dG-dC)(10), which has been well described, was characterized by a new VCD "marker" and it was shown that the interaction of Cu(II)TMPyP with (dA-dT)10 via external binding to the phosphate backbone and major groove binding caused transition from the B to the non-B conformer. TMAP interacted with the major groove of (dG-dC)10, was semi-intercalated into (dA-dT)10, and caused significant variation in the structure of both oligonucleotides at the higher concentration of porphyrin. The spectroscopic techniques used in this study revealed that porphyrin binding with AT sequences caused substantial variation of the DNA structure. It was shown that VCD spectroscopy is an effective tool for the conformational studies of nucleic acid-porphyrin complexes in solution. (c) 2007 Wiley Periodicals, Inc.
Garcia, Gustavo A.; Nahon, Laurent; Daly, Steven; Powis, Ivan
2013-01-01
Electron–nuclei coupling accompanying excitation and relaxation processes is a fascinating phenomenon in molecular dynamics. A striking and unexpected example of such coupling is presented here in the context of photoelectron circular dichroism measurements on randomly oriented, chiral methyloxirane molecules, unaffected by any continuum resonance. Here, we report that the forward-backward asymmetry in the electron angular distribution, with respect to the photon axis, which is associated with photoelectron circular dichroism can surprisingly reverse direction according to the ion vibrational mode excited. This vibrational dependence represents a clear breakdown of the usual Franck–Condon assumption, ascribed to the enhanced sensitivity of photoelectron circular dichroism (compared with other observables like cross-sections or the conventional anisotropy parameter-β) to the scattering phase off the chiral molecular potential, inducing a dependence on the nuclear geometry sampled in the photoionization process. Important consequences for the interpretation of such dichroism measurements within analytical contexts are discussed. PMID:23828557
Pérez-Mellor, Ariel; Zehnacker, Anne
2017-02-01
The diastereomer diketopiperazine (DKP) peptides built on phenylalanine, namely, cyclo diphenylalanine LPhe-LPhe and LPhe-DPhe, were studied in the solid phase by vibrational circular dichroism (VCD) coupled to quantum chemical calculations. The unit structure of cyclo LPhe-LPhe in KBr pellets is a dimer bridged by two strong NH…O hydrogen bonds. The intense bisignate signature in the CO stretch region is interpreted in terms of two contributions arising from the free COs of the dimer and the antisymmetrical combination of the bound COs. In contrast, cyclo LPhe-DPhe shows no VCD signal in relation to its symmetric nature. © 2017 Wiley Periodicals, Inc.
NASA Astrophysics Data System (ADS)
Rosen, David L.; Pendleton, J. David
1995-09-01
Light scattered from optically active spheres was theoretically analyzed for biodetection. The circularly polarized signal of near-forward scattering from circularly dichroic spheres was calculated. Both remote and point biodetection were considered. The analysis included the effect of a circular aperture and beam block at the detector. If the incident light is linearly polarized, a false signal would limit the sensitivity of the biodetector. If the incident light is randomly polarized, shot noise would limit the sensitivity. Suggested improvements to current techniques include a beam block, precise angular measurements, randomly polarized light, index-matching fluid, and larger apertures for large particles.
Sen, Ananya; Bouchet, Aude; Lepère, Valeria; Le Barbu-Debus, Katia; Scuderi, D; Piuzzi, F; Zehnacker-Rentien, A
2012-08-16
Laser-desorbed quinine and quinidine have been studied in the gas phase by combining supersonic expansion with laser spectroscopy, namely, laser-induced fluorescence (LIF), resonance-enhanced multiphoton ionization (REMPI), and IR-UV double resonance experiments. Density funtional theory (DFT) calculations have been done in conjunction with the experimental work. The first electronic transition of quinine and quinidine is of π-π* nature, and the studied molecules weakly fluoresce in the gas phase, in contrast to what was observed in solution (Qin, W. W.; et al. J. Phys. Chem. C2009, 113, 11790). The two pseudo enantiomers quinine and quinidine show limited differences in the gas phase; their main conformation is of open type as it is in solution. However, vibrational circular dichroism (VCD) experiments in solution show that additional conformers exist in condensed phase for quinidine, which are not observed for quinine. This difference in behavior between the two pseudo enantiomers is discussed.
Accuracy of Td-DFT in the Ultraviolet and Circular Dichroism Spectra of Deoxyguanosine and Uridine.
Miyahara, Tomoo; Nakatsuji, Hiroshi
2018-01-11
Accuracy of the time-dependent density functional theory (Td-DFT) was examined for the ultraviolet (UV) and circular dichroism (CD) spectra of deoxyguanosine (dG) and uridine, using 11 different DFT functionals and two different basis sets. The Td-DFT results of the UV and CD spectra were strongly dependent on the functionals used. The basis-set dependence was observed only for the CD spectral calculations. For the UV spectra, the B3LYP and PBE0 functionals gave relatively good results. For the CD spectra, the B3LYP and PBE0 with 6-311G(d,p) basis gave relatively permissible result only for dG. The results of other functionals were difficult to be used for the studies of the UV and CD spectra, though the symmetry adapted cluster-configuration interaction (SAC-CI) method reproduced well the experimental spectra of these molecules. To obtain valuable information from the theoretical calculations of the UV and CD spectra, the theoretical tool must be able to reproduce correctly both of the intensities and peak positions of the UV and CD spectra. Then, we can analyze the reasons of the changes of the intensity and/or the peak position to clarify the chemistry involved. It is difficult to recommend Td-DFT as such tools of science, at least from the examinations using dG and uridine.
NASA Astrophysics Data System (ADS)
Zhang, Xiang; Wang, Mingchao; Li, Li; Yin, Dali
2017-03-01
Asymmetric reactions often need to be evaluated during the synthesis of chiral compounds. However, traditional evaluation methods require the isolation of the individual enantiomer, which is tedious and time-consuming. Thus, it is desirable to develop simple, practical online detection methods. We developed a method based on high-performance liquid chromatography-electronic circular dichroism (HPLC-ECD) that simultaneously analyzes the material conversion ratio and absolute optical purity of each enantiomer. In particular, only a reverse-phase C18 column instead of a chiral column is required in our method because the ECD measurement provides a g-factor that describes the ratio of each enantiomer in the mixtures. We used our method to analyze the asymmetric hydrosilylation of β-enamino esters, and we discussed the advantage, feasibility, and effectiveness of this new methodology.
Bingham, Stephen J; Wolverson, Daniel; Thomson, Andrew J
2008-12-01
The simultaneous excitation of paramagnetic molecules with optical (laser) and microwave radiation in the presence of a magnetic field can cause an amplitude, or phase, modulation of the transmitted light at the microwave frequency. The detection of this modulation indicates the presence of coupled optical and ESR transitions. The phenomenon can be viewed as a coherent Raman effect or, in most cases, as a microwave frequency modulation of the magnetic circular dichroism by the precessing magnetization. By allowing the optical and magnetic properties of a transition metal ion centre to be correlated, it becomes possible to deconvolute the overlapping optical or ESR spectra of multiple centres in a protein or of multiple chemical forms of a particular centre. The same correlation capability also allows the relative orientation of the magnetic and optical anisotropies of each species to be measured, even when the species cannot be obtained in a crystalline form. Such measurements provide constraints on electronic structure calculations. The capabilities of the method are illustrated by data from the dimeric mixed-valence Cu(A) centre of nitrous oxide reductase (N(2)OR) from Paracoccus pantotrophus.
Magnetic circular dichroism of UCl 6– in the ligand-to-metal charge-transfer spectral region
Gendron, Frederic; Fleischauer, Valerie R.; Duignan, Thomas J.; ...
2017-06-23
Here, we present a combined ab initio theoretical and experimental study of the magnetic circular dichroism (MCD) spectrum of the octahedral UCl 6- complex ion in the UV-Vis spectral region. The ground state is an orbitally non-degenerate doublet E 5/2u and the MCD is a $C$-term spectrum caused by spin–orbit coupling. Calculations of the electronic spectrum at various levels of theory indicate that differential dynamic electron correlation has a strong influence on the energies of the dipole-allowed transitions and the envelope of the MCD spectrum. The experimentally observed bands are assigned to dipole-allowed ligand-to-metal charge transfer into the 5f shell,more » and 5f to 6d transitions. Charge transfer excitations into the U 6d shell appear at much higher energies. The MCD-allowed transitions can be assigned via their signs of the $C$-terms: Under O h double group symmetry, E 5/2u → E 5/2g transitions have negative $C$-terms whereas E 5/2u → F 3/2g transitions have positive $C$-terms if the ground state g-factor is negative, as it is the case for UCl 6-.« less
NASA Astrophysics Data System (ADS)
Pizzini, Stefania; Vogel, Jan; Bonfim, Marlio; Fontaine, Alain
Many synchrotron radiation techniques have been developed in the last 15 years for studying the magnetic properties of thin-film materials. The most attractive properties of synchrotron radiation are its energy tunability and its time structure. The first property allows measurements in resonant conditions at an absorption edge of each of the magnetic elements constituting the probed sample, and the latter allows time-resolved measurements on subnanosecond timescales. In this review, we introduce some of the synchrotron-based techniques used for magnetic investigations. We then describe in detail X-ray magnetic circular dichroism (XMCD) and how time-resolved XMCD studies can be carried out in the pump-probe mode. Finally, we illustrate some applications to magnetization reversal dynamics in spin valves and tunnel junctions, using fast magnetic field pulses applied along the easy magnetization axis of the samples. Thanks to the element-selectivity of X-ray absorption spectroscopy, the magnetization dynamics of the soft (Permalloy) and the hard (cobalt) layers can be studied independently. In the case of spin valves, this allowed us to show that two magnetic layers that are strongly coupled in a static regime can become uncoupled on nanosecond timescales.Present address: Universidade Federal do Paraná, Centro Politécnico CP 19011, Curitiba - PR CEP 81531-990, Brazil
Siligardi, Giuliano; Hussain, Rohanah; Patching, Simon G; Phillips-Jones, Mary K
2014-01-01
A great number of membrane proteins have proven difficult to crystallise for use in X-ray crystallographic structural determination or too complex for NMR structural studies. Circular dichroism (CD) is a fast and relatively easy spectroscopic technique to study protein conformational behaviour. In this review examples of the applications of CD and synchrotron radiation CD (SRCD) to membrane protein ligand binding interaction studies are discussed. The availability of SRCD has been an important advancement in recent progress, most particularly because it can be used to extend the spectral region in the far-UV region (important for increasing the accuracy of secondary structure estimations) and for working with membrane proteins available in only small quantities for which SRCD has facilitated molecular recognition studies. Such studies have been accomplished by probing in the near-UV region the local tertiary structure of aromatic amino acid residues upon addition of chiral or non-chiral ligands using long pathlength cells of small volume capacity. In particular, this review describes the most recent use of the technique in the following areas: to obtain quantitative data on ligand binding (exemplified by the FsrC membrane sensor kinase receptor); to distinguish between functionally similar drugs that exhibit different mechanisms of action towards membrane proteins (exemplified by secretory phospholipase A2); and to identify suitable detergent conditions to observe membrane protein-ligand interactions using stabilised proteins (exemplified by the antiseptic transporter SugE). Finally, the importance of characterising in solution the conformational behaviour and ligand binding properties of proteins in both far- and near-UV regions is discussed. This article is part of a Special Issue entitled: Structural and biophysical characterisation of membrane protein-ligand binding. © 2013.
Tanaka, Hiroki; Inoue, Yoshihisa; Nakano, Takeshi; Mori, Tadashi
2017-04-12
Circular dichroisms (CDs) of the o,p'-isomers of 1,1,1-trichloro- and 1,1-dichloro-2,2-bis(chlorophenyl)ethanes (DDT and DDD) were investigated experimentally and theoretically. A series of strong Cotton effect peaks in a characteristic negative-negative-positive-negative, or its mirror-imaged, pattern were observed in the CD spectra of these persistent organic pollutants. The theoretical CD spectra at the SAC-CI/B95(d) and RI-CC2/def2-TZVPP levels well reproduced the experimental ones, enabling us to unambiguously assign the absolute configuration of (+)-DDT and (-)-DDD as S.
Song, Dongsheng; Tavabi, Amir H.; Li, Zi-An; Kovács, András; Rusz, Ján; Huang, Wenting; Richter, Gunther; Dunin-Borkowski, Rafal E.; Zhu, Jing
2017-01-01
Electron energy-loss magnetic chiral dichroism is a powerful technique that allows the local magnetic properties of materials to be measured quantitatively with close-to-atomic spatial resolution and element specificity in the transmission electron microscope. Until now, the technique has been restricted to measurements of the magnetic circular dichroism signal in the electron beam direction. However, the intrinsic magnetization directions of thin samples are often oriented in the specimen plane, especially when they are examined in magnetic-field-free conditions in the transmission electron microscope. Here, we introduce an approach that allows in-plane magnetic signals to be measured using electron magnetic chiral dichroism by selecting a specific diffraction geometry. We compare experimental results recorded from a cobalt nanoplate with simulations to demonstrate that an electron magnetic chiral dichroism signal originating from in-plane magnetization can be detected successfully. PMID:28504267
DOE Office of Scientific and Technical Information (OSTI.GOV)
Lee, Geon Joon, E-mail: gjlee@kw.ac.kr; Sim, Geon Bo; Choi, Eun Ha
To understand the killing mechanism of fungal spores by plasma treatment, the optical, structural, and biological properties of the insect pathogenic fungus Cordyceps bassiana spores were studied. A nonthermal atmospheric-pressure plasma jet (APPJ) was used to treat the spores in aqueous solution. Optical emission spectra of the APPJ acquired in air indicated emission peaks corresponding to hydroxyl radicals and atomic oxygen. When the APPJ entered the aqueous solution, additional reactive species were derived from the interaction of plasma radicals with the aqueous solution. Fluorescence and absorption spectroscopy confirmed the generation of hydroxyl radicals and hydrogen peroxide in the plasma-activated watermore » (PAW). Spore counting showed that plasma treatment significantly reduced spore viability. Absorption spectroscopy, circular dichroism (CD) spectroscopy, and agarose gel electrophoresis of the DNA extracted from plasma-treated spores showed a reduction in spore DNA content. The magnitude of the dip in the CD spectrum was lower in the plasma-treated spores than in the control, indicating that plasma treatment causes structural modifications and/or damage to cellular components. Tryptophan fluorescence intensity was lower in the plasma-treated spores than in the control, suggesting that plasma treatment modified cell wall proteins. Changes in spore viability and DNA content were attributed to structural modification of the cell wall by reactive species coming from the APPJ and the PAW. Our results provided evidence that the plasma radicals and the derived reactive species play critical roles in fungal spore inactivation.« less
NASA Astrophysics Data System (ADS)
Lee, Geon Joon; Sim, Geon Bo; Choi, Eun Ha; Kwon, Young-Wan; Kim, Jun Young; Jang, Siun; Kim, Seong Hwan
2015-01-01
To understand the killing mechanism of fungal spores by plasma treatment, the optical, structural, and biological properties of the insect pathogenic fungus Cordyceps bassiana spores were studied. A nonthermal atmospheric-pressure plasma jet (APPJ) was used to treat the spores in aqueous solution. Optical emission spectra of the APPJ acquired in air indicated emission peaks corresponding to hydroxyl radicals and atomic oxygen. When the APPJ entered the aqueous solution, additional reactive species were derived from the interaction of plasma radicals with the aqueous solution. Fluorescence and absorption spectroscopy confirmed the generation of hydroxyl radicals and hydrogen peroxide in the plasma-activated water (PAW). Spore counting showed that plasma treatment significantly reduced spore viability. Absorption spectroscopy, circular dichroism (CD) spectroscopy, and agarose gel electrophoresis of the DNA extracted from plasma-treated spores showed a reduction in spore DNA content. The magnitude of the dip in the CD spectrum was lower in the plasma-treated spores than in the control, indicating that plasma treatment causes structural modifications and/or damage to cellular components. Tryptophan fluorescence intensity was lower in the plasma-treated spores than in the control, suggesting that plasma treatment modified cell wall proteins. Changes in spore viability and DNA content were attributed to structural modification of the cell wall by reactive species coming from the APPJ and the PAW. Our results provided evidence that the plasma radicals and the derived reactive species play critical roles in fungal spore inactivation.
NASA Astrophysics Data System (ADS)
Wu, Y. J.; Shen, C.; Tan, Q. H.; Shi, J.; Liu, X. F.; Wu, Z. H.; Zhang, J.; Tan, P. H.; Zheng, H. Z.
2018-04-01
The valley Zeeman splitting of monolayer two-dimensional (2D) materials in the magnetic field plays an important role in the valley and spin manipulations. In general, a high magnetic field (6-65 T) and low temperature (2-30 K) were two key measurement conditions to observe the resolvable valley Zeeman splitting of monolayer 2D materials in current reported experiments. In this study, we experimentally demonstrate an effective measurement scheme by employing magnetic circular dichroism (MCD) spectroscopy, which enables us to distinguish the valley Zeeman splitting under a relatively low magnetic field of 1 T at room temperature. MCD peaks related to both A and B excitonic transitions in monolayer MoS2 can be clearly observed. Based on the MCD spectra under different magnetic fields (-3 to 3 T), we obtained the valley Zeeman splitting energy and the g-factors of A and B excitons, respectively. Our results show that MCD spectroscopy is a high-sensitive magneto-optical technique to explore the valley and spin manipulation in 2D materials.
NASA Astrophysics Data System (ADS)
Staab, Maximilian; Kutnyakhov, Dmytro; Wallauer, Robert; Chernov, Sergey; Medjanik, Katerina; Elmers, Hans Joachim; Kläui, Mathias; Schönhense, Gerd
2017-04-01
The magnetic circular dichroism in threshold photoemission (TPMCD) for perpendicularly magnetized fcc Co films on Pt(111) has been revisited. A complete mapping of the spectral function I (EB,kx,ky) (binding energy EB, momentum parallel to surface kx, ky) and the corresponding TPMCD asymmetry distribution AMCD(EB,kx,ky) has been performed for one-photon and two-photon photoemission using time-of-flight momentum microscopy. The experimental results allow distinguishing direct from indirect transitions. The measurements reveal clear band features of direct transitions from bulk bands that show a nontrivial asymmetry pattern. A significant homogeneous background with substantial asymmetry stemming from indirect transitions superposes direct transitions. Two-photon photoemission reveals enhanced emission intensity via an image potential state, acting as intermediate state. The image potential state enhances not only intensity but also asymmetry. The present results demonstrate that two-photon photoemission is a powerful method for mapping the spin-polarized unoccupied band structures and points out pathways for applying TPMCD as a contrast mechanism for various classes of magnetic materials.
Cheng, Jiaji; Hao, Junjie; Liu, Haochen; Li, Jiagen; Li, Junzi; Zhu, Xi; Lin, Xiaodong; Wang, Kai; He, Tingchao
2018-05-30
Ligand-induced chirality in semiconductor nanocrystals (NCs) has attracted attention because of the tunable optical properties of the NCs. Induced circular dichroism (CD) has been observed in CdX (X = S, Se, Te) NCs and their hybrids, but circularly polarized luminescence (CPL) in these fluorescent nanomaterials has been seldom reported. Herein, we describe the successful preparation of l- and d-cysteine-capped CdSe-dot/CdS-rods (DRs) with tunable CD and CPL behaviors and a maximum anisotropic factor ( g lum ) of 4.66 × 10 -4 . The observed CD and CPL activities are sensitive to the relative absorption ratio of the CdS shell to the CdSe core, suggesting that the anisotropic g-factors in both CD and CPL increase to some extent for a smaller shell-to-core absorption ratio. In addition, the molar ratio of chiral cysteine to the DRs is investigated. Instead of enhancing the chiral interactions between the chiral molecules and DRs, an excess of cysteine molecules in aqueous solution inhibits both the CD and CPL activities. Such chiral and emissive NCs provide an ideal platform for the rational design of semiconductor nanomaterials with chiroptical properties.
Jangir, Deepak Kumar; Dey, Sanjay Kumar; Kundu, Suman; Mehrotra, Ranjana
2012-09-03
Proper understanding of the mechanism of binding of drugs to their targets in cell is a fundamental requirement to develop new drug therapy regimen. Amsacrine is a rationally designed anticancer drug, used to treat leukemia and lymphoma. Binding with cellular DNA is a crucial step in its mechanism of cytotoxicity. Despite numerous studies, DNA binding properties of amsacrine are poorly understood. Its reversible binding with DNA does not permit X-ray crystallography or NMR spectroscopic evaluation of amsacrine-DNA complexes. In the present work, interaction of amsacrine with calf thymus DNA is investigated at physiological conditions. UV-visible, FT-Raman and circular dichroism spectroscopic techniques were employed to determine the binding mode, binding constant, sequence specificity and conformational effects of amsacrine binding to native calf thymus DNA. Our results illustrate that amsacrine interacts with DNA by and large through intercalation between base pairs. Binding constant of the amsacrine-DNA complex was found to be K=1.2±0.1×10(4) M(-1) which is indicative of moderate type of binding of amsacrine to DNA. Raman spectroscopic results suggest that amsacrine has a binding preference of intercalation between AT base pairs of DNA. Minor groove binding is also observed in amsacrine-DNA complexes. These results are in good agreement with in silico investigation of amsacrine binding to DNA and thus provide detailed insight into DNA binding properties of amsacrine, which could ultimately, renders its cytotoxic efficacy. Copyright © 2012 Elsevier B.V. All rights reserved.
Miyahara, Tomoo; Nakatsuji, Hiroshi; Sugiyama, Hiroshi
2016-11-17
The helical structures of DNA and RNA are investigated experimentally using circular dichroism (CD) spectroscopy. The signs and the shapes of the CD spectra are much different between the right- and left-handed structures as well as between DNA and RNA. The main difference lies in the sign at around 295 nm of the CD spectra: it is positive for the right-handed B-DNA and the left-handed Z-RNA but is negative for the left-handed Z-DNA and the right-handed A-RNA. We calculated the SAC-CI CD spectra of DNA and RNA using the tetramer models, which include both hydrogen-bonding and stacking interactions that are important in both DNA and RNA. The SAC-CI results reproduced the features at around 295 nm of the experimental CD spectra of each DNA and RNA, and elucidated that the strong stacking interaction between the two base pairs is the origin of the negative peaks at 295 nm of the CD spectra for both DNA and RNA. On the basis of these facts, we discuss the similarities and differences between RNA and DNA double-helical structures in the CD spectroscopy based on the ChiraSac methodology.
Vujčić, Valerija; Radić Brkanac, Sandra; Radojčić Redovniković, Ivana; Ivanković, Siniša; Stojković, Ranko; Žilić, Irena; Radić Stojković, Marijana
2017-11-01
The phytochemical composition and biological activity of non-volatile components of Centaurea ragusina L. has not been studied previously. Our aim was to evaluate the phytochemical and bioactive potential (including interactions with polynucleotides) of C. ragusina L. depending on the origin of plant material (in vivo - leaves from natural habitats, ex vitro - leaves from plants acclimated from culture media, in vitro - leaves and calli from plants grown in culture media) and polarity of solvents used in extract preparation (80 and 96% ethanol and water combinations or single solvents). The polyphenol composition was determined by spectrophotometric and HPLC analysis. Biological activity of extracts was evaluated by following methods: 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) and 1,1-diphenyl-2-picrylhydrazyl (DPPH) methods for antioxidative activity, 2,3,5-triphenyl tetrazolium chloride (TTC) microdilution method for antibacterial activity, crystal-violet test for cytotoxic activity and thermal denaturation (TD) and circular dichroism (CD) for DNA/RNA interactions. Conditions for the most efficient polyphenol extraction were determined: the 80% ethanol/water solvent system was the most suitable for callus and leaf ex vitro samples and 80 or 96% ethanol for leaf in vivo samples. Significantly higher levels of chlorogenic acid and naringenin were detected in callus tissue than in vivo plant. Ethanolic extracts exhibited the significant antibacterial activity against Staphylococcus aureus ATCC 25923. DNA/RNA active compounds in plant extracts were detected by TD and CD methods. Callus tissue and ex vitro leaves represent a valuable source of polyphenols as in vivo leaves. TD and CD can be applied for detection of DNA/RNA active compounds in extracts from natural resources. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.
The circular dichroism properties of phi W-14 DNA containing alpha-putrescinylthymine.
Spetter, S; Chen, C; Warren, R A; Hanlon, S
1985-03-08
The circular dichroism properties of phi W-14 DNA containing alpha-putrescinylthymine and its acetylated derivative have been examined in a number of aqueous solvents. Native phi W-14 DNA exhibits a B-type CD spectrum whose characteristics do not entirely conform to what would be expected for its GC content (51%). The conformationally sensitive positive band above 260 nm has a rotational strength greater than that normally found in prokaryotic DNAs of comparable GC content, such as Escherichia coli DNA. The rotational strength of this band in the spectrum of the heat-denatured form of phi W-14 DNA, however, is similar to that of heat denatured E. coli DNA. Abolition of the positive charge on the putrescine residues of native phi W-14 DNA by reaction with CH2O or by acetylation reduces the rotational strength to a level appropriate for its GC content. Increases in the electrolyte content of the solvent have the same effect, although the rotational strength of this band in phi W-14 DNA does not become comparable to that of E. coli DNA until 6-7 M LiCl. Titration to pH 10.6 in solvents of modest electrolyte content, however, fails to appreciably affect the CD spectral properties of either native phi W-14 DNA or the derivative in which half of the secondary and all of the primary amino groups have been acetylated. On the basis of these results we have concluded that the enhanced rotational strength of the positive band above 260 nm in the CD spectrum of phi W-14 DNA is due to a conformational difference caused by an ion-pair interaction of the positively charged primary amino groups of putrescine with the phosphate backbone. The CD spectral properties, however, reveal that these differences, averaged over the entire basepair population, appear to be relatively small. The average conformation, at least in dilute aqueous solutions, seems to be an unexceptional B variant with conformational properties which would be more appropriate for a DNA of higher CG content.
Miyake, Hiroyuki; Terada, Keiko; Tsukube, Hiroshi
2014-06-01
A series of lanthanide tris(β-diketonates) functioned as useful chirality probes in the vibrational circular dichroism (VCD) characterization of biological amino alcohols. Various chiral amino alcohols induced intense VCD signals upon ternary complexation with racemic lanthanide tris(β-diketonates). The VCD signals observed around 1500 cm(-1) (β-diketonate IR absorption region) correlated well with the stereochemistry and enantiomeric purity of the targeted amino alcohol, while the corresponding monoalcohol, monoamine, and diol substrates induced very weak VCD signals. The high-coordination number and dynamic property of the lanthanide complex offer an effective chirality VCD probing of biological substrates. © 2014 Wiley Periodicals, Inc.
Thersleff, Thomas; Rusz, Jan; Rubino, Stefano; Hjörvarsson, Björgvin; Ito, Yasuo; J Zaluzec, Nestor; Leifer, Klaus
2015-08-17
Understanding the ramifications of reduced crystalline symmetry on magnetic behavior is a critical step in improving our understanding of nanoscale and interfacial magnetism. However, investigations of such effects are often controversial largely due to the challenges inherent in directly correlating nanoscale stoichiometry and structure to magnetic behavior. Here, we describe how to use Transmission Electron Microscope (TEM) to obtain Electron Magnetic Circular Dichroism (EMCD) signals as a function of scattering angle to locally probe the magnetic behavior of thin oxide layers grown on an Fe (1 1 0) surface. Experiments and simulations both reveal a strong dependence of the magnetic orbital to spin ratio on its scattering vector in reciprocal space. We exploit this variation to extract the magnetic properties of the oxide cladding layer, showing that it locally may exhibit an enhanced orbital to spin moment ratio. This finding is supported here by both spatially and angularly resolved EMCD measurements, opening up the way for compelling investigations into how magnetic properties are affected by nanoscale features.
Jose, K V Jovan; Raghavachari, Krishnan
2016-12-01
The molecules-in-molecules (MIM) fragment-based method has recently been adapted to evaluate the chiroptical (vibrational circular dichroism [VCD] and Raman optical activity [ROA]) spectra of large molecules such as peptides. In the MIM-VCD and MIM-ROA methods, the relevant higher energy derivatives of the parent molecule are assembled from the corresponding derivatives of smaller fragment subsystems. In addition, the missing long-range interfragment interactions are accounted at a computationally less expensive level of theory (MIM2). In this work we employed the MIM-VCD and MIM-ROA fragment-based methods to explore the evolution of the chiroptical spectroscopic characteristics of 3 10 -helix, α-helix, β-hairpin, γ-turn, and β-extended conformers of gas phase polyalanine (chain length n = 6-14). The different conformers of polyalanine show distinctive features in the MIM chiroptical spectra and the associated spectral intensities increase with evolution of system size. For a better understanding the site-specific effects on the vibrational spectra, isotopic substitutions were also performed employing the MIM method. An increasing redshift with the number of isotopically labeled 13 C=O functional groups in the peptide molecule was seen. For larger polypeptides, we implemented the two-step-MIM model to circumvent the high computational expense associated with the evaluation of chiroptical spectra at a high level of theory using large basis sets. The chiroptical spectra of α-(alanine) 20 polypeptide obtained using the two-step-MIM model, including continuum solvation effects, show good agreement with the full calculations and experiment. This benchmark study suggests that the MIM-fragment approach can assist in predicting and interpreting chiroptical spectra of large polypeptides. © 2016 Wiley Periodicals, Inc.
NASA Astrophysics Data System (ADS)
Antonov, V. N.; Bekenov, L. V.; Uba, S.; Ernst, A.
2017-12-01
We studied the structural, electronic, and magnetic properties of Mn-doped topological insulators Bi2Se3 and Bi2Te3 within the density-functional theory (DFT) using the generalized gradient approximation (GGA) in the framework of the fully relativistic spin-polarized Dirac linear muffin-tin orbital band-structure method. The x-ray absorption spectra (XAS) and x-ray magnetic circular dichroism at the Mn K and L2 ,3 edges were investigated theoretically from first principles. The calculated results are in good agreement with experimental data. The complex fine structure of the Mn L2 ,3 XAS in Mn-doped Bi2Se3 and Bi2Te3 was found to be not compatible with a pure Mn3 + valency state. Its interpretation demands mixed valent states. The theoretically calculated x-ray emission spectra at the Mn K and L2 ,3 edges are also presented and analyzed.
Bannwarth, Christoph; Seibert, Jakob; Grimme, Stefan
2016-05-01
The electronic circular dichroism (ECD) spectrum of the recently synthesized [16]helicene and a derivative comprising two triisopropylsilyloxy protection groups was computed by means of the very efficient simplified time-dependent density functional theory (sTD-DFT) approach. Different from many previous ECD studies of helicenes, nonequilibrium structure effects were accounted for by computing ECD spectra on "snapshots" obtained from a molecular dynamics (MD) simulation including solvent molecules. The trajectories are based on a molecule specific classical potential as obtained from the recently developed quantum chemically derived force field (QMDFF) scheme. The reduced computational cost in the MD simulation due to the use of the QMDFF (compared to ab-initio MD) as well as the sTD-DFT approach make realistic spectral simulations feasible for these compounds that comprise more than 100 atoms. While the ECD spectra of [16]helicene and its derivative computed vertically on the respective gas phase, equilibrium geometries show noticeable differences, these are "washed" out when nonequilibrium structures are taken into account. The computed spectra with two recommended density functionals (ωB97X and BHLYP) and extended basis sets compare very well with the experimental one. In addition we provide an estimate for the missing absolute intensities of the latter. The approach presented here could also be used in future studies to capture nonequilibrium effects, but also to systematically average ECD spectra over different conformations in more flexible molecules. Chirality 28:365-369, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
Orestes, Ednilsom; Bistafa, Carlos; Rivelino, Roberto; Canuto, Sylvio
2015-05-28
The vibrational circular dichroism (VCD) spectrum of l-alanine amino acid in aqueous solution in ambient conditions has been studied. The emphasis has been placed on the inclusion of the thermal disorder of the solute-solvent hydrogen bonds that characterize the aqueous solution condition. A combined and sequential use of molecular mechanics and quantum mechanics was adopted. To calculate the average VCD spectrum, the DFT B3LYP/6-311++G(d,p) level of calculation was employed, over one-hundred configurations composed of the solute plus all water molecules making hydrogen bonds with the solute. Simplified considerations including only four explicit solvent molecules and the polarizable continuum model were also made for comparison. Considering the large number of vibration frequencies with only limited experimental results a direct comparison is presented, when possible, and in addition a statistical analysis of the calculated values was performed. The results are found to be in line with the experiment, leading to the conclusion that including thermal disorder may improve the agreement of the vibrational frequencies with experimental results, but the thermal effects may be of greater value in the calculations of the rotational strengths.
Setnicka, Vladimír; Urbanová, Marie; Volka, Karel; Nampally, Sreenivasachary; Lehn, Jean-Marie
2006-11-24
The self-assembly of guanosine-5'-hydrazide G-1 in D(2)O, in the presence and absence of sodium cations, has been investigated by chiroptical techniques: electronic (ECD) and the newly introduced vibrational (VCD) circular dichroism spectroscopy. Using a combination of ECD and VCD with other methods such as IR, electron microscopy, and electrospray ionization mass spectrometry (ESI-MS) it was found that G-1 produces long-range chiral aggregates consisting of G-quartets, (G-1)(4), subsequently stacked into columns, [(G-1)(4)](n), induced by binding of metal cations between the (G-1)(4) species. This process, accompanied by gelation of the sample, is highly efficient in the presence of an excess of sodium cations, leading to aggregates with strong quartet-quartet interaction. Thermally induced conformational changes and conformational stability of guanosine-5'-hydrazide assemblies were studied by chiroptical techniques and the melting temperature of the hydrogels formed was obtained. The temperature-dependent experiments indicate that the long-range supramolecular aggregates are dissociated by increasing temperature into less ordered species, monomers, or other intermediates in equilibrium, as indicated by MS experiments.
Weisshoff, Hardy; Wenzel, Katrin; Schulze-Rothe, Sarah; Nikolenko, Heike; Davideit, Hanna; Becker, Niels-Peter; Göttel, Peter; Srivatsa, G Susan; Dathe, Margitta; Müller, Johannes; Haberland, Annekathrin
2018-04-18
Possible unwanted folding of biopharmaceuticals during manufacturing and storage has resulted in analysis schemes compared to small molecules that include bioanalytical characterization besides chemical characterization. Whether bioanalytical characterization is required for nucleotide-based drugs, may be decided on a case-by-case basis. Nucleotide-based pharmaceuticals, if chemically synthesized, occupy an intermediate position between small-molecule drugs and biologics. Here, we tested whether a physicochemical characterization of a nucleotide-based drug substance, BC 007, was adequate, using circular dichroism (CD) spectroscopy. Nuclear magnetic resonance confirmed CD data in one experimental setup. BC 007 forms a quadruplex structure under specific external conditions, which was characterized for its stability and structural appearance also after denaturation using CD and nuclear magnetic resonance. The amount of the free energy (ΔG 0 ) involved in quadruplex formation of BC 007 was estimated at +8.7 kJ/mol when dissolved in water and +1.4 kJ/mol in 154 mM NaCl, indicating structural instability under these conditions. However, dissolution of the substance in 5 mM of KCl reduced the ΔG 0 to -5.6 kJ/mol due to the stabilizing effect of cations. These results show that positive ΔG 0 of quadruplex structure formation in water and aqueous NaCl prevents BC 007 from preforming stable 3-dimensional structures, which could potentially affect drug function. Copyright © 2018 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.
Observation of circular dichroism in photoelectron angular distributions
DOE Office of Scientific and Technical Information (OSTI.GOV)
Appling, J.R.; White, M.G.; Orlando, T.M.
1986-12-01
The first observations of dichroic effects in photoelectron angular distributions are reported for photoionization of aligned molecular excited states with circularly polarized light. Photoelectron angular distributions resulting from the two-color, (2+1) REMPI of NO via the A /sup 2/summation/sup +/, v = 0, J = 3/2,5/2 excited states exhibit significant left--right asymmetry. The experimental CD angular distributions are found to be well described by the general theoretical framework recently developed by Dubs, Dixit, and McKoy and are in good qualitative agreement with their calculated REMPI--CD distributions.
Observation of circular dichroism in photoelectron angular distributions
NASA Astrophysics Data System (ADS)
Appling, Jeffrey R.; White, Michael G.; Orlando, Thomas M.; Anderson, Scott L.
1986-12-01
The first observations of dichroic effects in photoelectron angular distributions are reported for photoionization of aligned molecular excited states with circularly polarized light. Photoelectron angular distributions resulting from the two-color, (2+1) REMPI of NO via the A 2∑+, v=0, J=3/2,5/2 excited states exhibit significant left-right asymmetry. The experimental CD angular distributions are found to be well described by the general theoretical framework recently developed by Dubs, Dixit, and McKoy and are in good qualitative agreement with their calculated REMPI-CD distributions.
Fahleson, Tobias; Kauczor, Joanna; Norman, Patrick; Santoro, Fabrizio; Improta, Roberto; Coriani, Sonia
2015-05-28
We present a computational study of the magnetic circular dichroism (MCD) spectra in the 200-300 nm wavelength region of purine and its derivative hypoxanthine, as well as of the pyrimidine bases of nucleic acids uracil, thymine, and cytosine, using the B3LYP and CAM-B3LYP functionals. Solvent effects are investigated within the polarizable continuum model and by inclusion of explicit water molecules. In general, the computed spectra are found to be in good agreement with the experimental ones, apart from some overall blue shifts. Both the pseudo-A term shape of the MCD spectra of the purines and the B term shape of the spectra of pyrimidine bases are reproduced. Our calculations also correctly reproduce the reversed phase of the MCD bands in purine compared to that of its derivatives present in nucleic acids. Solvent effects are sizable and system specific, but they do not in general alter the qualitative shape of the spectra. The bands are dominated by the bright π → π* transitions, and our calculations in solution nicely reproduce their energy differences, improving the estimates obtained in the gas phase. Shoulders are predicted for purine and uracil due to n → π* excitations, but they are too weak to be observed in the experiment.
NASA Astrophysics Data System (ADS)
Takeda, Yukiharu; Saitoh, Yuji; Okane, Tetsuo; Yamagami, Hiroshi; Matsuda, Tatsuma D.; Yamamoto, Etsuji; Haga, Yoshinori; Ōnuki, Yoshichika
2018-05-01
We have performed soft x-ray magnetic circular dichroism (XMCD) experiments on the itinerant-electron metamagnet UCoAl at the U 4 d -5 f (N4 ,5) and Co 2 p -3 d (L2 ,3) absorption edges in order to investigate the magnetic properties of the U 5 f and Co 3 d electrons separately. From the line shape of the XMCD spectrum, it is deduced that the orbital magnetic moment of the Co 3 d electrons is unusually large. Through the systematic temperature (T )- and magnetic field (H )-dependent XMCD measurements, we have obtained two types of the magnetization curve as a function of H and T (M-H curve and M-T curve, respectively). The metamagnetic transition from a paramagnetic state to a field-induced ferromagnetic state was clearly observed under 15 K at HM. The value of the HM and its T dependence agree well between the U and Co sites, and the bulk magnetization. Whereas, we have discovered the remarkable differences in the M-H and M-T curves between the U and Co sites. The present findings clearly show that the role of the Co 3 d electrons should be considered more carefully in order to understand the origin of the magnetic ordering in UCoAl.
Janda, Alena; Casadevall, Arturo
2010-04-01
Antibodies (Ab) are bifunctional molecules with two domains, a constant region (C) that confers effector properties and a variable (V) region responsible of antigen (Ag) binding. Historically the C and V regions were considered to be functionally independent, with Ag specificity being solely determined by the V region. However, recent studies suggest that the C region can affect Ab fine specificity. This has led to the proposal that the C(H) domain influences the structure of the V region, thus affecting Ab affinity and fine specificity. An inference from this proposal is that V region identical monoclonal Abs (mAbs) differing in C region (eg isotype) would manifest different secondary structures arising from isotype-induced variation in the V-C regions after Ag binding. We hypothesized that such effects could translate into differences in Circular Dichroism (CD) upon Ag-Ab complexes formation. Consequently we studied the interaction of a set of V region identical IgG(1), IgG(2a), IgG(2b) and IgG(3) mAbs with glucuronoxylomannan (GXM). The native CD spectra of the pairs IgG(1)/IgG(2a) and IgG(3)/IgG(2b) were strikingly similar, implying similar secondary structure content. GXM binding by IgG(1), IgG(2a), IgG(2b) and IgG(3) produced different CD changes, with the pairs IgG(1)/IgG(2a) and IgG(3)/IgG(2b) again manifesting qualitatively similar trends in secondary structure changes. The magnitude of the changes differed among the isotypes with IgG(2a)>IgG(3)>IgG(2b)>IgG(1). These differences in CD changes were interpreted to reflect differences in V-C secondary structures. Copyright 2010 Elsevier Ltd. All rights reserved.
Benincori, Tiziana; Appoloni, Giulio; Mussini, Patrizia Romana; Arnaboldi, Serena; Cirilli, Roberto; Quartapelle Procopio, Elsa; Panigati, Monica; Abbate, Sergio; Mazzeo, Giuseppe; Longhi, Giovanna
2018-05-02
Two new inherently chiral oligothiophenes characterized by the atropisomeric 3,3'-bithianaphtene scaffold functionalized with fused ring bithiophene derivatives, namely 4H-cyclopenta [2,1-b3:4b']dithiophene (CPDT) and dithieno[3,3-b:2',3'-d]pyrrole (DTP), were synthesized. The racemates were fully characterized and resolved into antipodes by enantioselective HPLC. The enantiomers were analyzed through different chiroptical techniques: electronic circular dichroism (ECD) and vibrational circular dichroism (VCD) were employed to attribute the absolute configuration (AC). Comparison of experimental and calculated VCD spectra confirmed the DFT calculated conformational characteristics. The compound functionalized with two CPDT units was oxidized with FeCl3 and ECD and CPL of the resulting material were measured. Circularly Polarized Luminescence (CPL) was measured in order to verify if inherently chiral oligothiophenes could be promising systems for chiral photonics applications. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
What can we Learn on Gas Phase Chiral Compounds by Photoelectron Circular Dichroism ?
NASA Astrophysics Data System (ADS)
Nahon, Laurent
2017-06-01
Since 15 years, a new type of chiroptical effect has been the subject of a large array of both theoretical and experimental studies: Photoelectron Circular Dichroism (PECD) in the angular distribution of photoelectrons produced by CPL-ionization of pure enantiomers in the gas phase observed as a very intense (up to 35 %) forward/backward asymmetry with respect to the photon axis and which reveals the chirality of the molecule (configuration). PECD happens to be an orbital-specific, photon energy dependent effect and is a very subtle probe of the molecular potential being very sensitive to static molecular structures such as conformers, chemical substitution, clusters, as well as to vibrational motion, much more so than other observables in photoionization such as the cross section or the β asymmetry parameter (for a recent review see L. Nahon, G. A. Garcia, and I. Powis, J. Elec. Spec. Rel. Phen. 204, 322 (2015)). Therefore PECD studies have both a fundamental interest as well and analytical interest, especially since chiral species are ubiquitous in the biosphere, food and medical industry. This last aspect is probably the driving force for the recent extension of PECD studies by the laser community using UV REMPI schemes. After a large introduction to the PECD process itself, and a description of our double imaging electron/ion coincidence set-up, several recent results on one-photon VUV PECD will be presented, including: - Sensitivity to chemical substitutions, isomerism and conformation - Case of floppy biomolecules such as amino acids alanine and proline with a conformer analysis and possible consequences for the origin of life's homochirality - Analytical capabilities in terms of enantiomeric excess determination on a pure molecule as well as on a mixture of compounds. Future trends for PECD studies will be given regarding the case of more complex/structured chiral systems as well as opportunities for time-resolved PECD opened by the recent first performance
NASA Astrophysics Data System (ADS)
Miyawaki, Jun; Suga, Shigemasa; Fujiwara, Hidenori; Urasaki, Masato; Ikeno, Hidekazu; Niwa, Hideharu; Kiuchi, Hisao; Harada, Yoshihisa
2017-12-01
Fe L2 ,3-edge x-ray absorption spectra (XAS) and magnetic circular dichroism (MCD) in resonant inelastic x-ray scattering (RIXS) of α -Fe2O3 were measured to identify the electronic structure responsible for its weak ferromagnetism caused by the Dzyaloshinskii-Moriya interaction (DMI) at room temperature. In contrast to negligible MCD in XAS, MCD in RIXS (RIXS-MCD) was clearly observed in the d d excitation at 1.8 eV via excitation to charge-transfer states. Furthermore, RIXS-MCD showed a crystal orientation dependence, indicating that the observed RIXS-MCD originated from DMI. The observed RIXS-MCD is well described by ab initio charge-transfer multiplet calculations, revealing that the RIXS-MCD derives from spin flip excitations at delocalized eg orbitals. By the combination of the experiments and calculations, RIXS-MCD has unraveled that the origin of DMI in α -Fe2O3 is the eg orbitals, which are strongly hybridized with the 2 p orbitals of oxygen atoms. The results demonstrate the importance of RIXS-MCD for identifying the electronic structure related to DMI.
Thersleff, Thomas; Rusz, Jan; Rubino, Stefano; ...
2015-08-17
Understanding the ramifications of reduced crystalline symmetry on magnetic behavior is a critical step in improving our understanding of nanoscale and interfacial magnetism. However, investigations of such effects are often controversial largely due to the challenges inherent in directly correlating nanoscale stoichiometry and structure to magnetic behavior. Here, we describe how to use Transmission Electron Microscope (TEM) to obtain Electron Magnetic Circular Dichroism (EMCD) signals as a function of scattering angle to locally probe the magnetic behavior of thin oxide layers grown on an Fe (1 1 0) surface. Experiments and simulations both reveal a strong dependence of the magneticmore » orbital to spin ratio on its scattering vector in reciprocal space. We exploit this variation to extract the magnetic properties of the oxide cladding layer, showing that it locally may exhibit an enhanced orbital to spin moment ratio. This finding is supported here by both spatially and angularly resolved EMCD measurements, opening up the way for compelling investigations into how magnetic properties are affected by nanoscale features.« less
DOE Office of Scientific and Technical Information (OSTI.GOV)
Friese, Daniel H., E-mail: daniel.h.friese@uit.no
2015-09-07
This addendum shows the detailed derivation of the fundamental equations for two-photon circular dichroism which are given in a very condensed form in the original publication [I. Tinoco, J. Chem. Phys. 62, 1006 (1975)]. In addition, some minor errors are corrected and some of the derivations in the original publication are commented.
Goncharova, Iryna
2014-01-24
Ag(I)-containing compounds are attractive as antibacterial and antifungal agents. The renewed interest in the application of silver(I) compounds has led to the need for detailed knowledge of the mechanism of their action. One of the possible ways is the coordination of Ag(I) to G-C pairs of DNA, where Ag(+) ions form Ag(I)-mediated base pairs and inhibit the transcription. Herein, a systematic chiroptical study on silver(I)-mediated homo and mixed pairs of the C-G complementary-base derivatives cytidine(C) and 5'-guanosine monophosphate(G) in water is presented. Ag(I)-mediated homo and hetero pairs of G and C and their self-assembled species were studied under two pH levels (7.0 and 10.0) by vibrational (VCD) and electronic circular dichroism(ECD). VCD was used for the first time in this field and showed itself to be a powerful method for obtaining specific structural information in solution. Based on results of the VCD experiments, the different geometries of the homo pairs were proposed under pH 7.0 and 10.0. ECD was used as a diagnostic tool to characterize the studied systems and as a contact point between the previously defined structures of the metal or proton mediated pairs of nucleobases and the systems studied here. On the basis of the obtained data, the formation of the self-assembled species of cytidine with a structure similar to the i-motif structure in DNA was proposed at pH 10.0. Copyright © 2013 Elsevier B.V. All rights reserved.
NASA Astrophysics Data System (ADS)
Goncharova, Iryna
2014-01-01
Ag(I)-containing compounds are attractive as antibacterial and antifungal agents. The renewed interest in the application of silver(I) compounds has led to the need for detailed knowledge of the mechanism of their action. One of the possible ways is the coordination of Ag(I) to G-C pairs of DNA, where Ag+ ions form Ag(I)-mediated base pairs and inhibit the transcription. Herein, a systematic chiroptical study on silver(I)-mediated homo and mixed pairs of the C-G complementary-base derivatives cytidine(C) and 5‧-guanosine monophosphate(G) in water is presented. Ag(I)-mediated homo and hetero pairs of G and C and their self-assembled species were studied under two pH levels (7.0 and 10.0) by vibrational (VCD) and electronic circular dichroism(ECD). VCD was used for the first time in this field and showed itself to be a powerful method for obtaining specific structural information in solution. Based on results of the VCD experiments, the different geometries of the homo pairs were proposed under pH 7.0 and 10.0. ECD was used as a diagnostic tool to characterize the studied systems and as a contact point between the previously defined structures of the metal or proton mediated pairs of nucleobases and the systems studied here. On the basis of the obtained data, the formation of the self-assembled species of cytidine with a structure similar to the i-motif structure in DNA was proposed at pH 10.0.
NASA Astrophysics Data System (ADS)
Yuan, Lixia; Liu, Min; Liu, Guiqin; Li, Dacheng; Wang, Zhengping; Wang, Bingquan; Han, Jun; Zhang, Min
2017-02-01
Combination therapy with more than one therapeutic agent can improve therapeutic efficiency and decrease drug resistance. In this study, the interactions of human serum albumin (HSA) with individual or combined anticancer drugs, (-)-epigallocatechin-3-gallate (EGCG) and 5-fluorouracil (FU), were investigated by fluorescence and circular dichroism (CD) spectroscopy. The results demonstrated that the interaction of EGCG or FU with HSA is a process of static quenching and EGCG formed a more stable complex. The competitive experiments of site markers suggested that both anti-carcinogens mainly bound to site I (subdomain IIA). The interaction forces which play important roles in the binding process were discussed based on enthalpy and entropy changes. Moreover, the competition binding model for a ternary system was proposed so as to precisely calculate the binding parameters. The results demonstrated that one drug decreased the binding affinity of another drug with HSA, resulting in the increasing free drug concentration at the action sites. CD studies indicated that there was an alteration in HSA secondary structure due to the binding of EGCG and FU. It can be concluded that the combination of EGCG with FU may enhance anticancer efficacy. This finding may provide a theoretical basis for clinical treatments.
High-Energy Vacuum Birefringence and Dichroism in an Ultrastrong Laser Field
NASA Astrophysics Data System (ADS)
Bragin, Sergey; Meuren, Sebastian; Keitel, Christoph H.; Di Piazza, Antonino
2017-12-01
A long-standing prediction of quantum electrodynamics, yet to be experimentally observed, is the interaction between real photons in vacuum. As a consequence of this interaction, the vacuum is expected to become birefringent and dichroic if a strong laser field polarizes its virtual particle-antiparticle dipoles. Here, we derive how a generally polarized probe photon beam is influenced by both vacuum birefringence and dichroism in a strong linearly polarized plane-wave laser field. Furthermore, we consider an experimental scheme to measure these effects in the nonperturbative high-energy regime, where the Euler-Heisenberg approximation breaks down. By employing circularly polarized high-energy probe photons, as opposed to the conventionally considered linearly polarized ones, the feasibility of quantitatively confirming the prediction of nonlinear QED for vacuum birefringence at the 5 σ confidence level on the time scale of a few days is demonstrated for upcoming 10 PW laser systems. Finally, dichroism and anomalous dispersion in vacuum are shown to be accessible at these facilities.
Circular magnetoplasmonic modes in gold nanoparticles.
Pineider, Francesco; Campo, Giulio; Bonanni, Valentina; Fernández, César de Julián; Mattei, Giovanni; Caneschi, Andrea; Gatteschi, Dante; Sangregorio, Claudio
2013-10-09
The quest for efficient ways of modulating localized surface plasmon resonance is one of the frontiers in current research in plasmonics; the use of a magnetic field as a source of modulation is among the most promising candidates for active plasmonics. Here we report the observation of magnetoplasmonic modes on colloidal gold nanoparticles detected by means of magnetic circular dichroism (MCD) spectroscopy and provide a model that is able to rationalize and reproduce the experiment with unprecedented qualitative and quantitative accuracy. We believe that the steep slope observed at the plasmon resonance in the MCD spectrum can be very efficient in detecting changes in the refractive index of the surrounding medium, and we give a simple proof of principle of its possible implementation for magnetoplasmonic refractometric sensing.
Farkas, Viktor; Jákli, Imre; Tóth, Gábor K; Perczel, András
2016-09-19
Both far- and near-UV electronic circular dichroism (ECD) spectra have bands sensitive to thermal unfolding of Trp and Tyr residues containing proteins. Beside spectral changes at 222 nm reporting secondary structural variations (far-UV range), L b bands (near-UV range) are applicable as 3D-fold sensors of protein's core structure. In this study we show that both L b (Tyr) and L b (Trp) ECD bands could be used as sensors of fold compactness. ECD is a relative method and thus requires NMR referencing and cross-validation, also provided here. The ensemble of 204 ECD spectra of Trp-cage miniproteins is analysed as a training set for "calibrating" Trp↔Tyr folded systems of known NMR structure. While in the far-UV ECD spectra changes are linear as a function of the temperature, near-UV ECD data indicate a non-linear and thus, cooperative unfolding mechanism of these proteins. Ensemble of ECD spectra deconvoluted gives both conformational weights and insight to a protein folding↔unfolding mechanism. We found that the L b 293 band is reporting on the 3D-structure compactness. In addition, the pure near-UV ECD spectrum of the unfolded state is described here for the first time. Thus, ECD folding information now validated can be applied with confidence in a large thermal window (5≤T≤85 °C) compared to NMR for studying the unfolding of Trp↔Tyr residue pairs. In conclusion, folding propensities of important proteins (RNA polymerase II, ubiquitin protein ligase, tryptase-inhibitor etc.) can now be analysed with higher confidence. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Generation of Bright Phase-matched Circularly-polarized Extreme Ultraviolet High Harmonics
2014-12-08
circularly-polarized laser pulses field-ionize a gas in a hollow - core waveguide. We use this new light source for magnetic circular dichroism...polarized with opposite helicity in a gas-filled hollow waveguide (see Supplementary Section 6 for details on the important features of this source...mJ/pulse) driving lasers are focused into a 150-µm-diameter, 2-cm-long gas-filled hollow waveguide using lenses with focal lengths of 50 cm and 75 cm
Sato, Hisako; Taniguchi, Tohru; Nakahashi, Atsufumi; Monde, Kenji; Yamagishi, Akihiko
2007-08-06
Vibrational circular dichroism (VCD) spectra of a series of [M(III)(acac)3] (acac = acetylacetonato; M = Cr, Co, Ru, Rh, Ir, and Al) and [M(III)(acac)2(dbm)] (dbm = dibenzoylmethanato; M = Cr, Co, and Ru) have been investigated experimentally and/or theoretically in order to see the effect of the central metal ion on the vibrational dynamics of ligands. The optical antipodes give the mirror-imaged spectra in the region of 1700-1000 cm(-1). The remarkable effect of the central metal ion is observed experimentally on the VCD peaks due to C-O stretches (1500-1300 cm(-1)) for both [M(III)(acac)3] and [M(III)(acac)2(dbm)]. In the case of Delta-[M(III)(acac)3], for example, the order of frequency of two C-O stretches (E and A2 symmetries) is dependent on the kind of a central metal ion as follows: E (-) > A2 (+) for M = Co, Rh, and Ir, while A2 (+) > E (-) for M = Cr and Ru. In the case of Delta-[M(III)(acac)2(dbm)], the order of frequency of three C-O stretches (A, B, and B symmetries) is as follows: A (-) > B (+) > B (+) for Co(III), B (+) > A (-) > B (-) for Cr(III), and A (-) > B (+) > B (-) for Ru(III). These results imply that the energy levels of C-O stretches are delicately affected by the kind of central metal ion. Since such detailed information is not obtained from the IR spectra alone, the VCD spectrum can probe the effect of the central metal ion on interligand cooperative vibration modes.
NASA Astrophysics Data System (ADS)
Lee, Geon Joon; Park, Gyungsoon; Choi, Eun Ha
2017-11-01
We studied the effect of plasma treatment on the optical, structural and biological properties of Neurospora crassa ( N. crassa) spores. An atmospheric-pressure plasma jet (APPJ) was used to generate reactive oxygen and nitrogen species in aqueous solution. The APPJ treatment of N. crassa spores in water significantly reduced the viability of spores. The reduction in the spore viability can be attributed to the reactive species from the plasma itself and those derived from the reaction of plasma radicals with aqueous solution. These structural modifications were contingent on the medium in which N. crassa spores were suspended; plasma treatment of N. crassa spores in PBS did not significantly affect the viability of spores as compared with N. crassa spores in water. Scanning electron microscopy images and circular dichroism spectra indicated that the spore cell wall was damaged by plasma treatment. The optical absorption spectrum of untreated N. crassa spores exhibited two resonance absorption bands at approximately λ1 ≈ 260 nm and λ2 ≈ 472 nm, originating from deoxyribonucleic acid (DNA) and β-carotene. The Raman spectrum of untreated N. crassa spores exhibited three main peaks at 1519, 1157 and 1006 cm -1, attributed to β-carotene inside the cell wall. The Raman spectra showed that the APPJ treatment of N. crassa spores in water caused degradation of β-carotene, affecting the viability of spores.
NASA Astrophysics Data System (ADS)
Tanaka, H.; Bsatee, M.; Jadwisienczak, W. M.
2016-08-01
Systematic investigations of Ga1- x Mn x As grown on InP with different Mn concentrations have been conducted using magnetic circular dichroism (MCD) in reflection mode. The MCD spectrum of Ga0.97Mn0.03As/InP was decomposed into two dispersion curves originating from E 1 and E 1 + Δ1 optical transitions using the energy derivative of a Gaussian function. The Zeeman splitting energy E 1 at the L critical point (0.6 meV) of ferromagnetic Ga0.97Mn0.03As/InP was estimated using a rigid band shift model. Based on the relationship between E 1 and E 0 (Γ critical point) observed in Cd1- x Mn x Te dilute magnetic semiconductor (DMS), the Zeeman splitting energy E 1 (9.6 meV) of ferromagnetic Ga1- x Mn x As/InP was calculated. In addition, it was established that the peaks in the MCD spectra at L critical points shift toward the lower energy side as the Mn concentration is increased, and the observed shift saturates for Mn content of x = 0.001. Furthermore, the measured absorption spectra for Ga1- x Mn x As/InP did not show noticeable peak shifts with increasing Mn content. This suggests that the s, p- d exchange interaction induced in Ga1- x Mn x As/InP has localized nature due to the presence of a Mn rigid sphere of influence.
Circularly polarized light to study linear magneto-optics for ferrofluids: θ-scan technique
NASA Astrophysics Data System (ADS)
Meng, Xiangshen; Huang, Yan; He, Zhenghong; Lin, Yueqiang; Liu, Xiaodong; Li, Decai; Li, Jian; Qiu, Xiaoyan
2018-06-01
Circularly polarized light can be divided into two vertically linearly polarized light beams with ±π/2 phase differences. In the presence of an external magnetic field, when circularly polarized light travels through a ferrofluid film, whose thickness is no more than that of λ/4 plate, magneto-optical, magnetic birefringence and dichroism effects cause the transmitted light to behave as elliptically polarized light. Using angular scan by a continuously rotating polarizer as analyzer, the angular (θ) distribution curve of relative intensity (T) corresponding to elliptically polarized light can be measured. From the T ‑ θ curve having ellipsometry, the parameters such as the ratio of short to long axis, and angular orientation of the long axis to the vertical field direction can be obtained. Thus, magnetic birefringence and dichroism can be probed simultaneously by measuring magneto-optical, positive or negative birefringence and dichroism features from the transmission mode. The proposed method is called θ-scan technique, and can accurately determine sample stability, magnetic field direction, and cancel intrinsic light source ellipticity. This study may be helpful to further research done to ferrofluids and other similar colloidal samples with anisotropic optics.
NASA Astrophysics Data System (ADS)
Ferber, Steven Dwight
2005-11-01
The Vibrational Circular Dichroism (VCD) of Nucleic Acids is a sensitive function of their conformation. DeVoe's classically derived polarizability theory allows the calculation of polymer absorption and circular dichroism spectra in any frequency range. Following the approach of Tinoco and Cech as modified by Moore and Self, calculations were done in the infrared (IR) region with theoretically derived monomer input parameters. Presented herein are calculated absorption and CD spectra for nucleic acid oligomers and polymers. These calculations improve upon earlier attempts, which utilized frequencies, intensities and normal modes from empirical analysis of the nitrogenous base of the monomers. These more complete input polarizability parameters include all contributions to specific vibrational normal modes for the entire nucleotide structure. They are derived from density functional theory (DFT) vibrational analysis on quasi-nucleotide monomers using the GAUSSIAN '98/'03 program. The normal modes are "integrated" for the first time into single virtual (DeVoe) oscillators by incorporating "fixed partial charges" in the manner of Schellman. The results include the complete set of monomer normal modes. All of these modes may be analyzed, in a manner similar to those demonstrated here (for the 1500-1800 cm-1 region). A model is utilized for the polymer/oligomer monomers which maintains the actual electrostatic charge on the adjacent protonated phosphoryl groups (hydrogen phosphate, a mono-anion). This deters the optimization from "collapsing" into a hydrogen-bonded "ball" and thereby maintains the extended (polymer-like) conformation. As well, the precise C2 "endo" conformation of the sugar ring is maintained in the DNA monomers. The analogous C3 "endo" conformation is also maintained for the RNA monomers, which are constrained by massive "anchors" at the phosphates. The complete IR absorbance spectra (0-4,000 cm-1) are calculated directly in Gaussian. Calculated VCD
NASA Astrophysics Data System (ADS)
Sianglam, Pradthana; Kulchat, Sirinan; Tuntulani, Thawatchai; Ngeontae, Wittaya
2017-08-01
We demonstrate an advance in the fabrication of circular dichroism (CD) sensors for detection of Cd2 + and S2 - based on chiral CdS quantum dots (QDs) generated by a facile in-situ reaction. The chiral quantum dots are generated in solutions composed of Cd2 +, S2 -, cysteamine (CA) and L-penicillamine (L-PA), with the number of the generated particles limited by either the Cd2 + or S2 - concentration. We show that the magnitude of the CD signal produced by the QDs is linearly related to the initial concentration of Cd2 + and S2 -, with excellent selectivity over other ions. Our sensor functions over concentration ranges of 65-200 μM and 7-125 μM with detection limits of 59.7 and 1.6 μM for Cd2 + and S2 -, respectively. The sensor is applied in real water samples with results comparing favorably with those obtained from ICP-OES (for Cd2 +) and HPLC (for S2 -).
NASA Astrophysics Data System (ADS)
Kudrin, A. V.; Dorokhin, M. V.; Zdoroveishchev, A. V.; Demina, P. B.; Vikhrova, O. V.; Kalent'eva, I. L.; Ved', M. V.
2017-11-01
A photoconductive detector of circularly polarized radiation based on the metal-insulator-semiconductor structure of CoPt/(Al2O3/SiO2/Al2O3)/InGaAs/GaAs is created. The efficiency of detection of circularly polarized radiation is 0.75% at room temperature. The operation of the detector is based on the manifestation of the effect of magnetic circular dichroism in the CoPt layer, that is, the dependence of the CoPt transmission coefficient on the sign of the circular polarization of light and magnetization.
Griko, Yuri; Sreerama, Narasimha; Osumi-Davis, Patricia; Woody, Robert W.; Woody, A-Young Moon
2001-01-01
Structural changes in T7 RNA polymerase (T7RNAP) induced by temperature and urea have been studied over a wide range of conditions to obtain information about the structural organization and the stability of the enzyme. T7RNAP is a large monomeric enzyme (99 kD). Calorimetric studies of the thermal transitions in T7RNAP show that the enzyme consists of three cooperative units that may be regarded as structural domains. Interactions between these structural domains and their stability strongly depend on solvent conditions. The unfolding of T7RNAP under different solvent conditions induces a highly stable intermediate state that lacks specific tertiary interactions, contains a significant amount of residual secondary structure, and undergoes further cooperative unfolding at high urea concentrations. Circular dichroism (CD) studies show that thermal unfolding leads to an intermediate state that has increased β-sheet and reduced α-helix content relative to the native state. Urea-induced unfolding at 25°C reveals a two-step process. The first transition centered near 3 M urea leads to a plateau from 3.5 to 5.0 M urea, followed by a second transition centered near 6.5 M urea. The CD spectrum of the enzyme in the plateau region, which is similar to that of the enzyme thermally unfolded in the absence of urea, shows little temperature dependence from 15° to 60°C. The second transition leads to a mixture of poly(Pro)II and unordered conformations. As the temperature increases, the ellipticity at 222 nm becomes more negative because of conversion of poly(Pro)II to the unordered conformation. Near-ultraviolet CD spectra at 25°C at varying concentrations of urea are consistent with this picture. Both thermal and urea denaturation are irreversible, presumably because of processes that follow unfolding. PMID:11274475
Dafforn, Timothy R; Rajendra, Jacindra; Halsall, David J; Serpell, Louise C; Rodger, Alison
2004-01-01
High-resolution structure determination of soluble globular proteins relies heavily on x-ray crystallography techniques. Such an approach is often ineffective for investigations into the structure of fibrous proteins as these proteins generally do not crystallize. Thus investigations into fibrous protein structure have relied on less direct methods such as x-ray fiber diffraction and circular dichroism. Ultraviolet linear dichroism has the potential to provide additional information on the structure of such biomolecular systems. However, existing systems are not optimized for the requirements of fibrous proteins. We have designed and built a low-volume (200 microL), low-wavelength (down to 180 nm), low-pathlength (100 microm), high-alignment flow-alignment system (couette) to perform ultraviolet linear dichroism studies on the fibers formed by a range of biomolecules. The apparatus has been tested using a number of proteins for which longer wavelength linear dichroism spectra had already been measured. The new couette cell has also been used to obtain data on two medically important protein fibers, the all-beta-sheet amyloid fibers of the Alzheimer's derived protein Abeta and the long-chain assemblies of alpha1-antitrypsin polymers.
Optical Activity of Benzil Crystal
NASA Astrophysics Data System (ADS)
Říha, Jan; Vyšín, Ivo
2003-09-01
Optical activity of benzil as an example of optically active matter in the crystalline state only, not in solution, is studied for the wavelengths ranging from 0.320 m to 0.585 m. Previously measured experimental data are approximated by the theoretical set of formulas, which were derived by the use of the three coupled oscillators model. The earlier published formula consisting of six terms differed from the experimental data particularly in the wavelength region (0.380-0.510) m. This formula is replaced by the twelve-term formula which was computed by our specially worked computer program for the interpretation of the experimental data of optical activity based on the Marquardt-Levenberg method of the sum of least squares minimization. The possibility of molecular contribution to the resulting optical activity of benzil is mentioned. The use of Kramers-Kronig transforms for the determination of the circular dichroism curve based on the optical rotatory dispersion result is shown. The theoretically computed circular dichroism is compared with the available experimental data.
Demarque, Daniel P; Merten, Christian
2017-12-19
When predicting binding properties of small molecules or larger supramolecular aggregates, intra- and intermolecular hydrogen bonds are often considered the most important factor. Spectroscopic techniques such as 1 H NMR spectroscopy are typically utilized to characterize such binding events, but interpretation is often qualitative and follows chemical intuition. In this study, we compare the effects of intramolecular hydrogen bonding and solvation on two chiral 2,6-pyridinediyl-dialkylamides. In comparison with 1 H NMR spectroscopy, vibrational circular dichroism (VCD) spectroscopy proved to be more sensitive to conformational changes. In fact, the change of the solvent from CDCl 3 to [D 6 ]DMSO generates mirror-image VCD spectra for the same enantiomer. Here, the common sense that the sterically less hindered group is more prone to solvation proved to be wrong according predicted VCD spectra, which clearly show that both asymmetric amide hydrogens are equally likely to be solvated, but never simultaneously. The competition between intra- and intermolecular hydrogen bonding and their importance for a correct prediction of spectral properties are discussed. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Lerch, Michael T.; Horwitz, Joseph; McCoy, John; Hubbell, Wayne L.
2013-01-01
Excited states of proteins may play important roles in function, yet are difficult to study spectroscopically because of their sparse population. High hydrostatic pressure increases the equilibrium population of excited states, enabling their characterization [Akasaka K (2003) Biochemistry 42:10875–85]. High-pressure site-directed spin-labeling EPR (SDSL-EPR) was developed recently to map the site-specific structure and dynamics of excited states populated by pressure. To monitor global secondary structure content by circular dichroism (CD) at high pressure, a modified optical cell using a custom MgF2 window with a reduced aperture is introduced. Here, a combination of SDSL-EPR and CD is used to map reversible structural transitions in holomyoglobin and apomyoglobin (apoMb) as a function of applied pressure up to 2 kbar. CD shows that the high-pressure excited state of apoMb at pH 6 has helical content identical to that of native apoMb, but reversible changes reflecting the appearance of a conformational ensemble are observed by SDSL-EPR, suggesting a helical topology that fluctuates slowly on the EPR time scale. Although the high-pressure state of apoMb at pH 6 has been referred to as a molten globule, the data presented here reveal significant differences from the well-characterized pH 4.1 molten globule of apoMb. Pressure-populated states of both holomyoglobin and apoMb at pH 4.1 have significantly less helical structure, and for the latter, that may correspond to a transient folding intermediate. PMID:24248390
Micsonai, András; Wien, Frank; Bulyáki, Éva; Kun, Judit; Moussong, Éva; Lee, Young-Ho; Goto, Yuji; Réfrégiers, Matthieu; Kardos, József
2018-06-11
Circular dichroism (CD) spectroscopy is a widely used method to study the protein secondary structure. However, for decades, the general opinion was that the correct estimation of β-sheet content is challenging because of the large spectral and structural diversity of β-sheets. Recently, we showed that the orientation and twisting of β-sheets account for the observed spectral diversity, and developed a new method to estimate accurately the secondary structure (PNAS, 112, E3095). BeStSel web server provides the Beta Structure Selection method to analyze the CD spectra recorded by conventional or synchrotron radiation CD equipment. Both normalized and measured data can be uploaded to the server either as a single spectrum or series of spectra. The originality of BeStSel is that it carries out a detailed secondary structure analysis providing information on eight secondary structure components including parallel-β structure and antiparallel β-sheets with three different groups of twist. Based on these, it predicts the protein fold down to the topology/homology level of the CATH protein fold classification. The server also provides a module to analyze the structures deposited in the PDB for BeStSel secondary structure contents in relation to Dictionary of Secondary Structure of Proteins data. The BeStSel server is freely accessible at http://bestsel.elte.hu.
Kurouski, Dmitry; Dukor, Rina K; Lu, Xuefang; Nafie, Laurence A; Lednev, Igor K
2012-08-08
Fibrils are β-sheet-rich aggregates that are generally composed of several protofibrils and may adopt variable morphologies, such as twisted ribbons or flat-like sheets. This polymorphism is observed for many different amyloid associated proteins and polypeptides. In a previous study we proposed the existence of another level of amyloid polymorphism, namely, that associated with fibril supramolecular chirality. Two chiral polymorphs of insulin, which can be controllably grown by means of small pH variations, exhibit opposite signs of vibrational circular dichroism (VCD) spectra. Herein, using atomic force microscopy (AFM) and scanning electron microscopy (SEM), we demonstrate that indeed VCD supramolecular chirality is correlated not only by the apparent fibril handedness but also by the sense of supramolecular chirality from a deeper level of chiral organization at the protofilament level of fibril structure. Our microscopic examination indicates that normal VCD fibrils have a left-handed twist, whereas reversed VCD fibrils are flat-like aggregates with no obvious helical twist as imaged by atomic force microscopy or scanning electron microscopy. A scheme is proposed consistent with observed data that features a dynamic equilibrium controlled by pH at the protofilament level between left- and right-twist fibril structures with distinctly different aggregation pathways for left- and right-twisted protofilaments. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Andrew, Charles D; Bhattacharjee, Samita; Kokkoni, Nicoleta; Hirst, Jonathan D; Jones, Gareth R; Doig, Andrew J
2002-10-30
Here we investigate the structures and energetics of interactions between aromatic (Phe or Tyr) and basic (Lys or Arg) amino acids in alpha-helices. Side chain interaction energies are measured using helical peptides, by quantifying their helicities with circular dichroism at 222 nm and interpreting the results with Lifson-Roig-based helix/coil theory. A difficulty in working with Tyr is that the aromatic ring perturbs the CD spectrum, giving an incorrect helicity. We calculated the effect of Tyr on the CD at 222 nm by deriving the intensities of the bands directly from the electronic and magnetic transition dipole moments through the rotational strengths corresponding to each excited state of the polypeptide. This gives an improved value of the helix preference of Tyr (from 0.48 to 0.35) and a correction to the helicity for the peptides containing Tyr. We find that Phe-Lys, Lys-Phe, Phe-Arg, Arg-Phe, and Tyr-Lys are all stabilizing by -0.10 to -0.18 kcal.mol-1 when placed i, i + 4 on the surface of a helix in aqueous solution, despite the great difference in polarity between these residues. Interactions between these side chains have previously been attributed to cation-pi bonds. A survey of protein structures shows that they are in fact predominantly hydrophobic interactions between the CH2 groups of Lys or Arg and the aromatic rings.
Miyawaki, Jun; Suga, Shigemasa; Fujiwara, Hidenori; Niwa, Hideharu; Kiuchi, Hisao; Harada, Yoshihisa
2017-03-01
A compact and portable magnet system for measuring magnetic dichroism in resonant inelastic soft X-ray scattering (SX-RIXS) has been developed at the beamline BL07LSU in SPring-8. A magnetic circuit composed of Nd-Fe-B permanent magnets, which realised ∼0.25 T at the center of an 11 mm gap, was rotatable around the axis perpendicular to the X-ray scattering plane. Using the system, a SX-RIXS spectrum was obtained under the application of the magnetic field at an angle parallel, nearly 45° or perpendicular to the incident X-rays. A dedicated sample stage was also designed to be as compact as possible, making it possible to perform SX-RIXS measurements at arbitrary incident angles by rotating the sample stage in the gap between the magnetic poles. This system enables facile studies of magnetic dichroism in SX-RIXS for various experimental geometries of the sample and the magnetic field. A brief demonstration of the application is presented.
Song, Jintong; Wang, Man; Zhou, Xiangge; Xiang, Haifeng
2018-05-17
A series of chiral and helical Pt II -Salen complexes with 1,1'-binaphthyl linkers were synthesized and characterized. Owing to the restriction of intramolecular motions of central 1,1'-binaphthyls, the complexes exhibit unusual near-infrared aggregation-induced phosphorescence (AIP). The (R)/(S) enantiopure complexes were characterized by X-ray diffraction, circular dichroism spectra, time-dependent density functional theory calculations, and circularly polarized luminescence (CPL). The present work explores the use of tetradentate ligands that can be easily prepared from commercially available enantiopure compounds, and the subsequent preparation of stable CPL-active square planar Pt II complexes with AIP effect that may have interest in many applications. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
NASA Astrophysics Data System (ADS)
Antonov, V. N.; Shpak, A. P.; Yaresko, A. N.
2008-02-01
The present state of theoretical understanding of the x-ray magnetic circular dichroism (XMCD) of 4f and 5f compounds is reviewed. Energy band theory based upon the local spin-density approximation (LSDA) describes the XMCD spectra of transition metal compounds with high accuracy. However, the LSDA does not suffice for lanthanide compounds which have a correlated 4f shell. A satisfactory description of the XMCD spectra could be obtained by using a generalization of the LSDA, in which explicitly f electron Coulomb correlations are taken into account (LSDA +U approach). As examples of this group we consider the compound GdN. We also consider uranium 5f compounds. In those compounds where the 5f electrons are rather delocalized, the LSDA describes the XMCD spectra reasonably well. As an example of this group we consider UFe2. Particular differences occur for uranium compounds in which the 5f electrons are neither delocalized nor localized, but more or less semilocalized. Typical examples are UXAl (X =Co, Rh, and Pt), and UX (X =S, Se, Te). However, the semilocalized 5f's are not inert, but their interaction with conduction electrons plays an important role. We also consider the electronic structure and XMCD spectra of the heavy-fermion compounds UPt3, URu2Si2, UPd2Al3, UNi2Al3, and UBe13, where the degree of the 5f localization is increased in comparison with other uranium compounds. The electronic structure and XMCD spectra of UGe2 which possesses simultaneously ferromagnetism and superconductivity also presented. Recently achieved improvements for describing 5f compounds are discussed.
Iovescu, Alina; Băran, Adriana; Stîngă, Gabriela; Cantemir-Leontieş, Anca Ruxandra; Maxim, Monica Elisabeta; Anghel, Dan Florin
2015-12-01
The study systematically investigates aqueous mixtures of fixed bovine serum albumin (BSA) and various ethoxylated nonionic surfactants belonging to a homologous series or not. Mono-disperse tetra-(C12E4), hexa-(C12E6) and octa-ethyleneglycol mono-n-dodecyl ether (C12E8), and poly-disperse eicosa-ethyleneglycol mono-n-tetradecyl ether (C14EO20) are respectively employed. Fluorescence and circular dichroism measurements are performed at surfactant/protein molar ratios (rm)s lower and higher than one. We aim to get new insights into the binding mechanism of these species and to differentiate among the interaction abilities of these surfactants. The relative magnitude of the binding thermodynamic parameters by fluorescence, and the increase of α-helix prove that hydrogen bonding drives the interaction next to the hydrophobic attraction. C12En (n=4,6,8) develop more H bonds with the albumin than C14EO20 owing to a zigzag conformation of their short ethyleneoxide chains. Among the homologous surfactants, C12E6 has a slightly stronger interaction with BSA due to a maximal number of H bonds at a minimal hindering. Static fluorescence and dynamic fluorescence indicate an inter-conversion between the tryptophan (Trp) rotamers which happens around the surfactants critical micellar concentration. For C14EO20, the meander conformation of the polar group determines a less evident conversion of the Trp rotamers and smaller α-helix rise. Binding isotherms of the homologous surfactants and the fluorescence quenching mechanism by C12E6 are also provided. Copyright © 2015 Elsevier B.V. All rights reserved.
Dutta, Udayan; Cohenford, Menashi A; Dain, Joel A
2007-01-15
Advanced glycation end products (AGEs) play a significant role in the pathophysiology of diabetes leading to such conditions as atherosclerosis, cataract formation, and renal dysfunction. While the formation of nucleoside AGEs was previously demonstrated, no extensive studies have been performed to assess the effect of AGEs on DNA structure and folding. The objective of this study was to investigate the nonenzymatic glycation of two DNA oligonucleotide duplexes with one duplex consisting of deoxy-poly(A)15 and deoxy-poly(T)15 and the other consisting of deoxy-poly(GA)15 and deoxy-poly(CT)15. With D-glucose, D-galactose, D/L-glyceraldehyde, and D-glucosamine serving as the model glycating carbohydrates, D-glucosamine was found to exhibit the greatest effect on the stability and structure of the oligonucleotide duplexes, a finding that was confirmed by circular dichroism. The nonenzymatic glycation of deoxy-poly(AT) by D-glucosamine destabilized the deoxy-poly(AT) structure and changed its conformation from A form to X form. D-glucosamine also altered the conformation of deoxy-poly(GA)15 and deoxy-poly(CT)15 from A form to B form. Capillary electrophoresis and ultraviolet and fluorescence spectroscopy revealed that, of the various purines and pyrimidines, 2'-deoxyguanosine and guanine were most reactive with D-glucosamine. The nonenzymatic modification of nucleic acids warrants further investigation because this phenomenon may occur in vivo, altering DNA structure and/or function.
Kummer, K; Fondacaro, A; Jimenez, E; Velez-Fort, E; Amorese, A; Aspbury, M; Yakhou-Harris, F; van der Linden, P; Brookes, N B
2016-03-01
A new high-field magnet endstation for X-ray magnetic dichroism experiments has been installed and commissioned at the ESRF soft X-ray beamline ID32. The magnet consists of two split-pairs of superconducting coils which can generate up to 9 T along the beam and up to 4 T orthogonal to the beam. It is connected to a cluster of ultra-high-vacuum chambers that offer a comprehensive set of surface preparation and characterization techniques. The endstation and the beam properties have been designed to provide optimum experimental conditions for X-ray magnetic linear and circular dichroism experiments in the soft X-ray range between 400 and 1600 eV photon energy. User operation started in November 2014.
Kesting, Julie R; Olsen, Lars; Staerk, Dan; Tejesvi, Mysore V; Kini, Kukkundoor R; Prakash, Harishchandra S; Jaroszewski, Jerzy W
2011-10-28
The endophytic fungus Pestalotiopsis virgatula, derived from the plant Terminalia chebula and previously found to produce a large excess of a single metabolite when grown in the minimal M1D medium, was induced to produce a variety of unusual metabolites by growing in potato dextrose broth medium. Analysis of the fermentation medium extract was performed using an HPLC-PDA-MS-SPE-NMR hyphenated system, which led to the identification of a total of eight metabolites (1-8), six of which are new. Most of the metabolites are structurally related and are derivatives of benzo[c]oxepin, rare among natural products. This includes dispiro derivatives 7 and 8 (pestalospiranes A and B), having a novel 1,9,11,18-tetraoxadispiro[6.2.6.2]octadecane skeleton. Relative and absolute configurations of the latter were determined by a combination of NOESY spectroscopy and electronic circular dichroism spectroscopy supported by time-dependent density-functional theory calculations (B3LYP/TZVP level). This work demonstrates that a largely complete structure elucidation of numerous metabolites present in a raw fermentation medium extract can be performed by the HPLC-SPE-NMR technique using only a small amount of the extract, even with unstable metabolites that are difficult to isolate by traditional methods.
Sugimoto, Masumi; Liu, Xin-Ling; Tsunega, Seiji; Nakajima, Erika; Abe, Shunsuke; Nakashima, Takuya; Kawai, Tsuyoshi; Jin, Ren-Hua
2018-05-02
Recently, circularly polarized luminescence (CPL)-active systems have become a very hot and interesting subject in chirality- and optics-related areas. The CPL-active systems are usually available by two approaches: covalently combining a luminescent centre to chiral motif or associating the guest of luminescent probe to a chiral host. However, all the chiral components in CPL materials were organic, although the luminescent components were alternatively organics or inorganics. Herein, the first totally inorganic CPL-active system by "luminescent guest-chiral host" strategy is proposed. Luminescent sub-10 nm lanthanide oxides (Eu 2 O 3 or Tb 2 O 3 ) nanoparticles (guests) were encapsulated into chiral non-helical SiO 2 nanofibres (host) through calcination of chiral SiO 2 hybrid nanofibres, trapping Eu 3+ (or Tb 3+ ). These lanthanide oxides display circular dichroism (CD) optical activity in the ultraviolet wavelength and CPL signals around at 615 nm for Eu 3+ and 545 nm for Tb 3+ . This work has implications for inorganic-based CPL-active systems by incorporation of various luminescent guests within chiral inorganic hosts. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
DOE Office of Scientific and Technical Information (OSTI.GOV)
He, Junfeng; Mion, Thomas R.; Gao, Shang
2016-10-31
Unraveling the nature of pseudogap phase in high-temperature superconductors holds the key to understanding their superconducting mechanisms and potentially broadening their applications via enhancement of their superconducting transition temperatures. Angle-resolved photoemission spectroscopy (ARPES) experiments using circularly polarized light have been proposed to detect possible symmetry breaking state in the pseudogap phase of cuprates. Here, the presence (absence) of an electronic order which breaks mirror symmetry of the crystal would in principle induce a finite (zero) circular dichroism in photoemission. Different orders breaking reflection symmetries about different mirror planes can also be distinguished by the momentum dependence of the measured circularmore » dichroism.« less
NASA Astrophysics Data System (ADS)
Sikolenko, V. V.; Troyanchuk, I. O.; Karpinsky, D. V.; Rogalev, A.; Wilhelm, F.; Rosenberg, R.; Prabhakaran, D.; Efimova, E. A.; Efimov, V. V.; Tiutiunnikov, S. I.; Bobrikov, I. A.
2018-02-01
Spin transitions of cobalt ions in LaCoO3 single crystals have been studied by the method of X-ray magnetic circular dichroism (XMCD) at the K- and L 2,3-edges of Co3+ ions. The orbital momentum of cobalt ions obtained for the K-edge at the 3 d level in the region of the spin transition in the temperature range from 25 to 120 K increases by a factor of approximately 1.6, whereas the slope of the magnetization curve value in the same temperature range and magnetic field increases by a factor of more than 10. XMCD experiments at the cobalt L 2,3-edges demonstrate gradual growth of the ratio of the orbital momentum to the spin one L/ S from 0.48 to 0.53 in the temperature range from 60 K to 120 K.
Photo-induced optical activity in phase-change memory materials.
Borisenko, Konstantin B; Shanmugam, Janaki; Williams, Benjamin A O; Ewart, Paul; Gholipour, Behrad; Hewak, Daniel W; Hussain, Rohanah; Jávorfi, Tamás; Siligardi, Giuliano; Kirkland, Angus I
2015-03-05
We demonstrate that optical activity in amorphous isotropic thin films of pure Ge2Sb2Te5 and N-doped Ge2Sb2Te5N phase-change memory materials can be induced using rapid photo crystallisation with circularly polarised laser light. The new anisotropic phase transition has been confirmed by circular dichroism measurements. This opens up the possibility of controlled induction of optical activity at the nanosecond time scale for exploitation in a new generation of high-density optical memory, fast chiroptical switches and chiral metamaterials.
Gill, Pooria; Ranjbar, Bijan; Saber, Reza; Khajeh, Khosro; Mohammadian, Mehdi
2011-07-01
Cauliflower-like DNAs are stem-loop DNAs that are fabricated periodically in inverted repetitions from deoxyribonucleic acid phosphates (dNTPs) by loop-mediated isothermal amplification (LAMP). Cauliflower-like DNAs have ladder-shape behaviors on gel electrophoresis, and increasing the time of LAMP leads to multiplying the repetitions, stem-loops, and electrophoretic bands. Cauliflower-like DNAs were fabricated via LAMP using two loop primers, two bumper primers, dNTPs, a λ-phage DNA template, and a Bst DNA polymerase in 75- and 90-min periods. These times led to manufacturing two types of cauliflower-like DNAs with different contents of inverted repetitions and stem-loops, which were clearly indicated by two comparable electrophoresis patterns in agarose gel. LAMP-fabricated DNAs and natural dsB-DNA (salmon genomic DNA) were dialyzed in Gomori phosphate buffer (10 mM, pH 7.4) to be isolated from salts, nucleotides, and primers. Dialyzed DNAs were studied using UV spectroscopy, circular dichroism spectropolarimetry, and fluorescence spectrophotometry. Structural analyses indicated reduction of the molecular ellipticity and extinction coefficients in comparison with B-DNA. Also, cauliflower-like DNAs demonstrated less intrinsic and more extrinsic fluorescence in comparison with natural DNA. The overwinding and lengthening of the cauliflower-like configurations of LAMP DNAs led to changes in physical parameters of this type of DNA in comparison with natural DNA. The results obtained introduced new biomolecular characteristics of DNA macromolecules fabricated within a LAMP process and show the effects of more inverted repeats and stem-loops, which are manufactured by lengthening the process.
NASA Astrophysics Data System (ADS)
Juhin, Amélie; Sainctavit, Philippe; Ollefs, Katharina; Sikora, Marcin; Filipponi, Adriano; Glatzel, Pieter; Wilhelm, Fabrice; Rogalev, Andrei
2016-12-01
X-ray magnetic circular dichroism is measured at the Fe K pre-edge in yttrium iron garnet using two different procedures that allow reducing the intrinsic broadening due to the 1s corehole lifetime. First, deconvolution of XMCD data measured in total fluorescence yield (TFY) with an extremely high signal-to-noise ratio enables a factor of 2.4 to be gained in the XMCD intensity. Ligand field multiplet calculations performed with different values of intrinsic broadening show that deconvolving such high quality XMCD data is similar to reducing the lifetime broadening from a 1s corehole to a 2p corehole. Second, MCD is measured by resonant inelastic x-ray scattering spectroscopy as a function of incident energy and emission energy. Selection of a fixed emission energy, instead of using the TFY, allows enhancing the MCD intensity up to a factor of ˜4.7. However, this significantly changes the spectral shape of the XMCD signal, which cannot be interpreted any more as an absorption spectrum.
Circular dichroism studies of the mitochondrial channel, VDAC, from Neurospora crassa.
Shao, L; Kinnally, K W; Mannella, C A
1996-01-01
The protein that forms the voltage-gated channel VDAC (or mitochondrial porin) has been purified from Neurospora crassa. At room temperature and pH 7, the circular dichoism (CD) spectrum of VDAC suspended in octyl beta-glucoside is similar to those of bacterial porins, consistent with a high beta-sheet content. When VDAC is reconstituted into phospholipid liposomes at pH 7, a similar CD spectrum is obtained and the liposomes are rendered permeable to sucrose. Heating VDAC in octyl beta-glucoside or in liposomes results in thermal denaturation. The CD spectrum irreversibly changes to one consistent with total loss of beta-sheet content, and VDAC-containing liposomes irreversibly lose sucrose permeability. When VDAC is suspended at room temperature in octyl beta-glucoside at pH < 5 or in sodium dodecyl sulfate at pH 7, its CD spectrum is consistent with partial loss of beta-sheet content. The sucrose permeability of VDAC-containing liposomes is decreased at low pH and restored at pH 7. Similarly, the pH-dependent changes in the CD spectrum of VDAC suspended in octyl beta-glucoside also are reversible. These results suggest that VDAC undergoes a reversible conformational change at low pH involving reduced beta-sheet content and loss of pore-forming activity. Images FIGURE 1 PMID:8842216
NASA Astrophysics Data System (ADS)
Güler, Günnur; Vorob'ev, Mikhail M.; Vogel, Vitali; Mäntele, Werner
2016-05-01
Enzymatically-induced degradation of bovine serum albumin (BSA) by serine proteases (trypsin and α-chymotrypsin) in various concentrations was monitored by means of Fourier transform infrared (FT-IR) and ultraviolet circular dichroism (UV-CD) spectroscopy. In this study, the applicability of both spectroscopies to monitor the proteolysis process in real time has been proven, by tracking the spectral changes together with secondary structure analysis of BSA as proteolysis proceeds. On the basis of the FTIR spectra and the changes in the amide I band region, we suggest the progression of proteolysis process via conversion of α-helices (1654 cm- 1) into unordered structures and an increase in the concentration of free carboxylates (absorption of 1593 and 1402 cm- 1). For the first time, the correlation between the degree of hydrolysis and the concentration of carboxylic groups measured by FTIR spectroscopy was revealed as well. The far UV-CD spectra together with their secondary structure analysis suggest that the α-helical content decreases concomitant with an increase in the unordered structure. Both spectroscopic techniques also demonstrate that there are similar but less spectral changes of BSA for the trypsin attack than for α-chymotrypsin although the substrate/enzyme ratio is taken the same.
Polavarapu, Prasad L; Covington, Cody L
2014-09-01
For three different chiroptical spectroscopic methods, namely, vibrational circular dichroism (VCD), electronic circular dichroism (ECD), and Raman optical activity (ROA), the measures of similarity of the experimental spectra to the corresponding spectra predicted using quantum chemical theories are summarized. In determining the absolute configuration and/or predominant conformations of chiral molecules, these similarity measures provide numerical estimates of agreement between experimental observations and theoretical predictions. Selected applications illustrating the similarity measures for absorption, circular dichroism, and corresponding dissymmetry factor (DF) spectra, in the case of VCD and ECD, and for Raman, ROA, and circular intensity differential (CID) spectra in the case of ROA, are presented. The analysis of similarity in DF or CID spectra is considered to be much more discerning and accurate than that in absorption (or Raman) and circular dichroism (or ROA) spectra, undertaken individually. © 2014 Wiley Periodicals, Inc.
NASA Astrophysics Data System (ADS)
Asakura, D.; Koide, T.; Yamamoto, S.; Tsuchiya, K.; Shioya, T.; Amemiya, K.; Singh, V. R.; Kataoka, T.; Yamazaki, Y.; Sakamoto, Y.; Fujimori, A.; Taira, T.; Yamamoto, M.
2010-11-01
The magnetic states of Mn and Co atoms in Co-rich Co2MnGe Heusler alloy thin films facing an MgO barrier were studied by means of soft x-ray magnetic circular dichroism (XMCD). In particular, the Co2MnGe film-thickness dependence of the Mn and Co magnetic moments was investigated. With a decrease in the Co2MnGe film thickness to 1-2 monolayers (MLs), the spin magnetic moment of Mn decreased and the MnL2,3 -edge x-ray absorption spectra (XAS) showed a Mn2+ -like multiplet structure in MnO, in contrast to samples thicker than 4 ML, indicating that the Mn atoms of the 1 and 2 ML samples were oxidized. The Co spin magnetic moment increased slightly with decreasing thickness. A Co2+ -like multiplet structure in CoO was not observed in all the CoL2,3 -edge XAS and XMCD, indicating that, even in the ultrathin samples, the Co atoms were not oxidized, and were more strongly spin polarized than those in the thicker samples. Co spin magnetic moments of 1.40-1.77μB larger than the theoretical value for ideal stoichiometric Co2MnGe (˜1μB) and the Co-rich film composition imply the presence of Co antisites that would lower the spin polarization.
NASA Astrophysics Data System (ADS)
Dinh, Thanh-Chung; Renger, Thomas
2015-01-01
A challenge for the theory of optical spectra of pigment-protein complexes is the equal strength of the pigment-pigment and the pigment-protein couplings. Treating both on an equal footing so far can only be managed by numerically costly approaches. Here, we exploit recent results on a normal mode analysis derived spectral density that revealed the dominance of the diagonal matrix elements of the exciton-vibrational coupling in the exciton state representation. We use a cumulant expansion technique that treats the diagonal parts exactly, includes an infinite summation of the off-diagonal parts in secular and Markov approximations, and provides a systematic perturbative way to include non-secular and non-Markov corrections. The theory is applied to a model dimer and to chlorophyll (Chl) a and Chl b homodimers of the reconstituted water-soluble chlorophyll-binding protein (WSCP) from cauliflower. The model calculations reveal that the non-secular/non-Markov effects redistribute oscillator strength from the strong to the weak exciton transition in absorbance and they diminish the rotational strength of the exciton transitions in circular dichroism. The magnitude of these corrections is in a few percent range of the overall signal, providing a quantitative explanation of the success of time-local convolution-less density matrix theory applied earlier. A close examination of the optical spectra of Chl a and Chl b homodimers in WSCP suggests that the opening angle between Qy transition dipole moments in Chl b homodimers is larger by about 9∘ than for Chl a homodimers for which a crystal structure of a related WSCP complex exists. It remains to be investigated whether this change is due to a different mutual geometry of the pigments or due to the different electronic structures of Chl a and Chl b.
Padula, Daniele; Cerezo, Javier; Pescitelli, Gennaro; Santoro, Fabrizio
2017-12-13
Comparison between chiroptical spectra and theoretical predictions is the method of choice for the assignment of the absolute configuration of chiral compounds in solution. Here we report the case of an apparently simple biarylcarbinol, whose electronic circular dichroism (ECD) in the 1 L b region exhibits a peculiar alternation of negative and positive bands. Adopting Density Functional Theory, and describing solvent effects with implicit methods, we found three stable conformers in ethanol, each of them with two close lying states corresponding to similar local 1 L b excitations on the two phenyls. We computed the corresponding vibronic ECD spectra in harmonic approximation, including Duschinsky mixings as well as both Franck Condon (FC) and Herzberg Teller (HT) effects. Exploiting a recently developed mixed quantum/classical method, we further investigated the contribution of the vibronic spectra of out-of-equilibrium structures along the interconversion path connecting the different conformers. In this way, we achieved a reasonable agreement with experiment and attributed the alternating signs of the bands to the existence of different conformers. The remaining discrepancies with experiment indicate that specific solute-solvent interactions modulate the relative conformers' stabilities, calling for new methods able to combine Molecular Dynamics explorations and vibronic calculations. Moreover, the poor performance of HT approaches and the existence of two closely-lying states suggest the necessity of an improved fully-nonadiabatic vibronic approach. These findings demonstrate that even for such a simple system as the biarylcarbinol investigated here, a full reproduction of the fine details of the ECD spectrum requires the development of new improved methods.
Rizzo, Antonio; Vahtras, Olav
2011-06-28
A computational approach to the calculation of excited state electronic circular dichroism (ESECD) spectra of chiral molecules is discussed. Frequency dependent quadratic response theory is employed to compute the rotatory strength for transitions between excited electronic states, by employing both a magnetic gauge dependent and a (velocity-based) magnetic gauge independent approach. Application is made to the lowest excited states of two prototypical chiral molecules, propylene oxide, also known as 1,2-epoxypropane or methyl oxirane, and R-(+)-1,1'-bi(2-naphthol), or BINOL. The dependence of the rotatory strength for transitions between the lowest three excited states of methyl oxirane upon the quality and extension of the basis set is analyzed, by employing a hierarchy of correlation consistent basis sets. Once established that basis sets of at least triple zeta quality, and at least doubly augmented, are sufficient to ensure sufficiently converged results, at least at the Hartree-Fock self-consistent field (HF-SCF) level, the rotatory strengths for all transitions between the lowest excited electronic states of methyl oxirane are computed and analyzed, employing HF-SCF, and density functional theory (DFT) electronic structure models. For DFT, both the popular B3LYP and its recently highly successful CAM-B3LYP extension are exploited. The strong dependence of the spectra upon electron correlation is highlighted. A HF-SCF and DFT study is carried out also for BINOL, a system where excited states show the typical pairing structure arising from the interaction of the two monomeric moieties, and whose conformational changes following photoexcitation were studied recently with via time-resolved CD.
Lacy, Eilyn R.; Cox, Kari K.; Wilson, W. David; Lee, Moses
2002-01-01
An imidazole-containing polyamide trimer, f-ImImIm, where f is a formamido group, was recently found using NMR methods to recognize T·G mismatched base pairs. In order to characterize in detail the T·G recognition affinity and specificity of imidazole-containing polyamides, f-ImIm, f-ImImIm and f-PyImIm were synthesized. The kinetics and thermodynamics for the polyamides binding to Watson–Crick and mismatched (containing one or two T·G, A·G or G·G mismatched base pairs) hairpin oligonucleotides were determined by surface plasmon resonance and circular dichroism (CD) methods. f-ImImIm binds significantly more strongly to the T·G mismatch-containing oligonucleotides than to the sequences with other mismatched or with Watson–Crick base pairs. Compared with the Watson–Crick CCGG sequence, f-ImImIm associates more slowly with DNAs containing T·G mismatches in place of one or two C·G base pairs and, more importantly, the dissociation rate from the T·G oligonucleotides is very slow (small kd). These results clearly demonstrate the binding selectivity and enhanced affinity of side-by-side imidazole/imidazole pairings for T·G mismatches and show that the affinity and specificity increase arise from much lower kd values with the T·G mismatched duplexes. CD titration studies of f-ImImIm complexes with T·G mismatched sequences produce strong induced bands at ∼330 nm with clear isodichroic points, in support of a single minor groove complex. CD DNA bands suggest that the complexes remain in the B conformation. PMID:11937638
Ramsay, G; Ionescu, R; Eftink, M R
1995-08-01
In a previous paper (Ramsay and Eftink, Biophys. J. 66:516-523) we reported the development of a modified spectrophotometer that can make nearly simultaneous circular dichroism (CD) and fluorescence measurements. This arrangement allows multiple data sets to be collected during a single experiment, resulting in a saving of time and material, and improved correlation between the different types of measurements. The usefulness of the instrument was shown by thermal melting experiments on several different protein systems. This CD/fluorometer spectrophotometer has been further modified by interfacing with a syringe pump and a pH meter. This arrangement allows ligand, pH, and chemical denaturation titration experiments to be performed while monitoring changes in the sample's CD, absorbance, fluorescence, and light scattering properties. Our data acquisition program also has an ability to check whether the signals have approached equilibrium before the data is recorded. For performing pH titrations we have developed a procedure which uses the signal from a pH meter in a feedback circuit in order to collect data at evenly spaced pH intervals. We demonstrate the use of this instrument with studies of the unfolding of sperm whale apomyoglobin, as induced by acid pH and by the addition of guanidine-HCI.
Ramsay, G; Ionescu, R; Eftink, M R
1995-01-01
In a previous paper (Ramsay and Eftink, Biophys. J. 66:516-523) we reported the development of a modified spectrophotometer that can make nearly simultaneous circular dichroism (CD) and fluorescence measurements. This arrangement allows multiple data sets to be collected during a single experiment, resulting in a saving of time and material, and improved correlation between the different types of measurements. The usefulness of the instrument was shown by thermal melting experiments on several different protein systems. This CD/fluorometer spectrophotometer has been further modified by interfacing with a syringe pump and a pH meter. This arrangement allows ligand, pH, and chemical denaturation titration experiments to be performed while monitoring changes in the sample's CD, absorbance, fluorescence, and light scattering properties. Our data acquisition program also has an ability to check whether the signals have approached equilibrium before the data is recorded. For performing pH titrations we have developed a procedure which uses the signal from a pH meter in a feedback circuit in order to collect data at evenly spaced pH intervals. We demonstrate the use of this instrument with studies of the unfolding of sperm whale apomyoglobin, as induced by acid pH and by the addition of guanidine-HCI. Images FIGURE 2 PMID:8527683
NASA Astrophysics Data System (ADS)
Cid, R.; Alameda, J. M.; Valvidares, S. M.; Cezar, J. C.; Bencok, P.; Brookes, N. B.; Díaz, J.
2017-06-01
The origin of perpendicular magnetic anisotropy (PMA) in amorphous NdxCo1 -x thin films is investigated using x-ray magnetic circular dichroism (XMCD) spectroscopy at the Co L2 ,3 and Nd M4 ,5 edges. The magnetic orbital and spin moments of the 3 d cobalt and 4 f neodymium electrons were measured as a function of the magnetic field orientation, neodymium concentration, and temperature. In all the studied samples, the magnetic anisotropy of the neodymium subnetwork is always oriented perpendicular to the plane, whereas the anisotropy of the orbital moment of cobalt is in the basal plane. The ratio Lz/Sz of the neodymium 4 f orbitals changes with the sample orientation angle, being higher and closer to the atomic expected value at normal orientation and smaller at grazing angles. This result is well explained by assuming that the 4 f orbital is distorted by the effect of an anisotropic crystal field when it is magnetized along its hard axis, clearly indicating that the 4 f states are not rotationally invariant. The magnetic anisotropy energy associated to the neodymium subnetwork should be proportional to this distortion, which we demonstrate is accessible by applying the XMCD sum rules for the spin and intensity at the Nd M4 ,5 edges. The analysis unveils a significant portion of neodymium atoms magnetically uncoupled to cobalt, i.e., paramagnetic, confirming the inhomogeneity of the films and the presence of a highly disordered neodymium rich phase already detected by extended x-ray-absorption fine structure (EXAFS) spectroscopy. The presence of these inhomogeneities is inherent to the evaporation preparation method when the chosen concentration in the alloy is far from its eutectic concentrations. An interesting consequence of the particular way in which cobalt and neodymium segregates in this system is the enhancement of the cobalt spin moment which reaches 1.95 μB in the sample with the largest segregation.
NASA Astrophysics Data System (ADS)
Raju, Gembali; Vishwanath, S.; Prasad, Archana; Patel, Basant K.; Prabusankar, Ganesan
2016-03-01
New water soluble 4,5-bis imidazolium tagged acridines have been synthesized and structurally characterized by multinuclear NMR and single crystal X-ray diffraction techniques. The DNA binding and anti-microbial activities of these acridine derivatives were investigated by fluorescence and far-UV circular dichroism studies.
Komjáti, Balázs; Urai, Ákos; Hosztafi, Sándor; Kökösi, József; Kováts, Benjámin; Nagy, József; Horváth, Péter
2016-02-15
B3LYP is one of the most widely used functional for the prediction of electronic circular dichroism spectra, however if the studied molecule contains aromatic nitro group computations may fail to produce reliable results. A test set of molecules of known stereochemistry were synthesized to study this phenomenon in detail. Spectra were computed by B3LYP and CAM-B3LYP functionals with 6-311++G(2d,2p) basis set. It was found that the range separated CAM-B3LYP gives better predictions than B3LYP for all test molecules. Fragment population analysis revealed that the nitro groups form highly localized molecule orbitals but the exact composition depends on the functional. CAM-B3LYP allows sufficient spatial overlap between the nitro group and distant parts of the molecule, which is necessary for the accurate description of excited states especially for charge transfer states. This phenomenon and the synthesized test molecules can be used to benchmark theoretical methods as well as to help the development of new functionals intended for spectroscopical studies. Copyright © 2015 Elsevier B.V. All rights reserved.
Imai, Yuki; Nakano, Yuka; Kawai, Tsuyoshi; Yuasa, Junpei
2018-05-21
This work demonstrates a potential use of circularly polarized luminescence for object identification methodology in a sensor application. Towards this aim, we have developed new luminescence probes using pyrene derivatives as sensor luminophores. The probes [(R,R)- and (S,S)-Im2Py] contain two chiral imidazole moieties at 1,6-positions through ethynyl spacers (the angle between the spacers is close to 180°). The probe molecules spontaneously self-assemble into chiral stacks (P or M helicity) upon coordination to metal ions with tetrahedral coordination preference (e.g., Zn2+). The chiral probes display neither circular dichroism (CD) nor circularly polarized luminescence (CPL) in the absence of metal ions. However, [(R,R)- and (S,S)-Im2Py] begins to exhibit intense chiroptical activity (CD and CPL) upon self-assembly with Zn2+ ions. The unique chiroptical properties of [(R,R)- and (S,S)-Im2Py] with chemical stimuli-responsibility are capable of demonstrating the new sensing methodology using the CPL signal as detection output, enabling us to discriminate between a signal from the target analyte and that from non-target species. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
2017-01-01
Herein, a systematic study of a series of molecular iron model complexes has been carried out using Fe L2,3-edge X-ray absorption (XAS) and X-ray magnetic circular dichroism (XMCD) spectroscopies. This series spans iron complexes of increasing complexity, starting from ferric and ferrous tetrachlorides ([FeCl4]−/2–), to ferric and ferrous tetrathiolates ([Fe(SR)4]−/2–), to diferric and mixed-valent iron–sulfur complexes [Fe2S2R4]2–/3–. This test set of compounds is used to evaluate the sensitivity of both Fe L2,3-edge XAS and XMCD spectroscopy to oxidation state and ligation changes. It is demonstrated that the energy shift and intensity of the L2,3-edge XAS spectra depends on both the oxidation state and covalency of the system; however, the quantitative information that can be extracted from these data is limited. On the other hand, analysis of the Fe XMCD shows distinct changes in the intensity at both L3 and L2 edges, depending on the oxidation state of the system. It is also demonstrated that the XMCD intensity is modulated by the covalency of the system. For mononuclear systems, the experimental data are correlated with atomic multiplet calculations in order to provide insights into the experimental observations. Finally, XMCD is applied to the tetranuclear heterometal–iron–sulfur clusters [MFe3S4]3+/2+ (M = Mo, V), which serve as structural analogues of the FeMoco and FeVco active sites of nitrogenase. It is demonstrated that the XMCD data can be utilized to obtain information on the oxidation state distribution in complex clusters that is not readily accessible for the Fe L2,3-edge XAS data alone. The advantages of XMCD relative to standard K-edge and L2,3-edge XAS are highlighted. This study provides an important foundation for future XMCD studies on complex (bio)inorganic systems. PMID:28653855
2016-06-22
ARTICLE Received 16 Sep 2015 | Accepted 25 May 2016 | Published 22 Jun 2016 Experimental demonstration of the microscopic origin of circular...dissipation of the constituent metamolecules. Because such dissipation occurs on a nanoscale, this effect has never been experimentally probed and...never been experimentally verified because of the challenge of measuring non-radiative loss on the nanoscale. In this study we use a combination of
NASA Astrophysics Data System (ADS)
Heslar, John; Telnov, Dmitry A.; Chu, Shih-I.
2017-12-01
Recently, studies of bright circularly polarized high-harmonic beams from atoms in the soft-x-ray region as a source for x-ray magnetic circular dichroism measurement in a tabletop-scale setup have received considerable attention. In this paper, we address the problem with molecular targets and perform a detailed quantum study of H2 +, CO, and N2 molecules in bichromatic counter-rotating circularly polarized laser fields where we adopt wavelengths (1300 and 790 nm) and intensities (2 ×1014W /cm2 ) reported in a recent experiment [Proc. Natl. Acad. Sci. USA 112, 14206 (2015), 10.1073/pnas.1519666112]. Our treatment of multiphoton processes in homonuclear and heteronuclear diatomic molecules is nonperturbative and based on the time-dependent density-functional theory for multielectron systems. The calculated radiation spectrum contains doublets of left and right circularly polarized harmonics with high-energy photons in the XUV and soft-x-ray ranges. Our results reveal intriguing and substantially different nonlinear optical responses for homonuclear and heteronuclear diatomic molecules subject to circularly polarized intense laser fields. We study in detail the below- and above-threshold harmonic regions and analyze the ellipticity and phase of the generated harmonic peaks.
Rusz, Jan; Idrobo, Juan -Carlos; Bhowmick, Somnath
2014-09-30
The calculations presented here reveal that an electron probe carrying orbital angular momentum is just a particular case of a wider class of electron beams that can be used to measure electron magnetic circular dichroism (EMCD) with atomic resolution. It is possible to obtain an EMCD signal with atomic resolution by simply breaking the symmetry of the electron probe phase front using the aberration-corrected optics of a scanning transmission electron microscope. The probe’s required phase distribution depends on the sample’s magnetic symmetry and crystal structure. The calculations indicate that EMCD signals that use the electron probe’s phase are as strongmore » as those obtained by nanodiffraction methods.« less
Aboel Dahab, Ali; El-Hag, Dhia
2012-10-01
One of the relatively recent and most widely used approaches to reduce side effects associated with the use of nonsteroidal anti-inflammatory drugs (NSAIDs) is the complexation of NSAIDs with Cyclodextrins (CyD). So far, CyD interaction with drugs is not well understood. There have been many reports along these lines; however, rarely do these studies exploit the full potential of optical techniques. The purpose of this work is to produce a versatile, compact, low-volume, routine apparatus for the simultaneous measurements of absorbance and circular dichroism (CD) which allows for the concurrent use of three different pathlengths for binding studies of NSAIDs/CyD as a function of pH. A new rotating multi-cell holder which holds four cells was designed and manufactured. The work was achieved using an effective novel method for binding titration employing four separate flow cells connected in series in a flow system involving a titration flask and a pump. The pK(a), binding constants, stoichiometry and structural co-conformations of NSAIDs/β-CyD complexes were elucidated and determined with accuracy. The system proved to be efficient and the analysis time was reduced to less than or equal to one fourth of total analysis time used in one-cell systems, with possible automation for high-throughput analysis.
Komaromy, Andras Z; Kulsing, Chadin; Boysen, Reinhard I; Hearn, Milton T W
2015-03-01
Key requirements of protein purification by hydrophobic interaction chromatography (HIC) are preservation of the tertiary/quaternary structure, maintenance of biological function, and separation of the correctly folded protein from its unfolded forms or aggregates. This study examines the relationship between the HIC retention behavior of hen egg white lysozyme (HEWL) in high concentrations of several kosmotropic salts and its conformation, assessed by circular dichroism (CD) spectroscopy. Further, the physicochemical properties of HEWL in the presence of high concentrations of ammonium sulfate, sodium chloride and magnesium chloride were investigated by small angle X-ray scattering (SAXS) at different temperatures. Radii of gyration were extrapolated from Guinier approximations and the indirect transform program GNOM with protein-protein interaction and contrast variation taken into account. A bead model simulation provided information on protein structural changes using ab initio reconstruction with GASBOR. These results correlated to the secondary structure content obtained from CD spectroscopy of HEWL. These changes in SAXS and CD data were consistent with heat capacity ΔCp -values obtained from van't Hoff plot analyses of the retention data. Collectively, these insights enable informed decisions to be made on the choice of chromatographic conditions, leading to improved separation selectivity and opportunities for innovative column-assisted protein refolding methods. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
NASA Astrophysics Data System (ADS)
Kagoshima, Yasushi; Muto, Sadatsugu; Miyahara, Tsuneaki; Koide, Tsuneharu; Yamamoto, Shigeru; Kitamura, Hideo
1992-01-01
A branch beamline, BL28A, has been constructed for the application of circularly polarized vacuum ultraviolet radiation. The radiation can be obtained in the helical undulator operation mode of an insertion device, EMPW♯28, which is also cut for elliptically polarized hard x-ray radiation. T first harmonic of the helical undulator radiation can be tuned from 40 to 350 eV with its corresponding K value from 3 to 0.2. A monochromator working basically with constant deviation optics was installed, and has started its operation. A circularly polarized flux of ˜1010 photons/s has been achieved with energy resolution of around 500-1000 at the first harmonic peak. The circular polarization after the monochromator was estimated to be higher than 70% by comparing theory and experiment on the magnetic circular dichroism of nickel films in the 3p-3d excitation region. The design philosophy of the beamline and recent results on the performance tests are presented.
NASA Astrophysics Data System (ADS)
Zhan, Kangshu
evaluated. Full spectrum reconstruction using a set of selected optical filters was carried out and data visualization using a Matlab based 3D mapping method was demonstrated. The third chapter describes the introduction of biomolecules in chiral particle studies. By measuring the circular dichroism spectrum and image of nanorods during lysozyme adsorption and denaturation, I was able to monitor the conformation change of proteins on large gapped nanorods. Experiment results suggested that the conformational change of absorbed protein could lead to the change of chiral signal of nanoparticles, suggesting the potentials of detecting biomolecular structural changes at the single nanoparticle level, though much uncertainty still present. The inherent high background of large, gapped nanoparticles when they interact with biomolecules led to the research described in the 4th chapter where I studied small palladium-silver coreshell nanoparticle properties and its interaction with proteins. SEM was used to characterize particles structures; UV-Vis and darkfield microscopy was used to capture particles' optical responses; and the finite-difference time-domain (FDTD) method was used to simulate resulting spectra and to compare with experimental outcomes. Lysozyme and bovine serum albumin (BSA) were used as the model molecules to study their conformational changes after being adsorbed onto particles. Last but the least, the 5th chapter is dedicated to FDTD simulation of a pair of perfectly shaped triangle nanoprisms to illustrate possible CD responses to be expected from extreme particles with sharp corners and much concentrated local EM field. Different coupling modes of triangle nanoprism were analyzed. It is found that many factors, such as particle orientation, spacing, and their relative position, could lead to significantly different coupling efficient, for both homodimers and heterodimers. The modeling data suggested interesting potentials of nanoparticles of extreme geometric
NASA Astrophysics Data System (ADS)
Zhang, Zhiyin; Sun, Shuaishuai; Xu, Jianhua; Zhang, Jing; Huang, Yan; Zhang, Bingbing; Tao, Ye
2013-04-01
Alzheimer's disease (AD) is a progressive and devastating neurodegenerative pathology, clinically characterized by dementia, cognitive impairment, personality disorders and memory loss. It is generally accepted that, misfolding of Aβ peptides is the key element in pathogenesis and the secondary structure of Aβ can be changed to major β-strand with reasons unknown yet. Many studies have shown that the misfolding may be linked with some biometals, mainly copper and zinc ions. To characterize interactions of Aβ and metal ions, we utilized both the extended X-ray fine structure spectroscopy (EXAFS) and the synchrotron radiation circular dichroism spectroscopy (SRCD). Aβ (13-22), Aβ (13-21), Aβ (E22G) and Aβ(HH-AA) were selected to study the mechanism of copper and zinc binding to Aβ. We found that Cu interaction with H13 and H14 residues led to the disappearance of the PPΠ, while the Cu binding E22 residue caused a remarkable conformation change to β-sheet enrichment. The Zn ion, in contrast, made little effect on the conformation and it coordinated to only one histidine (H residue) or not.
Cristiglio, Viviana; Grillo, Isabelle; Fomina, Margarita; Wien, Frank; Shalaev, Evgenyi; Novikov, Alexey; Brassamin, Séverine; Réfrégiers, Matthieu; Pérez, Javier; Hennet, Louis
2017-01-01
The acoustic levitation technique is a useful sample handling method for small solid and liquids samples, suspended in air by means of an ultrasonic field. This method was previously used at synchrotron sources for studying pharmaceutical liquids and protein solutions using x-ray diffraction and small angle x-ray scattering (SAXS). In this work we combined for the first time this containerless method with small angle neutron scattering (SANS) and synchrotron radiation circular dichroism (SRCD) to study the structural behavior of proteins in solutions during the water evaporation. SANS results are also compared with SAXS experiments. The aggregation behavior of 45μl droplets of lysozyme protein diluted in water was followed during the continuous increase of the sample concentration by evaporating the solvent. The evaporation kinetics was followed at different drying stage by SANS and SAXS with a good data quality. In a prospective work using SRCD, we also studied the evolution of the secondary structure of the myoglobin protein in water solution in the same evaporation conditions. Acoustic levitation was applied for the first time with SANS and the high performances of the used neutron instruments made it possible to monitor fast container-less reactions in situ. A preliminary work using SRCD shows the potentiality of its combination with acoustic levitation for studying the evolution of the protein structure with time. This multi-techniques approach could give novel insights into crystallization and self-assembly phenomena of biological compound with promising potential applications in pharmaceutical, food and cosmetics industry. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo. Copyright © 2016 Elsevier B.V. All rights reserved.
Francis, Andrew J; Resendiz, Marino J E
2017-07-28
Solid-phase synthesis has been used to obtain canonical and modified polymers of nucleic acids, specifically of DNA or RNA, which has made it a popular methodology for applications in various fields and for different research purposes. The procedure described herein focuses on the synthesis, purification, and characterization of dodecamers of RNA 5'-[CUA CGG AAU CAU]-3' containing zero, one, or two modifications located at the C2'-O-position. The probes are based on 2-thiophenylmethyl groups, incorporated into RNA nucleotides via standard organic synthesis and introduced into the corresponding oligonucleotides via their respective phosphoramidites. This report makes use of phosphoramidite chemistry via the four canonical nucleobases (Uridine (U), Cytosine (C), Guanosine (G), Adenosine (A)), as well as 2-thiophenylmethyl functionalized nucleotides modified at the 2'-O-position; however, the methodology is amenable for a large variety of modifications that have been developed over the years. The oligonucleotides were synthesized on a controlled-pore glass (CPG) support followed by cleavage from the resin and deprotection under standard conditions, i.e., a mixture of ammonia and methylamine (AMA) followed by hydrogen fluoride/triethylamine/N-methylpyrrolidinone. The corresponding oligonucleotides were purified via polyacrylamide electrophoresis (20% denaturing) followed by elution, desalting, and isolation via reversed-phase chromatography (Sep-pak, C18-column). Quantification and structural parameters were assessed via ultraviolet-visible (UV-vis) and circular dichroism (CD) photometric analysis, respectively. This report aims to serve as a resource and guide for beginner and expert researchers interested in embarking in this field. It is expected to serve as a work-in-progress as new technologies and methodologies are developed. The description of the methodologies and techniques within this document correspond to a DNA/RNA synthesizer (refurbished and purchased in
All-optical switching in granular ferromagnets caused by magnetic circular dichroism
NASA Astrophysics Data System (ADS)
Ellis, Matthew O. A.; Fullerton, Eric E.; Chantrell, Roy W.
2016-07-01
Magnetic recording using circularly polarised femto-second laser pulses is an emerging technology that would allow write speeds much faster than existing field driven methods. However, the mechanism that drives the magnetisation switching in ferromagnets is unclear. Recent theories suggest that the interaction of the light with the magnetised media induces an opto-magnetic field within the media, known as the inverse Faraday effect. Here we show that an alternative mechanism, driven by thermal excitation over the anisotropy energy barrier and a difference in the energy absorption depending on polarisation, can create a net magnetisation over a series of laser pulses in an ensemble of single domain grains. Only a small difference in the absorption is required to reach magnetisation levels observed experimentally and the model does not preclude the role of the inverse Faraday effect but removes the necessity that the opto-magnetic field is 10 s of Tesla in strength.
Template Based Design of Anti-Metastatic Drugs from the Active Conformation of Laminin Peptide 11
2002-01-01
spectrometry, and the success of refolding column, lane D = molecular weight markers. the domain by circular dichroism (CD) spectroscopy . The recombinant...determine the active conformation of peptide 11 utilized Tr-NOESY (Transferred Nuclear Overhauser Effect Spectroscopy ) experiments where the peptide...activity. RNAase Nothing activity assayed for 20 hours of refolding using 2’:3’-cyclic cytidine monophosphate 0 01 1,5 2 Time, hrs A Final report
He, Wenni; Li, Yao; Qin, Yuejie; Tong, Xiaomei; Song, Zhijun; Zhao, Yu; Wei, Ran; Li, Li; Dai, Huanqin; Wang, Wenzhao; Luo, Houwei; Ye, Xin; Zhang, Lixin; Liu, Xueting
2017-08-01
This paper provides an efficient platform to diversify the structure and pharmaceutical potentials of known natural products. Seven metabolites were obtained via the biotransformation of cryptotanshinone by the fungus Mucor rouxii AS 3.3447, and assigned as 13R-14R-hydroxy-anhydride of 16R-cryptotanshinone (1), 1S-hydroxy-anhydride of 16R-cryptotanshinone (2), 1R-hydroxy-anhydride of 16R-cryptotanshinone (3), 3S-hydroxy-epicryptoacetalide (4), 3S-hydroxy-cryptoacetalide (5), epicryptoacetalide (6), and cryptoacetalide (7). Among these compounds, 1-5 are novel. The ortho-naphthoquinone chromophore of cryptotanshinone was degraded and rearranged by M. rouxii. 1 and 3 showed good anti-influenza A virus activities with the reduced cytotoxic activities compared to the parent substrate cryptotanshinone (8). The structures of all the new compounds were determined on the basis of HRESIMS (high-resolution electrospray ionization mass spectroscopy) spectrometry, NMR (nuclear magnetic resonance) spectroscopy, ECD (electronic circular dichroism) calculations, and the CD (circular dichroism) of "in situ" method with [Rh 2 (OCOCF 3 ) 4 ].
NASA Astrophysics Data System (ADS)
Natoli, Calogero R.; Krüger, Peter; Bartolomé, Juan; Bartolomé, Fernando
2018-04-01
We determine the magnetic ground state of the FePc molecule on Au-supported thin films based on the observed values of orbital anisotropy and spectroscopic x-ray magnetic circular dichroism (XMCD) measurements at the Fe K and L edges. Starting from ab initio molecular orbital multiplet calculations for the isolated molecule, we diagonalize the spin-orbit interaction in the subspace spanned by the three lowest spin triplet states of 3A2 g and 3Eg symmetry in the presence of a saturating magnetic field at a polar angle θ with respect to the normal to the plane of the film, plus an external perturbation representing the effect of the molecules in the stack on the FePc molecule under consideration. We find that the orbital moment of the ground state strongly depends on the magnetic field direction in agreement with the sum rule analysis of the L23-edge XMCD data. We calculate integrals over the XMCD spectra at the Fe K and L23 edges as used in the sum rules and explicitly show that they agree with the expectation values of the orbital moment and effective spin moment of the ground state. On the basis of this analysis, we can rule out alternative candidates proposed in the literature.
Wang, Shuai-Hua; Zheng, Fa-Kun; Zhang, Ming-Jian; Liu, Zhi-Fa; Chen, Jun; Xiao, Yu; Wu, A-Qing; Guo, Guo-Cong; Huang, Jin-Shun
2013-09-03
We employed two pairs of new in-situ-generated chiral amino acid-tetrazole ligands in constructing homochiral Zn(II) coordination compounds: [Zn(tzet)]n (1a for (S)-tzet and 1b for (R)-tzet, H2tzet = N-[2-(1H-tetrazol-5-yl)ethyl]tryptophan) and [Zn(tzep)(H2O)2]·H2O (2a for (S)-tzep and 2b for (R)-tzep, H2tzep = N-[2-(1H-tetrazol-5-yl)ethyl]proline), which were hydrothermally synthesized and structurally characterized by single-crystal X-ray diffraction. Structural analysis reveals that 1 features a 2D homochiral framework generated by both tetrazolate and carboxylate bridges in tzet(2-) ligands. The isolated structure of 2 is stabilized by extensive hydrogen bonds, which leads to formation of a supramolecular 2D architecture. The absolute configuration induced at the nitrogen atoms of 1 and 2 is strictly related to the neighboring chiral carbon atoms by hydrogen-bond interactions. To further investigate their chirality, the combined experimental and theoretical analyses of circular dichroism spectra reveal the absolute configurations and nature of the Cotton effects. Solid-state excitation and emission spectra for 1 and 2 at room temperature were investigated with relevant density of states calculation, and tunable photoluminescence emission of 1 under different excitation wavelengths was discussed. As nitrogen-rich tetrazolate compounds, 1 and 2 possess higher enthalpies of combustion and may serve as a new family of promising energetic materials.
Duman, Osman; Tunç, Sibel; Kancı Bozoğlan, Bahar
2013-07-01
The interactions of metoprolol tartrate (MPT) and guaifenesin (GF) drugs with human serum albumin (HSA) and human hemoglobin (HMG) proteins at pH 7.4 were studied by fluorescence and circular dichroism (CD) spectroscopy. Drugs quenched the fluorescence spectra of HSA and HMG proteins through a static quenching mechanism. For each protein-drug system, the values of Stern-Volmer quenching constant, bimolecular quenching constant, binding constant and number of binding site on the protein molecules were determined at 288.15, 298.15, 310.15 and 318.15 K. It was found that the binding constants of HSA-MPT and HSA-GF systems were smaller than those of HMG-MPT and HMG-GF systems. For both drugs, the affinity of HMG was much higher than that of HSA. An increase in temperature caused a negative effect on the binding reactions. The number of binding site on blood proteins for MPT and GF drugs was approximately one. Thermodynamic parameters showed that MPT interacted with HSA through electrostatic attraction forces. However, hydrogen bonds and van der Waals forces were the main interaction forces in the formation of HSA-GF, HMG-MPT and HMG-GF complexes. The binding processes between protein and drug molecules were exothermic and spontaneous owing to negative ∆H and ∆G values, respectively. The values of binding distance between protein and drug molecules were calculated from Förster resonance energy transfer theory. It was found from CD analysis that the bindings of MPT and GF drugs to HSA and HMG proteins altered the secondary structure of HSA and HMG proteins.
Employing Theories Far beyond Their Limits - Linear Dichroism Theory.
Mayerhöfer, Thomas G
2018-05-15
Using linear polarized light, it is possible in case of ordered structures, such as stretched polymers or single crystals, to determine the orientation of the transition moments of electronic and vibrational transitions. This not only helps to resolve overlapping bands, but also assigning the symmetry species of the transitions and to elucidate the structure. To perform spectral evaluation quantitatively, a sometimes "Linear Dichroism Theory" called approach is very often used. This approach links the relative orientation of the transition moment and polarization direction to the quantity absorbance. This linkage is highly questionable for several reasons. First of all, absorbance is a quantity that is by its definition not compatible with Maxwell's equations. Furthermore, absorbance seems not to be the quantity which is generally compatible with linear dichroism theory. In addition, linear dichroism theory disregards that it is not only the angle between transition moment and polarization direction, but also the angle between sample surface and transition moment, that influences band shape and intensity. Accordingly, the often invoked "magic angle" has never existed and the orientation distribution influences spectra to a much higher degree than if linear dichroism theory would hold strictly. A last point that is completely ignored by linear dichroism theory is the fact that partially oriented or randomly-oriented samples usually consist of ordered domains. It is their size relative to the wavelength of light that can also greatly influence a spectrum. All these findings can help to elucidate orientation to a much higher degree by optical methods than currently thought possible by the users of linear dichroism theory. Hence, it is the goal of this contribution to point out these shortcomings of linear dichroism theory to its users to stimulate efforts to overcome the long-lasting stagnation of this important field. © 2018 Wiley-VCH Verlag GmbH & Co. KGa
Menguy, Nicolas; Arrio, Marie-Anne; Sainctavit, Philippe; Juhin, Amélie; Wang, Yinzhao; Chen, Haitao; Bunau, Oana; Otero, Edwige; Ohresser, Philippe; Pan, Yongxin
2016-01-01
The biomineralization of magnetite nanocrystals (called magnetosomes) by magnetotactic bacteria (MTB) has attracted intense interest in biology, geology and materials science due to the precise morphology of the particles, the chain-like assembly and their unique magnetic properties. Great efforts have been recently made in producing transition metal-doped magnetosomes with modified magnetic properties for a range of applications. Despite some successful outcomes, the coordination chemistry and magnetism of such metal-doped magnetosomes still remain largely unknown. Here, we present new evidences from X-ray magnetic circular dichroism (XMCD) for element- and site-specific magnetic analyses that cobalt is incorporated in the spinel structure of the magnetosomes within Magnetospirillum magneticum AMB-1 through the replacement of Fe2+ ions by Co2+ ions in octahedral (Oh) sites of magnetite. Both XMCD at Fe and Co L2,3 edges, and energy-dispersive X-ray spectroscopy on transmission electron microscopy analyses reveal a heterogeneous distribution of cobalt occurring either in different particles or inside individual particles. Compared with non-doped one, cobalt-doped magnetosome sample has lower Verwey transition temperature and larger magnetic coercivity, related to the amount of doped cobalt. This study also demonstrates that the addition of trace cobalt in the growth medium can significantly improve both the cell growth and the magnetosome formation within M. magneticum AMB-1. Together with the cobalt occupancy within the spinel structure of magnetosomes, this study indicates that MTB may provide a promising biomimetic system for producing chains of metal-doped single-domain magnetite with an appropriate tuning of the magnetic properties for technological and biomedical applications. PMID:27512138
Li, Jinhua; Menguy, Nicolas; Arrio, Marie-Anne; Sainctavit, Philippe; Juhin, Amélie; Wang, Yinzhao; Chen, Haitao; Bunau, Oana; Otero, Edwige; Ohresser, Philippe; Pan, Yongxin
2016-08-01
The biomineralization of magnetite nanocrystals (called magnetosomes) by magnetotactic bacteria (MTB) has attracted intense interest in biology, geology and materials science due to the precise morphology of the particles, the chain-like assembly and their unique magnetic properties. Great efforts have been recently made in producing transition metal-doped magnetosomes with modified magnetic properties for a range of applications. Despite some successful outcomes, the coordination chemistry and magnetism of such metal-doped magnetosomes still remain largely unknown. Here, we present new evidences from X-ray magnetic circular dichroism (XMCD) for element- and site-specific magnetic analyses that cobalt is incorporated in the spinel structure of the magnetosomes within Magnetospirillum magneticum AMB-1 through the replacement of Fe(2+) ions by Co(2+) ions in octahedral (Oh) sites of magnetite. Both XMCD at Fe and Co L2,3 edges, and energy-dispersive X-ray spectroscopy on transmission electron microscopy analyses reveal a heterogeneous distribution of cobalt occurring either in different particles or inside individual particles. Compared with non-doped one, cobalt-doped magnetosome sample has lower Verwey transition temperature and larger magnetic coercivity, related to the amount of doped cobalt. This study also demonstrates that the addition of trace cobalt in the growth medium can significantly improve both the cell growth and the magnetosome formation within M. magneticum AMB-1. Together with the cobalt occupancy within the spinel structure of magnetosomes, this study indicates that MTB may provide a promising biomimetic system for producing chains of metal-doped single-domain magnetite with an appropriate tuning of the magnetic properties for technological and biomedical applications. © 2016 The Author(s).
NASA Astrophysics Data System (ADS)
Güler, Günnur; Džafić, Enela; Vorob'ev, Mikhail M.; Vogel, Vitali; Mäntele, Werner
2011-06-01
Fourier transform infrared (FT-IR)- and UV-circular dichroism (UV-CD) spectroscopy have been used to study real-time proteolytic digestion of β-lactoglobulin (β-LG) and β-casein (β-CN) by trypsin at various substrate/enzyme ratios in D 2O-buffer at 37 °C. Both techniques confirm that protein substrate looses its secondary structure upon conversion to the peptide fragments. This perturbation alters the backbone of the protein chain resulting in conformational changes and degrading of the intact protein. Precisely, the most significant spectral changes which arise from digestion take place in the amide I and amide II regions. The FT-IR spectra for the degraded β-LG show a decrease around 1634 cm -1, suggesting a decrease of β-sheet structure in the course of hydrolysis. Similarly, the intensity around the 1654 cm -1 band decreases for β-CN digested by trypsin, indicating a reduction in the α-helical part. On the other hand, the intensity around ˜1594 cm -1 and ˜1406 cm -1 increases upon enzymatic breakdown of both substrates, suggesting an increase in the antisymmetric and symmetric stretching modes of free carboxylates, respectively, as released digestion products. Observation of further H/D exchange in the course of digestion manifests the structural opening of the buried groups and accessibility to the core of the substrate. On the basis of the UV-CD spectra recorded for β-LG and β-CN digested by trypsin, the unordered structure increases concomitant with a decrease in the remaining structure, thus, revealing breakdown of the intact protein into smaller fragments. This model study in a closed reaction system may serve as a basis for the much more complex digestion processes in an open reaction system such as the stomach.
Cao, Xiaolin; Shah, Rekha D; Dukor, Rina K; Guo, Changning; Freedman, Teresa B; Nafie, Laurence A
2004-09-01
We report the first vibrational circular dichroism (VCD) spectra with continuous coverage from 800 cm(-1) in the mid-infrared (MIR) region to 10 000 cm(-1) in the near-infrared (NIR) region. This coverage is illustrated with MIR and NIR absorbance and VCD spectra of 2,2-dimethyl-dioxolane-4-methanol (DDM), alpha-pinene, and camphor that serve as calibration samples over this entire region. Commercially available, dual-source Fourier transform (FT) MIR and NIR VCD spectrometers were equipped with appropriate light sources, optics, and detectors, and were modified for dual-polarization-modulation (DPM) operation. The combination of liquid-nitrogen- and thermoelectric-cooled HgCdTe (MCT) detectors, as well as InGaAs and Germanium (Ge) detectors operating at room temperature, permitted collection of the desired absorbance and VCD spectra across the range of vibrational fundamental, combination band, and overtone frequencies. The spectra of DDM and alpha-pinene were measured as neat liquids and recorded for both enantiomers in the various spectral regions. Spectra for camphor were all measured in CCl(4) solution at a concentration of 0.6 M, except for the carbonyl-stretching region, where a more dilute concentration was used. The typical anisotropy ratios (g) of the three molecules were estimated with respect to their strongest VCD bands in each spectral region. It was found that for all three molecules in the spectral regions above 2000 cm(-1), anisotropy ratios are approximately the same order (10(-5)) of magnitude. However, in the MIR region, the typical anisotropy ratios are significantly different for the three molecules. This study demonstrates that with modern FT-VCD spectrometers modified for DPM operation, VCD spectra can be measured continuously across a wide spectral range from the MIR to nearly the visible region with an unsurpassed combination of signal-to-noise ratio and spectral resolution.
Simulation of circularly polarized luminescence spectra using coupled cluster theory
NASA Astrophysics Data System (ADS)
McAlexander, Harley R.; Crawford, T. Daniel
2015-04-01
We report the first computations of circularly polarized luminescence (CPL) rotatory strengths at the equation-of-motion coupled cluster singles and doubles (EOM-CCSD) level of theory. Using a test set of eight chiral ketones, we compare both dipole and rotatory strengths for absorption (electronic circular dichroism) and emission to the results from time-dependent density-functional theory (TD-DFT) and available experimental data for both valence and Rydberg transitions. For two of the compounds, we obtained optimized geometries of the lowest several excited states using both EOM-CCSD and TD-DFT and determined that structures and EOM-CCSD transition properties obtained with each structure were sufficiently similar that TD-DFT optimizations were acceptable for the remaining test cases. Agreement between EOM-CCSD and the Becke three-parameter exchange function and Lee-Yang-Parr correlation functional (B3LYP) corrected using the Coulomb attenuating method (CAM-B3LYP) is typically good for most of the transitions, though agreement with the uncorrected B3LYP functional is significantly worse for all reported properties. The choice of length vs. velocity representation of the electric dipole operator has little impact on the EOM-CCSD transition strengths for nearly all of the states we examined. For a pair of closely related β, γ-enones, (1R)-7-methylenebicyclo[2.2.1]heptan-2-one and (1S)-2-methylenebicyclo[2.2.1]heptan-7-one, we find that EOM-CCSD and CAM-B3LYP agree with the energetic ordering of the two possible excited-state conformations, resulting in good agreement with experimental rotatory strengths in both absorption and emission, whereas B3LYP yields a qualitatively incorrect result for the CPL signal of (1S)-2-methylenebicyclo[2.2.1]heptan-7-one. Finally, we predict that one of the compounds considered here, trans-bicyclo[3.3.0]octane-3,7-dione, is unique in that it exhibits an achiral ground state and a chiral first excited state, leading to a strong CPL
Simulation of circularly polarized luminescence spectra using coupled cluster theory
DOE Office of Scientific and Technical Information (OSTI.GOV)
McAlexander, Harley R.; Crawford, T. Daniel, E-mail: crawdad@vt.edu
2015-04-21
We report the first computations of circularly polarized luminescence (CPL) rotatory strengths at the equation-of-motion coupled cluster singles and doubles (EOM-CCSD) level of theory. Using a test set of eight chiral ketones, we compare both dipole and rotatory strengths for absorption (electronic circular dichroism) and emission to the results from time-dependent density-functional theory (TD-DFT) and available experimental data for both valence and Rydberg transitions. For two of the compounds, we obtained optimized geometries of the lowest several excited states using both EOM-CCSD and TD-DFT and determined that structures and EOM-CCSD transition properties obtained with each structure were sufficiently similar thatmore » TD-DFT optimizations were acceptable for the remaining test cases. Agreement between EOM-CCSD and the Becke three-parameter exchange function and Lee-Yang-Parr correlation functional (B3LYP) corrected using the Coulomb attenuating method (CAM-B3LYP) is typically good for most of the transitions, though agreement with the uncorrected B3LYP functional is significantly worse for all reported properties. The choice of length vs. velocity representation of the electric dipole operator has little impact on the EOM-CCSD transition strengths for nearly all of the states we examined. For a pair of closely related β, γ-enones, (1R)-7-methylenebicyclo[2.2.1]heptan-2-one and (1S)-2-methylenebicyclo[2.2.1]heptan-7-one, we find that EOM-CCSD and CAM-B3LYP agree with the energetic ordering of the two possible excited-state conformations, resulting in good agreement with experimental rotatory strengths in both absorption and emission, whereas B3LYP yields a qualitatively incorrect result for the CPL signal of (1S)-2-methylenebicyclo[2.2.1]heptan-7-one. Finally, we predict that one of the compounds considered here, trans-bicyclo[3.3.0]octane-3,7-dione, is unique in that it exhibits an achiral ground state and a chiral first excited state, leading to a
1999-08-01
and the digest proceeded for 25 minutes at room temperature. Column fractions were then collected in tubes containing soy- bean trypsin inhibitor (STI...characterization. C. Task 3: Analysis of Secondary Structure Composition using Circular Dichroism 1. Far-UV Circular Dichroism of P3 and P123 The University of...native protiens to determine functional activity of segments of a large modular protein, since non-native fragments and small peptides can yield
NASA Astrophysics Data System (ADS)
Takata, Fumiya; Ito, Keita; Takeda, Yukiharu; Saitoh, Yuji; Takanashi, Koki; Kimura, Akio; Suemasu, Takashi
2018-02-01
X-ray absorption spectroscopy (XAS) and x-ray magnetic circular dichroism measurements were performed at the Ni and Fe L2 ,3 absorption edges for N ixF e4 -xN (x =1 and 3) epitaxial films. Spectral line-shape analysis and element-specific magnetic moment evaluations are presented. Shoulders at approximately 2 eV above the Ni L2 ,3 main peaks in the XAS spectrum of N i3FeN were interpreted to originate from hybridization of orbitals between Ni 3 d at face-centered (II) sites and N 2 p at body-centered sites, while such features were missing in NiF e3N film. Similar shoulders were observed at Fe L2 ,3 edges in both films. These results indicate that the orbitals of Ni atoms did not hybridize with those of N atoms in the NiF e3N film. Hence, Ni atoms preferentially occupied corner (I) sites, where the hybridization was weak because of the relatively long distance between Ni at I sites and N atoms. The relatively large magnetic moment deduced from sum-rule analysis of NiF e3N also showed a good agreement with the presence of Ni atoms at I sites.
Statistical effects in the absorption and optical activity of particulate suspensions.
Bustamante, C; Maestre, M F
1988-01-01
The phenomenon of Duysens flattening of the absorption spectra resulting from the inhomogeneous distribution of the chromophores in the solution is analyzed. These inhomogeneities are treated as localized statistical fluctuations in the concentration of the absorbing species, by using the Gaussian distribution. A law of absorbance is obtained, and the effect of light scattering on the flattening is also characterized. The flattening in the circular dichroism spectra of particulate suspensions is then analyzed. It is shown that the degree of flattening of the circular dichroism of a suspension is, in general, different from the corresponding flattening of its absorption spectrum. A quantitative relationship between the two effects is established. PMID:3186738
Araujo, Thaís L S; Borges, Julio Cesar; Ramos, Carlos H; Meyer-Fernandes, José Roberto; Oliveira Júnior, Reinaldo S; Pascutti, Pedro G; Foguel, Debora; Palhano, Fernando L
2014-05-13
We investigated the folding of the 70 kDa human cytosolic inducible protein (Hsp70) in vitro using high hydrostatic pressure as a denaturing agent. We followed the structural changes in Hsp70 induced by high hydrostatic pressure using tryptophan fluorescence, molecular dynamics, circular dichroism, high-performance liquid chromatography gel filtration, dynamic light scattering, ATPase activity, and chaperone activity. Although monomeric, Hsp70 is very sensitive to hydrostatic pressure; after pressure had been removed, the protein did not return to its native sate but instead formed oligomeric species that lost chaperone activity but retained ATPase activity.
Banerjee, Raja; Sheet, Tridip
2017-11-01
Circular dichroism (CD) spectroscopy represents an important tool for characterization of the peptide and protein secondary structures that mainly arise from the conformational disposition of the peptide backbone in solution. In 1991 Manning and Woody proposed that, in addition to the signal intensity, the ratio between [θ]nπ* and [θ]ππ*ǁ ((R 2 ) ≅ [θ] 222 /[θ] 208 ), along with [θ]ππ*⊥ and [θ]ππ*ǁ ((R 1 ) ≅ [θ] 192 /[θ] 208 ), may be utilized towards identifying the peptide/protein conformation (especially 3 10 - and α-helices). However, till date the use of the ratiometric ellipticity component for helical structure analysis of peptides and proteins has not been reported. We studied a series of temperature dependent CD spectra of a thermally stable, model helical peptide and its related analogs in water as a function of added 2,2,2-trifluoroethanol (TFE) in order to explore their landscape of helicity. For the first time, we have experimentally shown here that the R 1 parameter can characterize better the individual helices, while the other parameter R 2 and the signal intensity do not always converge. We emphasize the use of the R 1 ratio of ellipticities for helical characterization because of the common origin of these two bands (exciton splitting of the amide π→ π* transition in a helical polypeptide). This approach may become worthwhile and timely with the increasing accessibility of CD synchrotron sources. © 2017 Wiley Periodicals, Inc.
Tomimatsu, Yoshio; Donovan, John W.
1981-01-01
Circular dichroism, differential scanning calorimetry and light-scattering measurements of ribulose 1,5-bisphosphate carboxylase (E.C. 4.1.1.39) from alfalfa, spinach and tobacco show: a) The conformation and thermal stability of the native carboxylases are sensitive to changes in pH and to activation of the enzyme with Mg2+ and CO2. The helical content, denaturation temperature (Td) and specific enthalpy of denaturation (Δq) decreased with increase in pH. Addition of Mg2+ and CO2 at pH 9 increased Td by 4 to 5 C; at pH 7.5 the changes in Td were smaller. b) Addition of mercurials produced changes in conformation and thermal stability. The decrease in helical content of the enzymes with increase in pH was enhanced by the addition of p-chloromercuribenzoate. At pH 9, addition of p-chloromercuribenzoate or of 1-(3-(chloromercuri)-2-methoxypropyl)urea decreased Td by 11.4 to 20.2 C and Δq by 2.1 to 2.8 calories per gram. c) The spinach carboxylase undergoes the largest and the tobacco the smallest changes in conformation and thermal stability upon change in pH or treatment with mercurials. d) The calorimetric data suggest that the large and small subunits are heat denatured independently but at the same temperature. e) Light scattering measurements at pH 9 of p-chloromercuribenzoate treated tobacco enzyme showed that there is no dissociation into subunits upon heating to temperatures greater than Td. A `ball and string' model for the carboxylase molecule is proposed to reconcile independence of subunit denaturation with apparent strong interactions between subunits. PMID:16662003
Polarized excitons and optical activity in single-wall carbon nanotubes
NASA Astrophysics Data System (ADS)
Chang, Yao-Wen; Jin, Bih-Yaw
2018-05-01
The polarized excitons and optical activity of single-wall carbon nanotubes (SWNTs) are studied theoretically by π -electron Hamiltonian and helical-rotational symmetry. By taking advantage of the symmetrization, the single-particle energy and properties of a SWNT are characterized with the corresponding helical band structure. The dipole-moment matrix elements, magnetic-moment matrix elements, and the selection rules can also be derived. Based on different selection rules, the optical transitions can be assigned as the parallel-polarized, left-handed circularly-polarized, and right-handed circularly-polarized transitions, where the combination of the last two gives the cross-polarized transition. The absorption and circular dichroism (CD) spectra are simulated by exciton calculation. The calculated results are well comparable with the reported measurements. Built on the foundation, magnetic-field effects on the polarized excitons and optical activity of SWNTs are studied. Dark-bright exciton splitting and interband Faraday effect in the CD spectrum of SWNTs under an axial magnetic field are predicted. The Faraday rotation dispersion can be analyzed according to the selection rules of circular polarizations and the helical band structure.
Optical activity in chiral stacks of 2D semiconductors
NASA Astrophysics Data System (ADS)
Poshakinskiy, Alexander V.; Kazanov, Dmitrii R.; Shubina, Tatiana V.; Tarasenko, Sergey A.
2018-03-01
We show that the stacks of two-dimensional semiconductor crystals with the chiral packing exhibit optical activity and circular dichroism. We develop a microscopic theory of these phenomena in the spectral range of exciton transitions that takes into account the spin-dependent hopping of excitons between the layers in the stack and the interlayer coupling of excitons via electromagnetic field. For the stacks of realistic two-dimensional semiconductors such as transition metal dichalcogenides, we calculate the rotation and ellipticity angles of radiation transmitted through such structures. The angles are resonantly enhanced at the frequencies of both bright and dark exciton modes in the stack. We also study the photoluminescence of chiral stacks and show that it is circularly polarized.
NASA Astrophysics Data System (ADS)
Gerard, Valerie; Govan, Joseph; Loudon, Alexander; Baranov, Alexander V.; Fedorov, Anatoly V.; Gun'ko, Yurii K.
2015-10-01
The main goal of our research is to develop new types of technologically important optically active quantum dot (QD) based materials, study their properties and explore their biological applications. For the first time chiral II-VI QDs have been prepared by us using microwave induced heating with the racemic (Rac), D- and L-enantiomeric forms of penicillamine as stabilisers. Circular dichroism (CD) studies of these QDs have shown that D- and L-penicillamine stabilised particles produced mirror image CD spectra, while the particles prepared with a Rac mixture showed only a weak signal. It was also demonstrated that these QDs show very broad emission bands between 400 and 700 nm due to defects or trap states on the surfaces of the nanocrystals. These QDs have demonstrated highly specific chiral recognition of various biological species including aminoacids. The utilisation of chiral stabilisers also allowed the preparation of new water soluble white emitting CdS nano-tetrapods, which demonstrated circular dichroism in the band-edge region of the spectrum. Biological testing of chiral CdS nanotetrapods displayed a chiral bias for an uptake of the D- penicillamine stabilised nano-tetrapods by cancer cells. It is expected that this research will open new horizons in the chemistry of chiral nanomaterials and their application in nanobiotechnology, medicine and optical chemo- and bio-sensing.
NASA Astrophysics Data System (ADS)
Vemuru, Krishnamurthy; Rosenberg, Richard; Mankey, Gary
Nanostructured FeCo thin films are interesting for magnetic recording applications due to their high saturation magnetization, high Curie temperature and low magnetocrystalline anisotropy. It is desirable to know how the magnetism is modified by the nanostructrure. We report Fe L 2 , 3 edge and Co L2 , 3 edge x-ray magnetic circular dichroism (XMCD) investigations of element specific spin and orbital magnetism of Fe and Co in two multilayer samples: (S1) Si/SiO2/[Co 0.8 nm/Fe 1.6 nm]x32/W (2nm) and (S2) Si/SiO2/[Co 1.6 nm/Fe 0.8 nm]x32/W (2nm) thin films at room temperature. Sum rule analysis of XMCD at Fe L2 , 3 edge in sample S1 shows that the orbital moment of Fe is strongly enhanced and the spin moment is strongly reduced as compared to the values found in bulk Fe. Details of sum rule analysis will be presented to compare and contrast spin magnetic moments and orbital magnetic moments of Fe and Co in the two multilayer samples. This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357.
Dobrikova, Anelia G; Várkonyi, Zsuzsanna; Krumova, Sashka B; Kovács, László; Kostov, Georgi K; Todinova, Svetla J; Busheva, Mira C; Taneva, Stefka G; Garab, Gyozo
2003-09-30
The thermo-optic mechanism in thylakoid membranes was earlier identified by measuring the thermal and light stabilities of pigment arrays with different levels of structural complexity [Cseh, Z., et al. (2000) Biochemistry 39, 15250-15257]. (According to the thermo-optic mechanism, fast local thermal transients, arising from the dissipation of excess, photosynthetically not used, excitation energy, induce elementary structural changes due to the "built-in" thermal instabilities of the given structural units.) The same mechanism was found to be responsible for the light-induced trimer-to-monomer transition in LHCII, the main chlorophyll a/b light-harvesting antenna of photosystem II (PSII) [Garab, G., et al. (2002) Biochemistry 41, 15121-15129]. In this paper, differential scanning calorimetry (DSC) and circular dichroism (CD) spectroscopy on thylakoid membranes of barley and pea are used to correlate the thermo-optically inducible structural changes with well-discernible calorimetric transitions. The thylakoid membranes exhibited six major DSC bands, with maxima between about 43 and 87 degrees C. The heat sorption curves were analyzed both by mathematical deconvolution of the overall endotherm and by a successive annealing procedure; these yielded similar thermodynamic parameters, transition temperature and calorimetric enthalpy. A systematic comparison of the DSC and CD data on samples with different levels of complexity revealed that the heat-induced disassembly of chirally organized macrodomains contributes profoundly to the first endothermic event, a weak and broad DSC band between 43 and 48 degrees C. Similarly to the main macrodomain-associated CD signals, this low enthalpy band could be diminished by prolonged photoinhibitory preillumination, the extent of which depended on the temperature of preillumination. By means of nondenaturing, "green" gel electrophoresis and CD fingerprinting, it is shown that the second main endotherm, around 60 degrees C
Circularly polarized antennas for active holographic imaging through barriers
McMakin, Douglas L [Richland, WA; Severtsen, Ronald H [Richland, WA; Lechelt, Wayne M [West Richland, WA; Prince, James M [Kennewick, WA
2011-07-26
Circularly-polarized antennas and their methods of use for active holographic imaging through barriers. The antennas are dielectrically loaded to optimally match the dielectric constant of the barrier through which images are to be produced. The dielectric loading helps to remove barrier-front surface reflections and to couple electromagnetic energy into the barrier.
Patty, C H Lucas; Luo, David A; Snik, Frans; Ariese, Freek; Buma, Wybren Jan; Ten Kate, Inge Loes; van Spanning, Rob J M; Sparks, William B; Germer, Thomas A; Garab, Győző; Kudenov, Michael W
2018-06-01
Spectropolarimetry of intact plant leaves allows to probe the molecular architecture of vegetation photosynthesis in a non-invasive and non-destructive way and, as such, can offer a wealth of physiological information. In addition to the molecular signals due to the photosynthetic machinery, the cell structure and its arrangement within a leaf can create and modify polarization signals. Using Mueller matrix polarimetry with rotating retarder modulation, we have visualized spatial variations in polarization in transmission around the chlorophyll a absorbance band from 650 nm to 710 nm. We show linear and circular polarization measurements of maple leaves and cultivated maize leaves and discuss the corresponding Mueller matrices and the Mueller matrix decompositions, which show distinct features in diattenuation, polarizance, retardance and depolarization. Importantly, while normal leaf tissue shows a typical split signal with both a negative and a positive peak in the induced fractional circular polarization and circular dichroism, the signals close to the veins only display a negative band. The results are similar to the negative band as reported earlier for single macrodomains. We discuss the possible role of the chloroplast orientation around the veins as a cause of this phenomenon. Systematic artefacts are ruled out as three independent measurements by different instruments gave similar results. These results provide better insight into circular polarization measurements on whole leaves and options for vegetation remote sensing using circular polarization. Copyright © 2018 The Author(s). Published by Elsevier B.V. All rights reserved.
Three-dimensional plasmonic chiral tetramers assembled by DNA origami.
Shen, Xibo; Asenjo-Garcia, Ana; Liu, Qing; Jiang, Qiao; García de Abajo, F Javier; Liu, Na; Ding, Baoquan
2013-05-08
Molecular chemistry offers a unique toolkit to draw inspiration for the design of artificial metamolecules. For a long time, optical circular dichroism has been exclusively the terrain of natural chiral molecules, which exhibit optical activity mainly in the UV spectral range, thus greatly hindering their significance for a broad range of applications. Here we demonstrate that circular dichroism can be generated with artificial plasmonic chiral nanostructures composed of the minimum number of spherical gold nanoparticles required for three-dimensional (3D) chirality. We utilize a rigid addressable DNA origami template to precisely organize four nominally identical gold nanoparticles into a three-dimensional asymmetric tetramer. Because of the chiral structural symmetry and the strong plasmonic resonant coupling between the gold nanoparticles, the 3D plasmonic assemblies undergo different interactions with left and right circularly polarized light, leading to pronounced circular dichroism. Our experimental results agree well with theoretical predictions. The simplicity of our structure geometry and, most importantly, the concept of resorting on biology to produce artificial photonic functionalities open a new pathway to designing smart artificial plasmonic nanostructures for large-scale production of optically active metamaterials.
Fu, Hengqing; Yang, Pengfei; Hai, Jinhui; Li, Huihui
2018-10-05
G-quadruplex DNAs are involved in a number of key biological processes, including gene expression, transcription, and apoptosis. The c-myb oncogene contains a number of GGA repeats in its promoter which forms G-quadruplex, thus it could be used as a target in cancer therapeutics. Several in-vitro studies have used Circular Dichroism (CD) spectroscopy or electrospray ionization mass spectrometry (ESI-MS) to demonstrate formation and stability of G-quadruplex DNA structure in the promoter region of human c-myb oncogene. The factors affecting the c-myb G-quadruplex structures were investigated, such as cations (i.e. K + , NH 4 + and Na + ) and co-solutes (methanol and polyethylene glycol). The results indicated that the presence of cations and co-solutes could change the G-quadruplex structural population and promote its thermodynamic stabilization as indicated by CD melting curves. It indicated that the co-solutes preferentially stabilize the c-myb G-quadruplex structure containing both homo- and hetero-stacking. In addition, protopine was demonstrated as a binder of c-myb G-quadruplex as screened from a library of natural alkaloids using ESI-MS method. CD spectra showed that it could selectively stabilize the c-myb G-quadruplex structure compared to other six G-quadruplexes from tumor-related G-rich sequences and the duplex DNAs (both long and short-chain ones). The binding of protopine could induce the change in the G-quadruplex structural populations. Therefore, protopine with its high binding specificity could be considered as a precursor for the design of drugs to target and regulate c-myb oncogene transcription. Copyright © 2018 Elsevier B.V. All rights reserved.
Zero-field dichroism in the solar chromosphere.
Sainz, R Manso; Bueno, J Trujillo
2003-09-12
We explain the linear polarization of the Ca ii infrared triplet observed close to the edge of the solar disk. In particular, we demonstrate that the physical origin of the enigmatic polarizations of the 866.2 and 854.2 nm lines lies in the existence of atomic polarization in their metastable (2)D(3)(/2, 5/2) lower levels, which produces differential absorption of polarization components (dichroism). To this end, we have solved the problem of the generation and transfer of polarized radiation by taking fully into account all the relevant optical pumping mechanisms in multilevel atomic models. We argue that "zero-field" dichroism may be of great diagnostic value in astrophysics.
NASA Astrophysics Data System (ADS)
Grum-Grzhimailo, A. N.; Cubaynes, D.; Heinecke, E.; Hoffmann, P.; Zimmermann, P.; Meyer, M.
2010-10-01
The generalized geometrical model for photoionization from polarized atoms is extended to include mixing of configurations in the initial atomic and/or the final photoion states. The theoretical results for angle-resolved linear and circular magnetic dichroism are in good agreement with new high-resolution photoelectron data for 3p-1 photoionization of potassium atoms polarized in the K 3p64s 2S1/2 ground state by laser optical pumping.
Karasawa, Masanobu; Ishii, Kazuyuki
2018-05-03
We have investigated the demagnetization of a ferrimagnetic substrate, Bi, Al-substituted dysprosium iron garnet (Bi0.8Dy2.2Fe4.3Al0.7O12), based on selective pulsed laser irradiation of a molecular thin film consisting of μ-oxo-bis[hydroxyl{2,9(or 10),16(or 17),23(or 24)-tetra-tert-butylphthalocyanato}silicon] ((SiPc)2) and poly(vinylidene fluoride), and succeeded in reproducing photothermal energy transfer from a molecular thin film to an inorganic magnetic substrate in a submicrometer-order and a submicrosecond time scale using numerical analysis. After the instant temperature rise due to nanosecond pulsed laser irradiation of the (SiPc)2-based film, followed by heat transfer from the film to the neighboring magnetic substrate, demagnetization of the magnetic substrate was spectroscopically monitored by the decrease in its magnetic circular dichroism (MCD) intensity. The MCD intensity decreased with increasing pulsed laser energy, which reflects the fact that the submicrometer-order region of the substrate was demagnetized as a result of temperature rise reaching high Curie temperature. This heat transfer phenomenon resulting in the demagnetization of the magnetic substrate was numerically analyzed in a submicrometer-order and a submicrosecond time scale using the finite difference method: the demagnetized regions were calculated to be the same order of magnitude as those experimentally evaluated. These results would provide a more detailed understanding of photothermal energy transfer in organic-inorganic hybrid materials, which would be useful for developing photofunctional materials.
Mefford, Melissa A.
2015-01-01
Telomerase is a specialized ribonucleoprotein complex that extends the 3′ ends of chromosomes to counteract telomere shortening. However, increased telomerase activity is associated with ∼90% of human cancers. The telomerase enzyme minimally requires an RNA (hTR) and a specialized reverse transcriptase protein (TERT) for activity in vitro. Understanding the structure-function relationships within hTR has important implications for human disease. For the first time, we have tested the physical-connectivity requirements in the 451-nucleotide hTR RNA using circular permutations, which reposition the 5′ and 3′ ends. Our extensive in vitro analysis identified three classes of hTR circular permutants with altered function. First, circularly permuting 3′ of the template causes specific defects in repeat-addition processivity, revealing that the template recognition element found in ciliates is conserved in human telomerase RNA. Second, seven circular permutations residing within the catalytically important core and CR4/5 domains completely abolish telomerase activity, unveiling mechanistically critical portions of these domains. Third, several circular permutations between the core and CR4/5 significantly increase telomerase activity. Our extensive circular permutation results provide insights into the architecture and coordination of human telomerase RNA and highlight where the RNA could be targeted for the development of antiaging and anticancer therapeutics. PMID:26503788
Magnetic x-ray linear dichroism of ultrathin Fe-Ni alloy films
DOE Office of Scientific and Technical Information (OSTI.GOV)
Schumann, F.O.; Willis, R.F.; Goodman, K.W.
1997-04-01
The authors have studied the magnetic structure of ultrathin Fe-Ni alloy films as a function of Fe concentration by measuring the linear dichroism of the 3p-core levels in angle-resolved photoemission spectroscopy. The alloy films, grown by molecular-beam epitaxy on Cu(001) surfaces, were fcc and approximately four monolayers thick. The intensity of the Fe dichroism varied with Fe concentration, with larger dichroisms at lower Fe concentrations. The implication of these results to an ultrathin film analogue of the bulk Invar effect in Fe-Ni alloys will be discussed. These measurements were performed at the Spectromicroscopy Facility (Beamline 7.0.1) of the Advanced Lightmore » Source.« less
Tao, Qiao-Qiao; Ma, Ke; Bao, Li; Wang, Kai; Han, Jun-Jie; Wang, Wen-Zhao; Zhang, Jin-Xia; Huang, Chen-Yang; Liu, Hong-Wei
2016-05-01
One new perhydrobenzannulated 5,5-spiroketal sesquiterpene, pleurospiroketal F (1), as well as six new modified bisabolene sesquiterpenes pleurotins A-F (2-7) were isolated from solid-state fermentation of Pleurotus citrinopileatus. The structures of compounds 1-7 were determined by NMR and MS spectroscopic analysis. The absolute configuration of 1 was determined by X-ray diffraction analysis, while the absolute configurations of 3-7 were assigned using the in situ dimolybdenum circular dichroism method and circular dichroism data comparison. Protein tyrosine phosphatase 1B plays a crucial role as a negative regulator of the insulin-dependent signal cascades. Therefore, the protein tyrosine phosphatase 1B inhibitor can be used for treating type 2 diabetes mellitus and obesity. Compounds 2 and 6 showed moderate inhibitory effects on protein tyrosine phosphatase 1B with IC50 s of 32.1 µM and 30.5 µM, respectively. The kinetic study confirmed compound 2 to be a noncompetitive inhibitor. Compounds 1-7 did not show cytotoxic activity against cancer cell lines (IC50 > 50 µM). Georg Thieme Verlag KG Stuttgart · New York.
Vector optical activity in the Weyl semimetal TaAs
Norman, M. R.
2015-12-15
Here, it is shown that the Weyl semimetal TaAs can have a significant polar vector contribution to its optical activity. This is quantified by ab initio calculations of the resonant x-ray diffraction at the Ta L1 edge. For the Bragg vector (400), this polar vector contribution to the circular intensity differential between left and right polarized x-rays is predicted to be comparable to that arising from linear dichroism. Implications this result has in regards to optical effects predicted for topological Weyl semimetals are discussed.
Wang, Z C; Zhong, X Y; Jin, L; Chen, X F; Moritomo, Y; Mayer, J
2017-05-01
Electron energy-loss magnetic chiral dichroism (EMCD) spectroscopy, which is similar to the well-established X-ray magnetic circular dichroism spectroscopy (XMCD), can determine the quantitative magnetic parameters of materials with high spatial resolution. One of the major obstacles in quantitative analysis using the EMCD technique is the relatively poor signal-to-noise ratio (SNR), compared to XMCD. Here, in the example of a double perovskite Sr 2 FeMoO 6 , we predicted the optimal dynamical diffraction conditions such as sample thickness, crystallographic orientation and detection aperture position by theoretical simulations. By using the optimized conditions, we showed that the SNR of experimental EMCD spectra can be significantly improved and the error of quantitative magnetic parameter determined by EMCD technique can be remarkably lowered. Our results demonstrate that, with enhanced SNR, the EMCD technique can be a unique tool to understand the structure-property relationship of magnetic materials particularly in the high-density magnetic recording and spintronic devices by quantitatively determining magnetic structure and properties at the nanometer scale. Copyright © 2017 Elsevier B.V. All rights reserved.
Mefford, Melissa A; Zappulla, David C
2016-01-15
Telomerase is a specialized ribonucleoprotein complex that extends the 3' ends of chromosomes to counteract telomere shortening. However, increased telomerase activity is associated with ∼90% of human cancers. The telomerase enzyme minimally requires an RNA (hTR) and a specialized reverse transcriptase protein (TERT) for activity in vitro. Understanding the structure-function relationships within hTR has important implications for human disease. For the first time, we have tested the physical-connectivity requirements in the 451-nucleotide hTR RNA using circular permutations, which reposition the 5' and 3' ends. Our extensive in vitro analysis identified three classes of hTR circular permutants with altered function. First, circularly permuting 3' of the template causes specific defects in repeat-addition processivity, revealing that the template recognition element found in ciliates is conserved in human telomerase RNA. Second, seven circular permutations residing within the catalytically important core and CR4/5 domains completely abolish telomerase activity, unveiling mechanistically critical portions of these domains. Third, several circular permutations between the core and CR4/5 significantly increase telomerase activity. Our extensive circular permutation results provide insights into the architecture and coordination of human telomerase RNA and highlight where the RNA could be targeted for the development of antiaging and anticancer therapeutics. Copyright © 2016, American Society for Microbiology. All Rights Reserved.
Harada, Takunori; Hayakawa, Hiroshi; Watanabe, Masayuki; Takamoto, Makoto
2016-07-01
A new solid-state dedicated circularly polarized luminescence (CPL) instrument (CPL-200CD) was successfully developed for measuring true CPL spectra for optically anisotropic samples on the basis of the Stokes-Mueller matrix approach. Electric components newly installed in the CPL-200CD include a pulse motor-driven sample rotation holder and a 100 kHz lock-in amplifier to achieve the linearly polarized luminescence measurement, which is essential for obtaining the true CPL signal for optically anisotropic samples. An acquisition approach devised for solid-state CPL analysis reduces the measurement times for a data set by ca. 98% compared with the time required in our previous method. As a result, the developed approach is very effective for samples susceptible to light-induced degradation. The theory and implementation of the method are described, and examples of its application to a CPL sample with macroscopic anisotropies are provided. An important advantage of the developed instrument is its ability to obtain molecular information for both excited and ground states because circular dichroism measurements can be performed by switching the monochromatic light to white light without rearrangement of the sample.
Microwave Magnetochiral Dichroism in the Chiral-Lattice Magnet Cu2OSeO3
NASA Astrophysics Data System (ADS)
Okamura, Y.; Kagawa, F.; Seki, S.; Kubota, M.; Kawasaki, M.; Tokura, Y.
2015-05-01
Through broadband microwave spectroscopy in Faraday geometry, we observe distinct absorption spectra accompanying magnetoelectric (ME) resonance for oppositely propagating microwaves, i.e., directional dichroism, in the multiferroic chiral-lattice magnet Cu2OSeO3. The magnitude of the directional dichroism critically depends on the magnetic-field direction. Such behavior is well accounted for by considering the relative direction of the oscillating electric polarizations induced via the ME effect with respect to microwave electric fields. Directional dichroism in a system with an arbitrary form of ME coupling can be also discussed in the same manner.
Influence of plasma-activated compounds on melanogenesis and tyrosinase activity
Ali, Anser; Ashraf, Zaman; Kumar, Naresh; Rafiq, Muhammad; Jabeen, Farukh; Park, Ji Hoon; Choi, Ki Hong; Lee, SeungHyun; Seo, Sung-Yum; Choi, Eun Ha; Attri, Pankaj
2016-01-01
Many organic chemists around the world synthesize medicinal compounds or extract multiple compounds from plants in order to increase the activity and quality of medicines. In this work, we synthesized new eugenol derivatives (ED) and then treated them with an N2 feeding gas atmospheric pressure plasma jet (APPJ) to increase their utility. We studied the tyrosinase-inhibition activity (activity test) and structural changes (circular dichroism) of tyrosinase with ED and plasma activated eugenol derivatives (PAED) in a cell-free environment. Later, we used docking studies to determine the possible interaction sites of ED and PAED compounds with tyrosinase enzyme. Moreover, we studied the possible effect of ED and PAED on melanin synthesis and its mechanism in melanoma (B16F10) cells. Additionally, we investigated the structural changes that occurred in activated ED after plasma treatment using nuclear magnetic resonance (NMR). Hence, this study provides a new perspective on PAED for the field of plasma medicine. PMID:26931617
Triterpenoids of Ganoderma theaecolum and their hepatoprotective activities.
Liu, Li-Ying; Chen, Hui; Liu, Chao; Wang, Hong-Qing; Kang, Jie; Li, Yan; Chen, Ruo-Yun
2014-10-01
Five new lanostane triterpenoids, ganoderic acid XL1 (1), ganoderic acid XL2 (2), 20-hydroxy-ganoderic acid AM1 (3), ganoderenic acid AM1 (4) and ganoderesin C (5), together with five known triterpenoids (6-10) were isolated from the fruiting bodies of Ganoderma theaecolum. Chemical structures were elucidated on the basis of spectroscopic evidence, including 1D, 2D NMR, mass spectrometric data and circular dichroism spectra. Compounds 1, 4, 5, 8, 9 and 10 (10 μM) exhibited hepatoprotective activities against DL-galactosamine-induced cell damage in HL-7702 cells. Copyright © 2014 Elsevier B.V. All rights reserved.
Probing the localization of magnetic dichroism by atomic-size astigmatic and vortex electron beams.
Negi, Devendra Singh; Idrobo, Juan Carlos; Rusz, Ján
2018-03-05
We report localization of a magnetic dichroic signal on atomic columns in electron magnetic circular dichroism (EMCD), probed by beam distorted by four-fold astigmatism and electron vortex beam. With astigmatic probe, magnetic signal to noise ratio can be enhanced by blocking the intensity from the central part of probe. However, the simulations show that for atomic resolution magnetic measurements, vortex beam is a more effective probe, with much higher magnetic signal to noise ratio. For all considered beam shapes, the optimal SNR constrains the signal detection at low collection angles of approximately 6-8 mrad. Irrespective of the material thickness, the magnetic signal remains strongly localized within the probed atomic column with vortex beam, whereas for astigmatic probes, the magnetic signal originates mostly from the nearest neighbor atomic columns. Due to excellent signal localization at probing individual atomic columns, vortex beams are predicted to be a strong candidate for studying the crystal site specific magnetic properties, magnetic properties at interfaces, or magnetism arising from individual atomic impurities.
Probing the localization of magnetic dichroism by atomic-size astigmatic and vortex electron beams
Negi, Devendra Singh; Idrobo, Juan Carlos; Rusz, Ján
2018-03-05
We report localization of a magnetic dichroic signal on atomic columns in electron magnetic circular dichroism (EMCD), probed by beam distorted by four-fold astigmatism and electron vortex beam. With astigmatic probe, magnetic signal to noise ratio can be enhanced by blocking the intensity from the central part of probe. However, the simulations show that for atomic resolution magnetic measurements, vortex beam is a more effective probe, with much higher magnetic signal to noise ratio. For all considered beam shapes, the optimal SNR constrains the signal detection at low collection angles of approximately 6–8 mrad. Irrespective of the material thickness, themore » magnetic signal remains strongly localized within the probed atomic column with vortex beam, whereas for astigmatic probes, the magnetic signal originates mostly from the nearest neighbor atomic columns. Due to excellent signal localization at probing individual atomic columns, vortex beams are predicted to be a strong candidate for studying the crystal site specific magnetic properties, magnetic properties at interfaces, or magnetism arising from individual atomic impurities.« less
Probing the localization of magnetic dichroism by atomic-size astigmatic and vortex electron beams
DOE Office of Scientific and Technical Information (OSTI.GOV)
Negi, Devendra Singh; Idrobo, Juan Carlos; Rusz, Ján
We report localization of a magnetic dichroic signal on atomic columns in electron magnetic circular dichroism (EMCD), probed by beam distorted by four-fold astigmatism and electron vortex beam. With astigmatic probe, magnetic signal to noise ratio can be enhanced by blocking the intensity from the central part of probe. However, the simulations show that for atomic resolution magnetic measurements, vortex beam is a more effective probe, with much higher magnetic signal to noise ratio. For all considered beam shapes, the optimal SNR constrains the signal detection at low collection angles of approximately 6–8 mrad. Irrespective of the material thickness, themore » magnetic signal remains strongly localized within the probed atomic column with vortex beam, whereas for astigmatic probes, the magnetic signal originates mostly from the nearest neighbor atomic columns. Due to excellent signal localization at probing individual atomic columns, vortex beams are predicted to be a strong candidate for studying the crystal site specific magnetic properties, magnetic properties at interfaces, or magnetism arising from individual atomic impurities.« less
Rafiee Fanood, Mohammad M; Ganjitabar, Hassan; Garcia, Gustavo A; Nahon, Laurent; Turchini, Stefano; Powis, Ivan
2018-04-17
Photoionization of the chiral monoterpene limonene has been investigated using polarized synchrotron radiation between the adiabatic ionization threshold, 8.505 and 23.5 eV. A rich vibrational structure is seen in the threshold photoelectron spectrum and is interpreted using a variety of computational methods. The corresponding photoelectron circular dichroism-measured in the photoelectron angular distribution as a forward-backward asymmetry with respect to the photon direction-was found to be strongly dependent on the vibronic structure appearing in the photoelectron spectra, with the observed asymmetry even switching direction in between the major vibrational peaks. This effect can be ultimately attributed to the sensitivity of this dichroism to small phase shifts between adjacent partial waves of the outgoing photoelectron. These observations have implications for potential applications of this chiroptical technique, where the enantioselective analysis of monoterpene components is of particular interest. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
The Secondary Structure of Human Hageman Factor (Factor XII) and its Alteration by Activating Agents
McMillin, Carl R.; Saito, Hidehiko; Ratnoff, Oscar D.; Walton, Alan G.
1974-01-01
Hageman factor (factor XII) is activated by exposure to surfaces such as glass or by solutions of certain compounds, notably ellagic acid. Changes in the structure of Hageman factor accompanying activation have been examined in this study by circular dichroism spectroscopy. The spectrum of unactivated Hageman factor in aqueous solutions suggests that its conformation is mainly aperiodic. Various perturbants altered the conformation of Hageman factor in differing ways, demonstrating the sensitivity of Hageman factor to its environment. After activation of Hageman factor with solutions of ellagic acid, a negative trough appeared in the region of the circular dichroism spectrum commonly assigned to tyrosine residues, along with other minor changes in the peptide spectral region. Some of these changes are similar to changes that occurred upon partial neutralization of the basic residues at alkali pH. Activation of Hageman factor by adsorption to quartz surfaces (in an aqueous environment) also produced changes similar to those in the ellagic acid-activated Hageman factor, including the negative ellipticity in the tyrosine region. These observations suggest that the activation process may be related to a change in status of some of the basic amino acid residues, coupled with a specific change in the environment of some tyrosine residues. The importance of these changes during the activation process remains to be determined. The sensitivity of Hageman factor to its environment is consistent with the view that the initiation of clotting by exposure of plasma to appropriate agents is brought about by alterations in the conformation of Hageman factor that occur in the apparent absence of Fletcher factor or other recognized clotting factors. Images PMID:4373492
Effects of Al(III) and Nano-Al13 Species on Malate Dehydrogenase Activity
Yang, Xiaodi; Cai, Ling; Peng, Yu; Li, Huihui; Chen, Rong Fu; Shen, Ren Fang
2011-01-01
The effects of different aluminum species on malate dehydrogenase (MDH) activity were investigated by monitoring amperometric i-t curves for the oxidation of NADH at low overpotential using a functionalized multi-wall nanotube (MWNT) modified glass carbon electrode (GCE). The results showed that Al(III) and Al13 can activate the enzymatic activity of MDH, and the activation reaches maximum levels as the Al(III) and Al13 concentration increase. Our study also found that the effects of Al(III) and Al13 on the activity of MDH depended on the pH value and aluminum speciation. Electrochemical and circular dichroism spectra methods were applied to study the effects of nano-sized aluminum compounds on biomolecules. PMID:22163924
Effects of Al(III) and nano-Al13 species on malate dehydrogenase activity.
Yang, Xiaodi; Cai, Ling; Peng, Yu; Li, Huihui; Chen, Rong Fu; Shen, Ren Fang
2011-01-01
The effects of different aluminum species on malate dehydrogenase (MDH) activity were investigated by monitoring amperometric i-t curves for the oxidation of NADH at low overpotential using a functionalized multi-wall nanotube (MWNT) modified glass carbon electrode (GCE). The results showed that Al(III) and Al(13) can activate the enzymatic activity of MDH, and the activation reaches maximum levels as the Al(III) and Al(13) concentration increase. Our study also found that the effects of Al(III) and Al(13) on the activity of MDH depended on the pH value and aluminum speciation. Electrochemical and circular dichroism spectra methods were applied to study the effects of nano-sized aluminum compounds on biomolecules.
Blasco, Salvador; Twamley, Brendan; O'Brien, John; Peacock, Robert D.; Kitchen, Jonathan A.; Martínez-Calvo, Miguel
2015-01-01
The binding of asymmetrical and optically pure tridentate ligands (L = 1(S) and 1(R)) containing one carboxylic group and 2-naphthyl as an antenna to lanthanide ions (M = La(iii) and Eu(iii)) was studied in CH3CN, showing the successive formation of M:L, M:L2 and M:L3 stoichiometric species in solution. The europium complexes EuL3 were also synthesised, structurally characterised and their photophysical properties probed in CH3OH and CH3CN. The changes in the chiroptical properties of both 1(S) and 1(R) were used (by circular dichroism (CD) spectroscopy) to monitor the formation of these chiral self-assemblies in solution. While circularly polarised luminescence (CPL) showed the formation of Eu(1(S))3 and Eu(1(R))3 as enantiomers, with high luminescence dissymmetry factors (g lum), fitting the CD changes allowed for binding constants to be determined that were comparable to those seen in the analyses of absorbance and luminescence changes. PMID:28936303
Circular RNA: New Regulatory Molecules.
Belousova, E A; Filipenko, M L; Kushlinskii, N E
2018-04-01
Circular RNA are a family of covalently closed circular RNA molecules, formed from pre-mRNA of coding genes by means of splicing (canonical and alternative noncanonical splicing). Maturation of circular RNA is regulated by cis- and trans-elements. Complete list of biological functions of these RNA is not yet compiled; however, their capacity to interact with specific microRNA and play a role of a depot attracts the greatest interest. This property makes circular RNA active regulatory transcription factors. Circular RNA have many advantages over their linear analogs: synthesis of these molecules is conservative, they are universal, characterized by clearly determined specificity, and are resistant to exonucleases. In addition, the level of their expression is often higher than that of their linear forms. It should be noted that expression of circular RNA is tissue-specific. Moreover, some correlations between changes in the repertoire and intensity of expression of circular RNA and the development of some pathologies have been detected. Circular RNA have certain advantages and can serve as new biomarkers for the diagnosis, prognosis, and evaluation of response to therapy.
Vitrified chiral-nematic liquid crystalline films for selective reflection and circular polarization
DOE Office of Scientific and Technical Information (OSTI.GOV)
Katsis, D.; Chen, P.H.M.; Mastrangelo, J.C.
Nematic and left-handed chiral-nematic liquid crystals comprising methoxybiphenylbenzoate and (S)-(-)-1-phenylethylamine pendants to a cyclohexane core were synthesized and characterized. Although pristine samples were found to be polycrystalline, thermal quenching following heating to and annealing at elevated temperatures permitted the molecular orders characteristic of liquid crystalline mesomorphism to be frozen in the glassy state. Left at room temperature for 6 months, the vitrified liquid crystalline films showed no evidence of recrystallization. An orientational order parameter of 0.65 was determined with linear dichroism of a vitrified nematic film doped with Exalite 428 at a mole fraction of 0.0025. Birefringence dispersion of amore » blank vitrified nematic film was determined using a phase-difference method complemented by Abbe refractometry. A series of vitrified chiral-nematic films were prepared to demonstrate selective reflection and circular polarization with a spectral region tunable from blue to the infrared region by varying the chemical composition. The experimentally measured circular polarization spectra were found to agree with the Good-Karali theory in which all four system parameters were determined a priori: optical birefringence, average refractive index, selective reflection wavelength, and film thickness.« less
The magnitude of linear dichroism of biological tissues as a result of cancer changes
NASA Astrophysics Data System (ADS)
Bojchuk, T. M.; Yermolenko, S. B.; Fedonyuk, L. Y.; Petryshen, O. I.; Guminetsky, S. G.; Prydij, O. G.
2012-01-01
The results of studies of linear dichroism values of different types of biological tissues (human prostate, esophageal epithelial human muscle tissue in rats) both healthy and infected tumor at different stages of development are shown here. The significant differences in magnitude of linear dichroism and its spectral dependence in the spectral range λ = 330 - 750 nm both among the objects of study, and between biotissues: healthy (or affected by benign tumors) and cancer patients are established. It is researched that in all cases in biological tissues (prostate gland, esophagus, human muscle tissue in rats) with cancer the linear dichroism arises, the value of which depends on the type of tissue and time of the tumor process. As for healthy tissues linear dichroism is absent, the results may have diagnostic value for detecting and assessing the degree of development of cancer.
The magnitude of linear dichroism of biological tissues as a result of cancer changes
NASA Astrophysics Data System (ADS)
Bojchuk, T. M.; Yermolenko, S. B.; Fedonyuk, L. Y.; Petryshen, O. I.; Guminetsky, S. G.; Prydij, O. G.
2011-09-01
The results of studies of linear dichroism values of different types of biological tissues (human prostate, esophageal epithelial human muscle tissue in rats) both healthy and infected tumor at different stages of development are shown here. The significant differences in magnitude of linear dichroism and its spectral dependence in the spectral range λ = 330 - 750 nm both among the objects of study, and between biotissues: healthy (or affected by benign tumors) and cancer patients are established. It is researched that in all cases in biological tissues (prostate gland, esophagus, human muscle tissue in rats) with cancer the linear dichroism arises, the value of which depends on the type of tissue and time of the tumor process. As for healthy tissues linear dichroism is absent, the results may have diagnostic value for detecting and assessing the degree of development of cancer.
Enantiomeric resolution and X-ray optical activity of a tricobalt extended metal atom chain.
Srinivasan, Anandi; Cortijo, Miguel; Bulicanu, Vladimir; Naim, Ahmad; Clérac, Rodolphe; Sainctavit, Philippe; Rogalev, Andrei; Wilhelm, Fabrice; Rosa, Patrick; Hillard, Elizabeth A
2018-02-07
A simple procedure based on anion exchange was employed for the enantiomeric resolution of the extended metal atom chain (EMAC) [Co 3 (dpa) 4 (MeCN) 2 ] 2+ . Use of the chiral salt (NBu 4 ) 2 [As 2 (tartrate) 2 ], (Λ- 1 or Δ- 1 ), resulted in the selective crystallization of the EMAC enantiomers as [Δ-Co 3 (dpa) 4 (MeCN) 2 ](NBu 4 ) 2 [Λ-As 2 (tartarte) 2 ] 2 , (Δ- 2 ) and [Λ-Co 3 (dpa) 4 (MeCN) 2 ](NBu 4 ) 2 [Δ-As 2 (tartrate) 2 ] 2 (Λ- 2 ), respectively, in the P 42 1 2 space group, whereas a racemic mixture of 1 yielded [Co 3 (dpa) 4 (MeCN) 2 ][As 2 (tartrate) 2 ]·2MeCN ( rac - 3 ), which crystallized in the C 2/ c space group. The local electronic and magnetic structure of the EMAC enantiomers was studied, exploiting a variety of dichroisms in single crystals. A strong linear dichroism at the Co K-edge was observed in the orthoaxial configuration, whereas it vanished in the axial orientation, thus spectroscopically confirming the D 4 crystal symmetry. Compounds Δ- 2 and Λ- 2 are shown to be enantiopure materials as evidenced by mirror-image natural circular dichroism spectra in the UV/vis in solution and in the X-ray range at the Co K-edge in single crystals. The surprising absence of detectable X-ray magnetic circular dichroism or X-ray magnetochiral dichroism signals at the Co K-edge, even at low temperature (3 K) and a high magnetic field (17 T), is ascribed to a strongly delocalized spin density on the tricobalt core.
Optical activities of steroid ketones - Elucidation of the octant rule
NASA Astrophysics Data System (ADS)
Hatanaka, Masashi; Sayama, Daisuke; Miyasaka, Makoto
2018-07-01
Theoretical calculations of optical activities in steroid ketones are presented by using modern semi-empirical PM7 wavefunctions. Both circular dichroism (CD) and specific rotation, which is proportional to optical rotation dispersion (ORD), are well simulated, and signs of the Cotton effect at the most long-wavelength region are fully in accordance with the experimental results. The good accordance is related to the octant rule, which is deduced within the framework of the perturbation theory. Our treatment is promising to predict the signs of the Cotton effect of large molecules, and thus, the absolute configurations can also be grasped without demanding procedures.
Active fluids at circular boundaries: swim pressure and anomalous droplet ripening.
Jamali, Tayeb; Naji, Ali
2018-06-13
We investigate the swim pressure exerted by non-chiral and chiral active particles on convex or concave circular boundaries. Active particles are modeled as non-interacting and non-aligning self-propelled Brownian particles. The convex and concave circular boundaries are used to model a fixed inclusion immersed in an active bath and a cavity (or container) enclosing the active particles, respectively. We first present a detailed analysis of the role of convex versus concave boundary curvature and of the chirality of active particles in their spatial distribution, chirality-induced currents, and the swim pressure they exert on the bounding surfaces. The results will then be used to predict the mechanical equilibria of suspended fluid enclosures (generically referred to as 'droplets') in a bulk with active particles being present either inside the bulk fluid or within the suspended droplets. We show that, while droplets containing active particles behave in accordance with standard capillary paradigms when suspended in a normal bulk, those containing a normal fluid exhibit anomalous behaviors when suspended in an active bulk. In the latter case, the excess swim pressure results in non-monotonic dependence of the inside droplet pressure on the droplet radius; hence, revealing an anomalous regime of behavior beyond a threshold radius, in which the inside droplet pressure increases upon increasing the droplet size. Furthermore, for two interconnected droplets, mechanical equilibrium can occur also when the droplets have different sizes. We thus identify a regime of anomalous droplet ripening, where two unequal-sized droplets can reach a final state of equal size upon interconnection, in stark contrast with the standard Ostwald ripening phenomenon, implying shrinkage of the smaller droplet in favor of the larger one.
Bandara, D M Indika; Sono, Masanori; Bruce, Grant S; Brash, Alan R; Dawson, John H
2011-12-01
Bovine liver catalase (BLC), catalase-related allene oxide synthase (cAOS) from Plexaura homomalla, and a recently isolated protein from the cattle pathogen Mycobacterium avium ssp. paratuberculosis (MAP-2744c (MAP)) are all tyrosinate-ligated heme enzymes whose crystal structures have been reported. cAOS and MAP have low (<20%) sequence similarity to, and significantly different catalytic functions from, BLC. cAOS transforms 8R-hydroperoxy-eicosatetraenoic acid to an allene epoxide, whereas the MAP protein is a putative organic peroxide-dependent peroxidase. To elucidate factors influencing the functions of these and related heme proteins, we have investigated the heme iron coordination properties of these tyrosinate-ligated heme enzymes in their ferric and ferrous states using magnetic circular dichroism and UV-visible absorption spectroscopy. The MAP protein shows remarkable spectral similarities to cAOS and BLC in its native Fe(III) state, but clear differences from ferric proximal heme ligand His93Tyr Mb (myoglobin) mutant, which may be attributed to the presence of an Arg(+)-N(ω)-H···¯O-Tyr (proximal heme axial ligand) hydrogen bond in the first three heme proteins. Furthermore, the spectra of Fe(III)-CN¯, Fe(III)-NO, Fe(II)-NO (except for five-coordinate MAP), Fe(II)-CO, and Fe(II)-O(2) states of cAOS and MAP, but not H93Y Mb, are also similar to the corresponding six-coordinate complexes of BLC, suggesting that a tyrosinate (Tyr-O¯) is the heme axial ligand trans to the bound ligands in these complexes. The Arg(+)-N(ω)-H to ¯O-Tyr hydrogen bond would be expected to modulate the donor properties of the proximal tyrosinate oxyanion and, combined with the subtle differences in the catalytic site structures, affect the activities of cAOS, MAP and BLC. Copyright © 2011 Elsevier Inc. All rights reserved.
[A turning point in the knowledge of the structure-function-activity relations of elastin].
Alix, A J
2001-01-01
confirms our hypothesis that intra-molecular elasticity of tropoelastin could be explained by the possibility of transitions between conformations involving short beta-strands and beta-turns. This result is of great interest in the construction (by using molecular biology) of elastic biomaterials derived from the elastin sequence (particularly, the elastin derived peptides corresponding to the sequence exon 21--(exon 24--exon 24...). Our study permit also to predict the conformations of specific elastin derived peptides which could have interesting biological activity. Peptides resulting from the degradation of elastin, the insoluble polymer of tropoelastin and responsible for the elasticity of vertebrate tissues, can induce biological effects and notably the regulation of matrix metalloproteinases (MMP-s) activity. Recently, it was proposed that some elastin derived hexapeptides resulting from circular permutations of VGVAPG (a three fold repetition sequence in exon 24 of human tropoelastin) possess MMP-1 production and activation regulation properties. This effect depends on the presence of the tropoelastin specific membraneous receptor 67 KDa EBP (Elastin Binding Protein). Our results obtained by using both circular dichroism spectroscopy and linear predictions confirmed the hypothesis of a structure dependent mechanism with a possibly occurring type VIII beta-turn on the first four residues of the GXXPG sequence consensus which is only present among all active peptides. Thus, we have performed extensive molecular dynamics studies, in both implicit and explicit solvent, on these active and inactive elastin derived hexapeptides. Using our own analysis method of pattern recognition of the types of the beta-reverse-turns followed during the molecular dynamics trajectory, we found that active and inactive peptides effectively form two well distinct conformational groups in which active peptides preferentially adopt conformation close to type VIII GXXP (beta
Nakahara, Shiro; Yamaguchi, Takanori; Hori, Yuichi; Anjo, Naofumi; Hayashi, Akiko; Kobayashi, Sayuki; Komatsu, Takaaki; Sakai, Yoshihiko; Fukui, Akira; Tsuchiya, Takeshi; Taguchi, Isao
2016-05-01
Atrial low-voltage zones (LVZs) may be related to maintenance of atrial fibrillation (AF). The influence of left atrial (LA) contact areas (CoAs) on reentrant or rotor-like sources maintaining AF has not been investigated. Forty patients with persistent AF (PsAF) were analyzed. Three representative CoA regions in the LA (ascending aorta: anterior wall; descending aorta: left inferior pulmonary vein; and vertebrae: posterior wall) were visualized by enhanced CT. Using circular catheters, the LVZs (<0.5 mV) were assessed after restoration of SR, and local activation mapping and frequency domain analyses were performed after induction of AF. Circular activation during AF was visually defined as sites with ≥2 rotations by serial electrograms encompassing >80% of the mean AF cycle length. A pivot was defined as the core of the localized circular activation. Anterior (39/40 patients, 98%), left pulmonary vein antrum (27/40, 68%), and posterior (19/40, 48%) CoAs were identified, and 80% (68/85) of those sites were overlapped by or close (<3 mm) to LVZs. Thirty-six (90%) patients demonstrated circular activation (3.1±1.7 sites/patients) along with significantly higher organized dominant frequencies (6.3 ± 0.5 Hz, regularity-index: 0.26 [0.23-0.41]) within the LA, and the average electrogram amplitude of those pivots was 0.30 mV (0.18-0.52). Of those sites, 55% (66/120) were located at or close to CoA regions. Catheter ablation including of LVZs neighboring CoAs terminated AF in 9 (23%) patients. External anatomical structures contacting the LA may be related to unique conduction properties in diseased myocardium necessary for PsAF maintenance. © 2016 Wiley Periodicals, Inc.
Wang, Ai; Wang, Yuekui; Jia, Jie; Feng, Lixia; Zhang, Chunxia; Liu, Linlin
2013-06-20
To assess the contributions of configurational and vicinal effects as well as chelate-ring size to rotational strengths, the geometries of a series of cobalt(III) complexes [Co(EDDA-type)(L)](±) with the tetradentate EDDA-type ligands, EDDA (ethylenediamine-N,N'-diacetate), DMEDDA (N,N'-dimethylethylenediamine-N,N'-diacetate), DEEDDA (N,N'-diethylethylenediamine-N,N'-diacetate), and a bidentate ancillary ligand L (L = ethylenediamine, oxalate, carbonate, (S)-alanine, and malonate) in aqueous solution have been optimized at the DFT/B3LYP/6-311++G(2d,p) level of theory. Based on the optimized geometries, the excitation energies and oscillator and rotational strengths have been calculated using the time-dependent density functional theory (TDDFT) method with the same functional and basis set. The calculated circular dichroism (CD) curves are in excellent agreement with the observed ones except for some small red or blue shifts in peak wavelengths. For the influence of chelate-ring size of the bidentate ligands on the CD intensities, a qualitative analysis together with the quantitative TDDFT calculation reveal that it depends on the symmetry of the cobalt-EDDA backbone. For the s-cis-isomers, the influence is negligible due to the perturbation is symmetric. For the uns-cis-isomers, the perturbation is unsymmetric. Since a small ring size means a large perturbation, this leads to the integral CD intensities decreasing with increasing the chelate ring size. The vicinal effects of asymmetric nitrogens incorporate both the substitutent effects and conformational relaxation effects, with the former being dominant. By analyzing the contributions of chiral arrays to rotational strengths, we found that the part of contributions dominated by the S-type chiral nitrogens could be considered as a good measure for the vicinal effects of chiral nitrogens. In addition, we found that the twist form (δ/λ) of the backbone ethylenediamine ring (E-ring) of the coordinated EDDA
Dendup, Tshewang; Prachyawarakorn, Vilailak; Pansanit, Acharavadee; Mahidol, Chulabhorn; Ruchirawat, Somsak; Kittakoop, Prasat
2014-05-01
Three new isoflavanones (1-3) and thirteen known compounds (4-16) were isolated from the roots of Mucuna pruriens. The absolute configurations of isoflavanones 1-3 and parvisoflavanone (4), lespedeol C (5), and uncinanone C (6) were addressed by a circular dichroism technique. Isoflavanones, isoflavones, and pterocarpans of M. pruriens were found to be α-glucosidase inhibitors. Medicarpin (7) and parvisoflavone B (9) were potent α-glucosidase inhibitors (twofold less active than the standard drug acarbose). The production of bioactive metabolites in M. pruriens seems to be season-dependent. Georg Thieme Verlag KG Stuttgart · New York.
Bloino, Julien; Biczysko, Malgorzata; Barone, Vincenzo
2017-01-01
The aim of this paper is twofold. First, we want to report the extension of our virtual multifrequency spectrometer (VMS) to anharmonic intensities for Raman Optical Activity (ROA) with the full inclusion of first- and second-order resonances for both frequencies and intensities in the framework of the generalized second-order vibrational perturbation theory (GVPT2) for all kinds of vibrational spectroscopies. Then, from a more general point of view, we want to present and validate the performance of VMS for the parallel analysis of different vibrational spectra for medium-sized molecules (IR, Raman, VCD, ROA) including both mechanical and electric/magnetic anharmonicity. For the well-known methyloxirane benchmark, careful selection of density functional, basis set, and resonance tresholds permitted to reach qualitative and quantitative vis-à-vis comparison between experimental and computed band positions and shapes. Next, the whole series of halogenated azetidinones is analyzed, showing that it is now possible to interpret different spectra in terms of electronegativity, polarizability, and hindrance variation between closely related substituents, chiral spectroscopies being particular effective in this connection. PMID:26580121
Balinski, K; Schneider, L; Wöllermann, J; Buling, A; Joly, L; Piamonteze, C; Feltham, H L C; Brooker, S; Powell, A K; Delley, B; Kuepper, K
2018-06-20
We apply X-ray magnetic circular dichroism to study the internal magnetic structure of two very promising star shaped macrocyclic complexes with a CuII3TbIII core. These complexes are rare examples prepared with a macrocyclic ligand that show indications of SMM (Single Molecule Magnet) behavior, and they differ only in ring size: one has a propylene linked macrocycle, [CuII3TbIII(LPr)(NO3)2(MeOH)(H2O)2](NO3)·3H2O (nickname: Cu3Tb(LPr)), and the other has the butylene linked analogue, [CuII3TbIII(LBu)(NO3)2(MeOH)(H2O)](NO3)·3H2O (nickname: Cu3Tb(LBu)). We analyze the orbital and spin contributions to the Cu and Tb ions quantitatively by applying the spin and orbital sum rules concerning the L2 (M4)/L3 (M5) edges. In combination with appropriate ligand field simulations, we demonstrate that the Tb(iii) ions contribute with high orbital magnetic moments to the magnetic anisotropy, whereas the ligand field determines the easy axis of magnetization. Furthermore, we confirm that the Cu(ii) ions in both molecules are in a divalent valence state, the magnetic moments of the three Cu ions appear to be canted due to 3d-3d intramolecular magnetic interactions. For Cu3Tb(LPr), the corresponding element specific magnetization loops reflect that the Cu(ii) contribution to the overall magnetic picture becomes more important as the temperature is lowered. This implies a low value for the 3d-4f coupling.
Circular dichroism and DNA secondary structure.
Baase, W A; Johnson, W C
1979-01-01
The change in average rotation of the DNA helix has been determined for the transfer from 0.05 M NaCl to 3.0 M CsCl, 6.2 M LiCl and 5.4 M NH4Cl. This work, combined with data at lower salt from other laboratories, allows us to relate the intensity of the CD of DNA at 275 nm directly to the change in the number of base pairs per turn. The change in secondary structure for the transfer of DNA from 0.05 M NaCl (where it is presumably in the B-form) to high salt (where the characteristic CD has been interpreted as corresponding to C-form geometry) is found to be -0.22 (+/- 0.02) base pairs per turn. In the case of mononucleosomes, where the CD indicates the "C-form", the change in secondary structure (including temperature effects) would add -0.31 (+/- 0.03) turns about the histone core to the -1.25 turns estimated from work on SV40 chromatin. Accurate winding angles and molar extinction coefficients were determined for ethidium. PMID:424316
NASA Astrophysics Data System (ADS)
Ushenko, A. G.; Dubolazov, A. V.; Ushenko, V. A.; Ushenko, Yu. A.; Sakhnovskiy, M. Y.; Pavlyukovich, O.; Pavlyukovich, N.; Novakovskaya, O.; Gorsky, M. P.
2016-09-01
The model of Mueller-matrix description of mechanisms of optical anisotropy that typical for polycrystalline layers of the histological sections of biological tissues and fluids - optical activity, birefringence, as well as linear and circular dichroism - is suggested. Within the statistical analysis distributions quantities of linear and circular birefringence and dichroism the objective criteria of differentiation of myocardium histological sections (determining the cause of death); films of blood plasma (liver pathology); peritoneal fluid (endometriosis of tissues of women reproductive sphere); urine (kidney disease) were determined. From the point of view of probative medicine the operational characteristics (sensitivity, specificity and accuracy) of the method of Mueller-matrix reconstruction of optical anisotropy parameters were found.
USDA-ARS?s Scientific Manuscript database
ToxA is a proteinaceous necrotrophic effector produced by Stagonospora nodorum and Pyrenophora tritici-repentis. In this study, all eight mature isoforms of the ToxA protein were purified and compared. Circular dichroism spectra indicated that all isoforms were structurally intact and had indistingu...
Dichroism, chirality, and polarization eigenstates in Babinet nanoslot-dimer membrane metamaterials
NASA Astrophysics Data System (ADS)
Zhukovsky, Sergei V.; Chigrin, Dmitry N.; Kremers, Christian; Lavrinenko, Andrei V.
2013-11-01
We present a detailed theoretical description of the optical properties of planar metamaterials comprising a metal membrane patterned with openings (microslots) arranged in closely located couples (dimers). Using the covariant coupled-dipole approach, the effective material tensors of such a metamaterial are recovered, and contributions responsible for elliptical dichroism and optical activity are identified. Polarization conversion properties of II-shaped and V-shaped dimers are determined and explained in terms of elliptically polarized eigenmodes of the metamaterial. Good agreement with direct numerical simulations is demonstrated. The results obtained are promising for the design of thin-film frequency selective polarization shapers for terahertz waves.
Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants
Llauro, Christel; Jobet, Edouard; Robakowska-Hyzorek, Dagmara; Lasserre, Eric; Ghesquière, Alain; Panaud, Olivier
2017-01-01
Retrotransposons are mobile genetic elements abundant in plant and animal genomes. While efficiently silenced by the epigenetic machinery, they can be reactivated upon stress or during development. Their level of transcription not reflecting their transposition ability, it is thus difficult to evaluate their contribution to the active mobilome. Here we applied a simple methodology based on the high throughput sequencing of extrachromosomal circular DNA (eccDNA) forms of active retrotransposons to characterize the repertoire of mobile retrotransposons in plants. This method successfully identified known active retrotransposons in both Arabidopsis and rice material where the epigenome is destabilized. When applying mobilome-seq to developmental stages in wild type rice, we identified PopRice as a highly active retrotransposon producing eccDNA forms in the wild type endosperm. The mobilome-seq strategy opens new routes for the characterization of a yet unexplored fraction of plant genomes. PMID:28212378
Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants.
Lanciano, Sophie; Carpentier, Marie-Christine; Llauro, Christel; Jobet, Edouard; Robakowska-Hyzorek, Dagmara; Lasserre, Eric; Ghesquière, Alain; Panaud, Olivier; Mirouze, Marie
2017-02-01
Retrotransposons are mobile genetic elements abundant in plant and animal genomes. While efficiently silenced by the epigenetic machinery, they can be reactivated upon stress or during development. Their level of transcription not reflecting their transposition ability, it is thus difficult to evaluate their contribution to the active mobilome. Here we applied a simple methodology based on the high throughput sequencing of extrachromosomal circular DNA (eccDNA) forms of active retrotransposons to characterize the repertoire of mobile retrotransposons in plants. This method successfully identified known active retrotransposons in both Arabidopsis and rice material where the epigenome is destabilized. When applying mobilome-seq to developmental stages in wild type rice, we identified PopRice as a highly active retrotransposon producing eccDNA forms in the wild type endosperm. The mobilome-seq strategy opens new routes for the characterization of a yet unexplored fraction of plant genomes.
NASA Technical Reports Server (NTRS)
Rosu, Grigore; Goguen, Joseph; Norvig, Peter (Technical Monitor)
2001-01-01
Circular coinduction is a technique for behavioral reasoning that extends cobasis coinduction to specifications with circularities. Because behavioral satisfaction is not recursively enumerable, no algorithm can work for every behavioral statement. However. algorithms using circular coinduction can prove every practical behavioral result that we know. This paper proves the correctness of circular coinduction and some consequences.
Large birefringence and linear dichroism in TiS3 nanosheets.
Papadopoulos, Nikos; Frisenda, Riccardo; Biele, Robert; Flores, Eduardo; Ares, Jose R; Sánchez, Carlos; van der Zant, Herre S J; Ferrer, Isabel J; D'Agosta, Roberto; Castellanos-Gomez, Andres
2018-06-21
TiS3 nanosheets have proven to be promising candidates for ultrathin optoelectronic devices due to their direct narrow band-gap and the strong light-matter interaction. In addition, the marked in-plane anisotropy of TiS3 is appealing for the fabrication of polarization sensitive optoelectronic devices. Herein, we study the optical contrast of TiS3 nanosheets of variable thickness on SiO2/Si substrates, from which we obtain the complex refractive index in the visible spectrum. We find that TiS3 exhibits very large birefringence, larger than that of well-known strong birefringent materials like TiO2 or calcite, and linear dichroism. These findings are in qualitative agreement with ab initio calculations that suggest an excitonic origin for the birefringence and linear dichroism of the material.
Novel designed VmCT1 analogs with increased antimicrobial activity.
Pedron, Cibele Nicolaski; Torres, Marcelo Der Torossian; Lima, Julia Aparecida da Silva; Silva, Pedro Ismael; Silva, Fernanda Dias; Oliveira, Vani Xavier
2017-01-27
Antimicrobial peptides are biologically active molecules produced by a wide range of organisms as an essential component of the innate immune response. They have recently attracted great interest, since they have antimicrobial activity against a broad spectrum of microorganisms. VmCT1 is a cationic peptide from the venom of Vaejovis mexicanus smithi scorpions, which presents antibacterial activity and tends to helical structures. Its analogs were synthesized, characterized and the conformational studies were performed by circular dichroism. The peptides were designed to verify if the single and double substitutions proposed at the hydrophilic and hydrophobic portions of the amphipathic structure would alter antimicrobial activity against Gram-negative and Gram-positive bacteria, yeast and filamentous fungus, besides the hemolytic activity in human erythrocytes. Total charge of the peptides were modified from +2 to +3 by the introduction of a Lysine residue in the hydrophilic face of the amphiphilic helical structure leading to enhanced antimicrobial activity. [K] 11 -VmCT1-NH 2 presented the lower MIC value against the microorganisms (from 0.39 to 6.25 μmol L -1 ), however it showed higher hemolytic activity. The other Lysine-substituted analogs presented also lower MIC values ranging from 0.39 to 25 μmol L -1 for the microorganisms assessed. The circular dichroism spectra analyses suggest that the Lysine-substituted analogs tend to adopt helical structures in trifluoroethanol solution and vesicles (f H : 0.43-1), however they were coiled in water. Alanine substitution by a Glutamic acid residue in the hydrophilic face promotes the increase of polar angle in [E] 4 -VmCT1-NH 2 analog, which was important to led lower hemolytic activity (MHC value = 25 μmol L -1 ). [W] 9 -VmCT1-NH 2 and [E] 4 [W] 9 -VmCT1-NH 2 were designed to favors hydrophobic interactions by the introduction of Tryptophan residue. [W] 9 -VmCT1-NH 2 presented MIC values lower or
Anti-inflammatory Flavanones and Flavanols from the Roots of Pongamia pinnata.
Wen, Ran; Lv, Haining; Jiang, Yong; Tu, Pengfei
2018-05-18
A phytochemical study of the roots of Pongamia pinnata afforded 29 flavanones and flavanols, including 7 previously undescribed compounds. The structures of the isolated compounds were determined by 1D and 2D NMR and mass spectroscopy data. The absolute configurations of the compounds were assigned via analysis of the specific rotations and electronic circular dichroism spectra, application of Mosher's method, and by comparing the calculated and experimental electronic circular dichroism spectra. The isolates were evaluated for their inhibitory effects on nitric oxide production in lipopolysaccharide-stimulated BV-2 microglial cells. All of the isolated compounds exhibited inhibitory effects against nitric oxide production, and most of them showed obvious anti-inflammatory activities (IC 50 < 20 µM), among which 26: was the most active compound with an IC 50 of 9.6 µM. Georg Thieme Verlag KG Stuttgart · New York.
Spectroscopic characterization of metal bound phytochelatin analogue (Glu-Cys)4-Gly.
Cheng, Yongsheng; Yan, Yong-Bin; Liu, Jinyuan
2005-10-01
The metal ion binding properties of a phytochelatin (PC) analogue, (Glu-Cys)4-Gly (named as EC4), have been studied by a divalent metal ion binding assay monitored by UV-visible spectroscopy, circular dichroism and NMR spectroscopy. Spectro- photometric titration with different divalent metal ions have revealed that the stiochoimetry of metal-bound EC4 was 1:1, and its metal binding affinities with different divalent metal ions in the order of Cd(II)>Cu(II)>Zn(II)>Pb(II)>Ni(II)>Co(II). UV-visible spectroscopic analysis of metal complexes indicated that four sulfur atoms in cysteine residues are attributable to ligand-to-metal charge transfer (LMCT) between divalent metal ions and EC4, and further confirmed by 1D H1 NMR study and Circular Dichroism. In addition, Circular Dichroism spectra of both free and metal-bound forms of EC4 revealed that metal coordination drives the nonapeptide chain to fold into a turned conformation. The comprehensive analysis of spectroscopic properties of the nonapeptide complexed with metal ions not only provides a fundamental description of the metal ion binding properties of PC analogue, but also shows a correlation between metal binding affinity of PC analogue and the induction activity of metal ions.
Galinato, Mary Grace I.; Spolitak, Tatyana; Ballou, David P.; Lehnert, Nicolai
2011-01-01
Although there has been extensive research on various Cytochrome P450s, especially Cyt P450cam, there is much to be learned about the mechanism of how its functional unit, a heme b ligated by an axial cysteine, is finely tuned for catalysis by its second coordination sphere. Here we study how the hydrogen bonding network affects the proximal cysteine and the Fe-S(Cys) bond in ferric Cyt P450cam. This is accomplished using low-temperature magnetic circular dichroism (MCD) spectroscopy on wild-type (wt) Cyt P450cam, and on the mutants Q360P (pure ferric high-spin at low temperature) and L358P with which the “Cys pocket” has been altered (by removing amino acids involved in the hydrogen bonding network), and Y96W (pure ferric low-spin). The MCD spectrum of Q360P reveals fourteen electronic transitions between 15200 and 31050 cm-1. Variable-temperature variable-field (VTVH) saturation curves were used to determine the polarizations of these electronic transitions, with respect to in-plane (xy) and out-of-plane (z) polarization relative to the heme. The polarizations, oscillator strengths, and TD-DFT calculations were then used to assign the observed electronic transitions. In the lower energy region, prominent bands at 15909 and 16919 cm-1 correspond to porphyrin (P) → Fe charge transfer (CT) transitions. The band at 17881 cm-1 has distinct sulfur S(π)→ Fe CT contributions. The Q band is observed as a pseudo A-term (derivative shape) at 18604 and 19539 cm-1. In the case of the Soret band, the negative component of the expected pseudo A-term is split into two features due to mixing with another π → π* and potentially a P → Fe CT excited state. These features are observed at 23731, 24859, and 25618 cm-1. Most importantly, the broad, prominent band at 28570 cm-1 is assigned to the S(σ)→ Fe CT transition, whose intensity is generated through a multitude of CT transitions with strong iron character. For wt, Q360P, and L358P, this band occurs at 28724
Depletion forces on circular and elliptical obstacles induced by active matter
NASA Astrophysics Data System (ADS)
Leite, L. R.; Lucena, D.; Potiguar, F. Q.; Ferreira, W. P.
2016-12-01
Depletion forces exerted by self-propelled particles on circular and elliptical passive objects are studied using numerical simulations. We show that a bath of active particles can induce repulsive and attractive forces which are sensitive to the shape and orientation of the passive objects (either horizontal or vertical ellipses). The resultant force on the passive objects due to the active particles is studied as a function of the shape and orientation of the passive objects, magnitude of the angular noise, and distance between the passive objects. By increasing the distance between obstacles the magnitude of the repulsive depletion force increases, as long as such a distance is less than one active particle diameter. For longer distances, the magnitude of the force always decreases with increasing distance. We also found that attractive forces may arise for vertical ellipses at high enough area fraction.
Depletion forces on circular and elliptical obstacles induced by active matter.
Leite, L R; Lucena, D; Potiguar, F Q; Ferreira, W P
2016-12-01
Depletion forces exerted by self-propelled particles on circular and elliptical passive objects are studied using numerical simulations. We show that a bath of active particles can induce repulsive and attractive forces which are sensitive to the shape and orientation of the passive objects (either horizontal or vertical ellipses). The resultant force on the passive objects due to the active particles is studied as a function of the shape and orientation of the passive objects, magnitude of the angular noise, and distance between the passive objects. By increasing the distance between obstacles the magnitude of the repulsive depletion force increases, as long as such a distance is less than one active particle diameter. For longer distances, the magnitude of the force always decreases with increasing distance. We also found that attractive forces may arise for vertical ellipses at high enough area fraction.
76 FR 62148 - Title VI; Proposed Circular, Environmental Justice; Proposed Circular
Federal Register 2010, 2011, 2012, 2013, 2014
2011-10-06
...-0055] Title VI; Proposed Circular, Environmental Justice; Proposed Circular AGENCY: Federal Transit... the September 29, 2011, Federal Register Notices titled ``Title VI; Proposed Circular'' and... September 29, 2011, Federal Register Notices titled ``Title VI; Proposed Circular'' (76 FR 60593) and...
Tao, Qiao-Qiao; Ma, Ke; Bao, Li; Wang, Kai; Han, Jun-Jie; Zhang, Jin-Xia; Huang, Chen-Yang; Liu, Hong-Wei
2016-06-01
Nine new sesquiterpenoids, clitocybulol derivatives, clitocybulols G-O (1-9) and three known sesquiterpenoids, clitocybulols C-E (10-12), were isolated from the solid culture of the edible fungus Pleurotus cystidiosus. The structures of compounds 1-12 were determined by spectroscopic methods. The absolute configurations of compounds 1-9 were assigned via the circular dichroism (CD) data analysis. Compounds 1, 6 and 10 showed moderate inhibitory activity against protein tyrosine phosphatase-1B (PTP1B) with IC50 values of 49.5, 38.1 and 36.0μM, respectively. Copyright © 2016. Published by Elsevier B.V.
Spontaneous ordering and vortex states of active fluids in circular confinement
NASA Astrophysics Data System (ADS)
Theillard, Maxime; Ezhilan, Barath; Saintillan, David
2015-11-01
Recent experimental, theoretical and simulation studies have shown that confinement can profoundly affect self-organization in active suspensions leading to striking features such as directed fluid pumping in planar confinement, formation of steady and spontaneous vortices in radial confinement. Motivated by this, we study the dynamics in a suspension of biologically active particles confined in spherical geometries using a mean-field kinetic theory for which we developed a novel numerical solver. In the case of circular confinement, we conduct a systematic exploration of the entire parameter space and distinguish 3 broad states: no-flow, stable vortex and chaotic and several interesting sub-states. Our efficient numerical framework is also employed to study 3D effects and dynamics in more complex geometries.
NASA Astrophysics Data System (ADS)
Merz, M.; Nagel, P.; Pinta, C.; Samartsev, A.; v. Löhneysen, H.; Wissinger, M.; Uebe, S.; Assmann, A.; Fuchs, D.; Schuppler, S.
2010-11-01
Epitaxial thin films of undoped LaCoO3 , of electron-doped La0.7Ce0.3CoO3 , and of hole-doped La0.7Sr0.3CoO3 exhibit ferromagnetic order with a transition temperature TC≈84K , 23 K, and 194 K, respectively. The spin-state structure for these compounds was studied by soft x-ray magnetic circular dichroism and by near-edge x-ray absorption fine structure at the CoL2,3 and OK edges. It turns out that superexchange between Co3+ high-spin and Co3+ low-spin states is responsible for the ferromagnetism in LaCoO3 . For La0.7Ce0.3CoO3 the Co3+ ions are in a low-spin state and the spin and orbital moments are predominantly determined by a Co2+ high-spin configuration. A spin blockade naturally explains the low transition temperature and the insulating characteristics of La0.7Ce0.3CoO3 . For La0.7Sr0.3CoO3 , on the other hand, the magnetic moments in the epitaxial films originate from high-spin Co3+ and high-spin Co4+ states. Ferromagnetism is induced by t2g double exchange between the two high-spin configurations. For all systems, a strong magnetic anisotropy is observed, with the magnetic moments essentially oriented within the film plane.
Cheng, John T.J.; Hale, John D.; Kindrachuk, Jason; Jessen, Havard; Elliott, Melissa; Hancock, Robert E.W.; Straus, Suzana K.
2010-01-01
Previous studies on aurein 2.2 and 2.3 in DMPC/DMPG and POPC/POPG membranes have shown that bilayer thickness and phosphatidylglycerol content have a significant impact on the interaction of these peptides with membrane bilayers. Further examination with the DiSC35 assay has indicated that aurein 2.2 induces greater membrane leakage than aurein 2.3 in Staphylococcus aureus C622. The only difference between these peptides is a Leu to Ile mutation at residue 13. To better understand the importance of this residue, the structure and activity of the L13A, L13F, and L13V mutants were investigated. In addition, we investigated a number of peptides with truncations at the C-terminus to determine whether the C-terminus, which contains residue 13, is crucial for antimicrobial activity. Solution circular dichroism results demonstrated that the L13F mutation and the truncation of the C-terminus by six residues resulted in decreased helical content, whereas the L13A or L13V mutation and the truncation of the C-terminus by three residues showed little to no effect on the structure. Oriented circular dichroism results demonstrated that only an extensive C-terminal truncation reduced the ability of the peptide to insert into lipid bilayers. 31P NMR spectroscopy showed that all peptides disorder the headgroups. The implications of these results in terms of antimicrobial activity and the ability of these peptides to induce leakage in S. aureus are discussed. The results suggest that the presence of the 13th residue in aurein 2.2 is important for structure and activity, but the exact nature of residue 13 is less important as long as it is a hydrophobic residue. PMID:21044590
2. Northwest circular bastion, seen from edge of southwest circular ...
2. Northwest circular bastion, seen from edge of southwest circular bastion wall. Metal roof beams extend up to form peak. World War II gun installation at right. - Fort Hamilton, Northwest Circular Bastion, Rose Island, Newport, Newport County, RI
Fernández-Lucas, Jesús; Acebal, Carmen; Sinisterra, José V.; Arroyo, Miguel; de la Mata, Isabel
2010-01-01
A novel type II nucleoside 2′-deoxyribosyltransferase from Lactobacillus reuteri (LrNDT) has been cloned and overexpressed in Escherichia coli. The recombinant LrNDT has been structural and functionally characterized. Sedimentation equilibrium analysis revealed a homohexameric molecule of 114 kDa. Circular dichroism studies have showed a secondary structure containing 55% α-helix, 10% β-strand, 16% β-sheet, and 19% random coil. LrNDT was thermostable with a melting temperature (Tm) of 64°C determined by fluorescence, circular dichroism, and differential scanning calorimetric studies. The enzyme showed high activity in a broad pH range (4.6 to 7.9) and was also very stable between pH 4 and 7.9. The optimal temperature for activity was 40°C. The recombinant LrNDT was able to synthesize natural and nonnatural nucleoside analogues, improving activities described in the literature, and remarkably, exhibited unexpected new arabinosyltransferase activity, which had not been described so far in this kind of enzyme. Furthermore, synthesis of new arabinonucleosides and 2′-fluorodeoxyribonucleosides was carried out. PMID:20048065
Snyder, Rae Ana; Bell, Caleb B.; Diao, Yinghui; Krebs, Carsten; Bollinger, J. Martin; Solomon, Edward I.
2013-01-01
Myo-inositol oxygenase (MIOX) catalyzes the 4e− oxidation of myo-inositol (MI) to D-glucuronate using a substrate activated Fe(II)Fe(III) site. The biferrous and Fe(II)Fe(III) forms of MIOX were studied with circular dichroism (CD), magnetic circular dichroism (MCD), and variable temperature variable field (VTVH) MCD spectroscopies. The MCD spectrum of biferrous MIOX shows two ligand field (LF) transitions near 10,000 cm−1, split by ~2,000 cm−1, characteristic of 6 coordinate (6C) Fe(II) sites, indicating that the modest reactivity of the biferrous form toward O2 can be attributed to the saturated coordination of both irons. Upon oxidation to the Fe(II)Fe(III) state, MIOX shows two LF transitions in the ~10,000 cm−1 region, again implying a coordinatively saturated Fe(II) site. Upon MI binding, these split in energy to 5,200 cm−1 and 11,200 cm−1, showing that MI binding causes the Fe(II) to become coordinately unsaturated. VTVH MCD magnetization curves of unbound and MI-bound Fe(II)Fe(III) forms show that upon substrate binding, the isotherms become more nested, requiring that the exchange coupling and ferrous zero field splitting (ZFS) both decrease in magnitude. These results imply that MI binds to the ferric site, weakening the Fe(III)-μ-OH bond and strengthening the Fe(II)-μ-OH bond. This perturbation results in the release of a coordinated water from the Fe(II) that enables its O2 activation. PMID:24066857
Theoretical Prediction of Vibrational Circular Dichroism Spectra
1990-01-01
Chabalowski U.S. ARMY BALLISTIC RESEARCH LABORATORY January 1990 DTIC ELECTESMAR 6U99 CHEMICAL COMMAN4D Aberden Proving Ground . MeMand 21010-5423 IDWPM...TASK [WORK UNIT ELEMENT NO. NO.11 46 2 6 2 2 NO. A5531 ACCESSION NO. Aberdeen Proving Ground , MD 21010-5423 IC4648061 D020 1 11. TITLE (Include...Engineering Center ATITN: SDCCR-RSP-C Aberdeen Proving Ground , MD 21010-5423 U.S. Army Ballistic Research Laboratory Aberdeen Proving Ground , MD
Electronic and vibrational exciton coupling in oxidized trianglimines.
Szymkowiak, Joanna; Kwit, Marcin
2018-02-01
Readily available chiral trianglimine and their (poly)oxygenated congeners represent a unique class of macrocyclic rigid compounds optimal for testing electronic and vibrational circular dichroism exciton chirality methods. Electronic and vibrational circular dichroism spectra of such trianglimines are strongly affected by polar substituents in macrocycle skeletons. Double substitution by OH groups in each aromatic fragment of the macrocycle causes sign reversal of the exciton couplet in the region of the strongest UV absorption. On the other hand, electronic circular dichroism spectrum of the macrocycle having 2 methoxy groups shows 2 exciton couplets-the long-wavelength positive and the second of the negative sign, observed at the shorter wavelengths. VCD spectra of macrocyclic imines show vibrational exciton couplets in the region of strong C=N stretches. The signs of these couplets are positive and the opposite of the diamine chirality. For trianglimine macrocycles the interpretation of VCD spectra in terms of excitons is much more convincing than for electronic circular dichroism spectra. By contrast, trans-1,2-diaminocyclohexane-based vicinal diimines, being a one-third of the respective macrocycle, do not exhibit any vibrational exciton effect. Experimental data were confronted with DFT calculations. We observed good-to-excellent agreement between experimental and computed data. © 2017 Wiley Periodicals, Inc.
Optically active molecular magnets
NASA Astrophysics Data System (ADS)
Gruselle, Michel; Malezieux, Bernard; Train, Cyrille; Guyard-Duhayon, Carine; Clement, Rene; Benard, Sophie; Gredin, Patrick; Tonsuaadu, Kaia
2005-08-01
We describe the synthesis of two-dimensional {[MnIICrIII(C2O4)3]C} bimetallic networks that include as template cations C stilbazolium salts 4-[4-(N,N-dimethylamino)-α-styryl]-N-alkylpyridinium with alkyl = methyl (DAMS), 4-[4-methoxy- α-styryll-N-isopentylpyridinium (MIPS), and DAZOP, which is a DAMS analogue with the central [C=C] core replaced by an azo N=N] moiety. These networks are obtained in their optically active forms, using the resolved - or Λ- [CrIII(C204)3]3- anionic bricks as chiral-inducing reagents. The UV-visible properties of the networks and their natural circular dichroism (Cotton effects) demonstrate that the MIPS, DAZOP, and DAMS become chiral in [MnIICrIII(C204)3]- anionic matrices. The absolute configurations of the template cations inside the anionic framework depend on the configuration of the starting anionic reagent.
Brau, Charles A.; Kurnit, Norman A.; Cooper, Richard K.
1984-01-01
A high efficiency, free electron laser utilizing a circular relativistic electron beam accelerator and a circular whispering mode optical waveguide for guiding optical energy in a circular path in the circular relativistic electron beam accelerator such that the circular relativistic electron beam and the optical energy are spatially contiguous in a resonant condition for free electron laser operation. Both a betatron and synchrotron are disclosed for use in the present invention. A free electron laser wiggler is disposed around the circular relativistic electron beam accelerator for generating a periodic magnetic field to transform energy from the circular relativistic electron beam to optical energy.
Azimuthally invariant Mueller-matrix mapping of biological optically anisotropic network
NASA Astrophysics Data System (ADS)
Ushenko, Yu. O.; Vanchuliak, O.; Bodnar, G. B.; Ushenko, V. O.; Grytsyuk, M.; Pavlyukovich, N.; Pavlyukovich, O. V.; Antonyuk, O.
2017-09-01
A new technique of Mueller-matrix mapping of polycrystalline structure of histological sections of biological tissues is suggested. The algorithms of reconstruction of distribution of parameters of linear and circular dichroism of histological sections liver tissue of mice with different degrees of severity of diabetes are found. The interconnections between such distributions and parameters of linear and circular dichroism of liver of mice tissue histological sections are defined. The comparative investigations of coordinate distributions of parameters of amplitude anisotropy formed by Liver tissue with varying severity of diabetes (10 days and 24 days) are performed. The values and ranges of change of the statistical (moments of the 1st - 4th order) parameters of coordinate distributions of the value of linear and circular dichroism are defined. The objective criteria of cause of the degree of severity of the diabetes differentiation are determined.
NASA Astrophysics Data System (ADS)
Lee, Jae-Hoon; Park, Hyun-Sang; Jeon, Jae-Hong; Han, Min-Koo
2008-03-01
We have proposed a new poly-Si TFT pixel, which can suppress TFT leakage current effect on active matrix organic diode (AMOLED) displays, by employing a new circular switching TFT and additional signal line for compensating the leakage current. When the leakage current of switching TFT is increased, the VGS of the current driving TFT in the proposed pixel is not altered by the variable data voltages due to the circular switching TFT. Our simulation results show that OLED current variation of the proposed pixel can be suppressed less than 3%, while that of conventional pixel exceeds 30%. The proposed pixel may be suitable to suppress the leakage current effect on AMOLED display.
Quantitation of protein orientation in flow-oriented unilamellar liposomes by linear dichroism
NASA Astrophysics Data System (ADS)
Rajendra, Jascindra; Damianoglou, Angeliki; Hicks, Matthew; Booth, Paula; Rodger, P. Mark; Rodger, Alison
2006-07-01
The linear dichroism of the visible wavelength transitions of retinal have been used to analyse linear dichroism spectra to determine the orientation of aromatic and peptide structural motifs of Bacteriorhodopsin incorporated into unilamellar soy bean liposomes. The results are consistent with the available X-ray data. This proves that visible light absorbing chromophores can be used to analyse linear dichroism data to give the orientation of membrane proteins in membrane mimicking environments. The work has been extended by screening a wide range of hydrophobic molecules with high extinction coefficients in transitions above 300 nm to find molecules that could be used as independent probes of liposome orientation for experiments involving proteins incorporated into liposomes. Three probes were found to have potential for future work: bis-(1,3-dibutylbarbituric acid)pentamethine oxonol (DiBAC 4), retinol and rhodamine B. All three can be used to determine the orientation of the porphyrin of cytochrome c, the aromatic residues of gramicidin and the helices of both proteins. The orientation parameter, S, for the liposomes varied from batch to batch of unilamellar liposomes prepared by extruding through a 100 nm membrane. The value and variation in S was 0.030 ± 0.010. Repeat experiments with the same batch of liposomes showed less variation. Film LD data were measured for DiBAC 4 and rhodamine B to determine the polarisations of their long wavelength transitions.
NASA Astrophysics Data System (ADS)
Eso, R.; Safiuddin, L. O.; Agusu, L.; Arfa, L. M. R. F.
2018-04-01
We propose a teaching instrument demonstrating the circular membrane waves using the excel interactive spreadsheets with the Visual Basic for Application (VBA) programming. It is based on the analytic solution of circular membrane waves involving Bessel function. The vibration modes and frequencies are determined by using Bessel approximation and initial conditions. The 3D perspective based on the spreadsheets functions and facilities has been explored to show the 3D moving objects in transitional or rotational processes. This instrument is very useful both in teaching activity and learning process of wave physics. Visualizing of the vibration of waves in the circular membrane which is showing a very clear manner of m and n vibration modes of the wave in a certain frequency has been compared and matched to the experimental result using resonance method. The peak of deflection varies in time if the initial condition was working and have the same pattern with matlab simulation in zero initial velocity
Enantioselective binding of L, D-phenylalanine to ct DNA
NASA Astrophysics Data System (ADS)
Zhang, Lijin; Xu, Jianhua; Huang, Yan; Min, Shungeng
2009-10-01
The enantioselective binding of L, D-phenylalanine to calf thymus DNA was studied by absorption, circular dichroism, fluorescence quenching, viscosity, salt effect and emission experiments. The results obtained from absorption, circular dichroism, fluorescence quenching and viscosity experiments excluded the intercalative binding and salt effect experiments did not support electrostatic binding. So the binding of L, D-phenylalanine to ct DNA should be groove binding. Furthermore, the emission spectra revealed that the binding is enantioselective.
Enantioselective binding of L,D-phenylalanine to ct DNA.
Zhang, Lijin; Xu, Jianhua; Huang, Yan; Min, Shungeng
2009-10-15
The enantioselective binding of L,D-phenylalanine to calf thymus DNA was studied by absorption, circular dichroism, fluorescence quenching, viscosity, salt effect and emission experiments. The results obtained from absorption, circular dichroism, fluorescence quenching and viscosity experiments excluded the intercalative binding and salt effect experiments did not support electrostatic binding. So the binding of l,d-phenylalanine to ct DNA should be groove binding. Furthermore, the emission spectra revealed that the binding is enantioselective.
Arvinte, Tudor; Bui, Tam T T; Dahab, Ali A; Demeule, Barthélemy; Drake, Alex F; Elhag, Dhia; King, Peter
2004-09-01
Circular dichroism (CD) is an important spectroscopic technique for monitoring chirality and biological macromolecule conformation. However, during a CD measurement, absorbance, light scattering/turbidity, and fluorescence can also be detected. The simultaneous measurement of these different spectral features for a single sample is the basis of a multi-mode optical spectrometer. This allows time-efficient gathering of complementary information and provides a scheme to ensure that CD measurements are reliable. Aspects of circular polarization differential light scattering, pH, and temperature variation of a protein (antibody) solution are described. A procedure to help ensure that CD measurements are reliable is described.
Górecki, Marcin; Carpita, Luca; Arrico, Lorenzo; Zinna, Francesco; Di Bari, Lorenzo
2018-05-29
We studied enantiopure chiral trivalent lanthanide (Ln3+ = La3+, Sm3+, Eu3+, Gd3+, Tm3+, and Yb3+) complexes with two fluorinated achiral tris(β-diketonate) ligands (HFA = hexafluoroacetylacetonate and TTA = 2-thenoyltrifluoroacetonate), incorporating a chiral bis(oxazolinyl)pyridine (PyBox) unit as a neutral ancillary ligand, by the combined use of optical and chiroptical methods, ranging from UV to IR both in absorption and circular dichroism (CD), and including circularly polarized luminescence (CPL). Ultimately, all the spectroscopic information is integrated into a total and a chiroptical super-spectrum, which allows one to characterize a multidimensional chemical space, spanned by the different Ln3+ ions, the acidity and steric demand of the diketone and the chirality of the PyBox ligand. In all cases, the Ln3+ ions endow the systems with peculiar chiroptical properties, either allied to f-f transitions or induced by the metal onto the ligand. In more detail, we found that Sm3+ complexes display interesting CPL features, which partly superimpose and partly integrate the more common Eu3+ properties. Especially, in the context of security tags, the pair Sm/Eu may be a winning choice for chiroptical barcoding.
Lin, Xionghao; Ji, Shuai; Li, Rui; Dong, Yinhui; Qiao, Xue; Hu, Hongbo; Yang, Wenzhi; Guo, Dean; Tu, Pengfei; Ye, Min
2012-12-28
Terpecurcumins A-I (1-9), together with three known analogues (10-12), were isolated from the rhizomes of Curcuma longa (turmeric). They were derived from the hybridization of curcuminoids and bisabolanes. The structures and absolute configurations of 1-9 were elucidated on the basis of extensive spectroscopic data analysis, including NMR and electronic circular dichroism spectra. The configuration of 10 was further confirmed by X-ray crystallography. A plausible biogenetic relationship for 1-12 is proposed. Compounds 4, 6, 7, 10, and 11 showed higher cytotoxic activities (IC(50), 10.3-19.4 μM) than curcumin (IC(50), 31.3-49.2 μM) against human cancer cell lines (A549, HepG2, and MDA-MB-231).
Basu, Anirban; Kumar, Gopinatha Suresh
2016-12-01
Interaction of proflavine with hemoglobin (Hgb) was studied employing spectroscopy, calorimetry, and atomic force microscopy. The equilibrium constant was found to be of the order 10 4 M -1 . The quenching of Hgb fluorescence by proflavine was due to the complex formation. Calculation of the molecular distance (r) between the donor (β-Trp37 of Hgb) and acceptor (proflavine) suggested that energy can be efficiently transferred from the β-Trp37 residue at the α1β2 interface of the protein to the dye. Proflavine induced significant secondary structural changes in Hgb. Synchronous fluorescence studies showed that proflavine altered the microenvironment around the tryptophan residues to a greater extent than the tyrosine residues. Circular dichroism spectral studies showed that proflavine caused significant reduction in the α-helical content of Hgb. The esterase activity assay further complemented the circular dichroism data. The Soret band intensity of Hgb decreased upon complexation. Differential scanning calorimetry and circular dichroism melting results revealed that proflavine induced destabilization of Hgb. The binding was driven by both positive entropy and negative enthalpy. Atomic force microscopy studies revealed that the essential morphological features of hemoglobin were retained in the presence of proflavine. Overall, insights on the photophysical aspects and energetics of the binding of proflavine with Hgb are presented. Copyright © 2016 Elsevier B.V. All rights reserved.
Peroxide Activation for Electrophilic Reactivity by the Binuclear Non-heme Iron Enzyme AurF
Park, Kiyoung; Li, Ning; Kwak, Yeonju; ...
2017-05-01
Binuclear non-heme iron enzymes activate O 2 for diverse chemistries that include oxygenation of organic substrates and hydrogen atom abstraction. This process often involves the formation of peroxo-bridged biferric intermediates, only some of which can perform electrophilic reactions. To elucidate the geometric and electronic structural requirements to activate peroxo reactivity, the active peroxo intermediate in 4-aminobenzoate N-oxygenase (AurF) has been characterized spectroscopically and computationally. A magnetic circular dichroism study of reduced AurF shows that its electronic and geometric structures are poised to react rapidly with O 2. Nuclear resonance vibrational spectroscopic definition of the peroxo intermediate formed in this reactionmore » shows that the active intermediate has a protonated peroxo bridge. Density functional theory computations on the structure established here show that the protonation activates peroxide for electrophilic/single-electron-transfer reactivity. As a result, this activation of peroxide by protonation is likely also relevant to the reactive peroxo intermediates in other binuclear non-heme iron enzymes.« less
Peroxide Activation for Electrophilic Reactivity by the Binuclear Non-heme Iron Enzyme AurF
DOE Office of Scientific and Technical Information (OSTI.GOV)
Park, Kiyoung; Li, Ning; Kwak, Yeonju
Binuclear non-heme iron enzymes activate O 2 for diverse chemistries that include oxygenation of organic substrates and hydrogen atom abstraction. This process often involves the formation of peroxo-bridged biferric intermediates, only some of which can perform electrophilic reactions. To elucidate the geometric and electronic structural requirements to activate peroxo reactivity, the active peroxo intermediate in 4-aminobenzoate N-oxygenase (AurF) has been characterized spectroscopically and computationally. A magnetic circular dichroism study of reduced AurF shows that its electronic and geometric structures are poised to react rapidly with O 2. Nuclear resonance vibrational spectroscopic definition of the peroxo intermediate formed in this reactionmore » shows that the active intermediate has a protonated peroxo bridge. Density functional theory computations on the structure established here show that the protonation activates peroxide for electrophilic/single-electron-transfer reactivity. As a result, this activation of peroxide by protonation is likely also relevant to the reactive peroxo intermediates in other binuclear non-heme iron enzymes.« less
Fishman, Randy Scott; Lee, Jun Hee; Bordacs, Sandor; ...
2015-09-14
A microscopic model for the room-temperature multiferroic BiFeO 3 that includes two Dzyaloshinskii-Moriya interactions and single-ion anisotropy along the ferroelectric polarization predicts both the zero-field spectroscopic modes as well as their splitting and evolution in a magnetic field. Due to simultaneously broken time-reversal and spatial-inversion symmetries, the absorption of light changes as the magnetic field or the direction of light propagation is reversed. We discuss three physical mechanisms that may contribute to this absorption asymmetry known as directional dichroism: the spin current, magnetostriction, and single-ion anisotropy. We conclude that the directional dichroism in BiFeO 3 is dominated by the spin-currentmore » polarization and is insensitive to the magnetostriction and easy-axis anisotropy. With three independent spin-current parameters, our model accurately describes the directional dichroism observed for magnetic field along [1, -1, 0]. Since some modes are almost transparent to light traveling in one direction but opaque for light traveling in the opposite direction, BiFeO 3 can be used as a room-temperature optical diode at certain frequencies in the GHz to THz range. This work demonstrates that an analysis of the directional dichroism spectra based on an effective spin model supplemented by first-principles calculations can produce a quantitative microscopic theory of the magnetoelectric couplings in multiferroic materials.« less
High-energy vacuum birefringence and dichroism in an ultrastrong laser field
NASA Astrophysics Data System (ADS)
Meuren, Sebastian; Bragin, Sergey; Keitel, Christoph H.; di Piazza, Antonino
2017-10-01
The interaction between real photons in vacuum is a long-standing prediction of quantum electrodynamics, which has never been observed experimentally. Upcoming 10 PW laser systems like the Extreme Light Infrastructure (ELI) will provide laser pulses with unprecedented intensities. If combined with highly energetic gamma photons - obtainable via Compton backscattering from laser-wakefield accelerated electron beams - the QED critical field becomes accessible. In we have derived how a generally polarized probe photon beam is influenced by both vacuum birefringence and dichroism in a strong linearly polarized plane-wave laser field. We put forward an experimental scheme to measure these effects in the nontrivial high-energy regime, where the QED critical field is reached and the Euler-Heisenberg approximation, valid for low-frequency electromagnetic fields, breaks down. Our results suggest the feasibility of verifying/rejecting the QED prediction for vacuum birefringence/dichroism at the 3 σ confidence level on the time scale of a few days at several upcoming laser facilities. Now at Princeton University, Princeton, NJ.
Rončević, Tomislav; Vukičević, Damir; Ilić, Nada; Krce, Lucija; Gajski, Goran; Tonkić, Marija; Goić-Barišić, Ivana; Zoranić, Larisa; Sonavane, Yogesh; Benincasa, Monica; Juretić, Davor; Maravić, Ana; Tossi, Alessandro
2018-04-12
Antimicrobial peptides often show broad-spectrum activity due to a mechanism based on bacterial membrane disruption, which also reduces development of permanent resistance, a desirable characteristic in view of the escalating multidrug resistance problem. Host cell toxicity however requires design of artificial variants of natural AMPs to increase selectivity and reduce side effects. Kiadins were designed using rules obtained from natural peptides active against E. coli and a validated computational algorithm based on a training set of such peptides, followed by rational conformational alterations. In vitro activity, tested against ESKAPE strains (ATCC and clinical isolates), revealed a varied activity spectrum and cytotoxicity that only in part correlated with conformational flexibility. Peptides with a higher proportion of Gly were generally less potent and caused less bacterial membrane alteration, as observed by flow cytometry and AFM, which correlate to structural characteristics as observed by circular dichroism spectroscopy and predicted by molecular dynamics calculations.
Laurencin, Mathieu; Legrand, Baptiste; Duval, Emilie; Henry, Joël; Baudy-Floc'H, Michèle; Zatylny-Gaudin, Céline; Bondon, Arnaud
2012-01-01
Incorporation of aza-β3-amino acids into endogenous neuropeptide from mollusks (ALSGDAFLRF-NH2) with weak antimicrobial activities allows us to design new AMPs sequences. We find that, depending on the nature of the substitution, these could result either in inactive pseudopeptides or in a drastic enhancement of the antimicrobial activity without high cytotoxicity resulted. Structural studies perform by NMR and circular dichroism on the pseudopeptides show the impact of aza-β3-amino acids on the peptide structures. We obtain the first three-dimensional structures of pseudopeptides containing aza-β3-amino acids in aqueous micellar SDS and demonstrate that hydrazino turn can be formed in aqueous solution. Overall, these results demonstrate the ability to modulate AMPs activities through structural modifications induced by the nature and the position of these amino acid analogs in the peptide sequences. PMID:22320306
Circular electrode geometry metal-semiconductor-metal photodetectors
NASA Technical Reports Server (NTRS)
Mcaddo, James A. (Inventor); Towe, Elias (Inventor); Bishop, William L. (Inventor); Wang, Liang-Guo (Inventor)
1994-01-01
The invention comprises a high speed, metal-semiconductor-metal photodetector which comprises a pair of generally circular, electrically conductive electrodes formed on an optically active semiconductor layer. Various embodiments of the invention include a spiral, intercoiled electrode geometry and an electrode geometry comprised of substantially circular, concentric electrodes which are interposed. These electrode geometries result in photodetectors with lower capacitances, dark currents and lower inductance which reduces the ringing seen in the optical pulse response.
Yadav, Dharmendra K; Bharitkar, Yogesh P; Hazra, Abhijit; Pal, Uttam; Verma, Sugreev; Jana, Sayantan; Singh, Umesh P; Maiti, Nakul C; Mondal, Nirup B; Swarnakar, Snehasikta
2017-05-26
Neem (Azadirachta indica) is a well-known medicinal and insecticidal plant. Although previous studies have reported the antiulcer activity of neem leaf extract, the lead compound is still unidentified. The present study reports tamarixetin 3-O-β-d-glucopyranoside (1) from a methanol extract of neem leaves and its gastroprotective activity in an animal model. Compound 1 showed significant protection against indomethacin-induced gastric ulceration in mice in a dose-dependent manner. Moreover, ex vivo and circular dichroism studies confirmed that 1 inhibited the enzyme matrix metalloproteinase-9 (MMP-9) activity with an IC 50 value of ca. 50 μM. Molecular docking and dynamics showed the binding of 1 into the pocket of the active site of MMP-9, forming a coordination complex with the catalytic zinc, thus leading to inhibition of MMP-9 activity.
Liu, Na; Li, Rui-Juan; Wang, Xiao-Ning; Zhu, Rong-Xiu; Wang, Lei; Lin, Zhao-Min; Zhao, Yu; Lou, Hong-Xiang
2013-09-27
Ten highly oxygenated ent-pimarane-type diterpenoids, pedinophyllols A-J (1-10), were isolated from the Chinese liverwort Pedinophyllum interruptum. Their structures were determined by comprehensive analysis of spectroscopic data together with single-crystal X-ray diffraction analysis. The absolute configurations were elucidated by comparison of experimental and theoretically calculated electronic circular dichroism spectra. Allelopathic testing showed that several new diterpenoids inhibited germination of Arabidopsis thaliana seeds.
Yang, Xinhe; Huang, Mingjun; Qin, Caiqin; Lv, Bangyu; Mao, Qingli; Liu, Zhonghua
2017-08-01
The crude tea polysaccharides (CTPS) from Qingzhuan brick tea(QZBT) were extracted and fractionated to afford two fractions, namely TPS-1 and TPS-2. Analyses were conducted concerning the structural characterization and antioxidant activities of these samples. Component analysis revealed that the carbohydrate, uronic acid, protein and polyphenol contents of these samples differed significantly. Fourier transform infrared analysis showed that these samples showed similar characteristic absorption peaks for polysaccharides. Ultraviolet-visible spectroscopy, circular dichroism, scanning electron microscopy and thermogravimetric analyses indicated that there were considerable differences in the presence of protein, surface features, conformational characteristics and thermodynamic behaviors. For antioxidant activities in vitro, CTPS, TPS-1 and TPS-2 exhibited concentration-dependent antioxidant activities, with TPS-2 showing significantly higher antioxidant activity than CTPS and TPS-1. These results provide a scientific and strong foundation for the use of tea polysaccharides(TPS) from QZBT and further research towards the relationships between the characteristics and antioxidant activities of TPS. Copyright © 2017 Elsevier B.V. All rights reserved.
Raffaini, Giuseppina; Milani, Roberto; Ganazzoli, Fabio; Resnati, Giuseppe; Metrangolo, Pierangelo
2016-01-01
Hydrophobins are proteins of interest for numerous applications thanks to their unique conformational and surface properties and their ability to self-assemble at interfaces. Here we report fully atomistic molecular mechanics and molecular dynamics results together with circular dichroism experimental data, aimed to study the conformational properties of the hydrophobin HFBII in a fluorinated solvent in comparison with a water solution and/or at an aqueous/vacuum interface. Both the atomistic simulations and the circular dichroism data show the remarkable structural stability of HFBII at all scales in all these environments, with no significant structural change, although a small cavity is formed in the fluorinated solvent. The combination of theoretical calculations and circular dichroism data can describe in detail the protein conformation and flexibility in different solvents and/or at an interface, and constitutes a first step towards the study of their self-assembly. Copyright © 2015 Elsevier Inc. All rights reserved.
NASA Astrophysics Data System (ADS)
Chen, Kai; Sundermann, Martin; Strigari, Fabio; Kawabata, Jo; Takabatake, Toshiro; Tanaka, Arata; Bencok, Peter; Choueikani, Fadi; Severing, Andrea
2018-04-01
Here we present linear and circular polarized soft x-ray absorption spectroscopy (XAS) data at the Ce M4 ,5 edges of the electron (Ir) and hole-doped (Re) Kondo semiconductor CeOs2Al10 . Both substitutions have a strong impact on the unusual high Néel temperature TN=28.5 K, and also the direction of the ordered moment in case of Ir. The substitution dependence of the linear dichroism is weak thus validating the crystal-field description of CeOs2Al10 being representative for the Re and Ir substituted compounds. The impact of electron and hole doping on the hybridization between conduction and 4 f electrons is related to the amount of f0 in the ground state and reduction of x-ray magnetic circular dichroism. A relationship of c f -hybridization strength and enhanced TN is discussed. The direction and doping dependence of the circular dichroism strongly supports the idea of strong Kondo screening along the crystallographic a direction.
Dichrometer errors resulting from large signals or improper modulator phasing.
Sutherland, John C
2012-09-01
A single-beam spectrometer equipped with a photoelastic modulator can be configured to measure a number of different parameters useful in characterizing chemical and biochemical materials including natural and magnetic circular dichroism, linear dichroism, natural and magnetic fluorescence-detected circular dichroism, and fluorescence polarization anisotropy as well as total absorption and fluorescence. The derivations of the mathematical expressions used to extract these parameters from ultraviolet, visible, and near-infrared light-induced electronic signals in a dichrometer assume that the dichroic signals are sufficiently small that certain mathematical approximations will not introduce significant errors. This article quantifies errors resulting from these assumptions as a function of the magnitude of the dichroic signals. In the case of linear dichroism, improper modulator programming can result in errors greater than those resulting from the assumption of small signal size, whereas for fluorescence polarization anisotropy, improper modulator phase alone gives incorrect results. Modulator phase can also impact the values of total absorbance recorded simultaneously with linear dichroism and total fluorescence. Copyright © 2012 Wiley Periodicals, Inc., A Wiley Company.
Lipase in aqueous-polar organic solvents: Activity, structure, and stability
Kamal, Md Zahid; Yedavalli, Poornima; Deshmukh, Mandar V; Rao, Nalam Madhusudhana
2013-01-01
Studying alterations in biophysical and biochemical behavior of enzymes in the presence of organic solvents and the underlying cause(s) has important implications in biotechnology. We investigated the effects of aqueous solutions of polar organic solvents on ester hydrolytic activity, structure and stability of a lipase. Relative activity of the lipase monotonically decreased with increasing concentration of acetone, acetonitrile, and DMF but increased at lower concentrations (upto ∼20% v/v) of dimethylsulfoxide, isopropanol, and methanol. None of the organic solvents caused any appreciable structural change as evident from circular dichorism and NMR studies, thus do not support any significant role of enzyme denaturation in activity change. Change in 2D [15N, 1H]-HSQC chemical shifts suggested that all the organic solvents preferentially localize to a hydrophobic patch in the active-site vicinity and no chemical shift perturbation was observed for residues present in protein's core. This suggests that activity alteration might be directly linked to change in active site environment only. All organic solvents decreased the apparent binding of substrate to the enzyme (increased Km); however significantly enhanced the kcat. Melting temperature (Tm) of lipase, measured by circular dichroism and differential scanning calorimetry, altered in all solvents, albeit to a variable extent. Interestingly, although the effect of all organic solvents on various properties on lipase is qualitatively similar, our study suggest that magnitudes of effects do not appear to follow bulk solvent properties like polarity and the solvent effects are apparently dictated by specific and local interactions of solvent molecule(s) with the protein. PMID:23625694
Barteri, Mario; De Carolis, Roberta; Marinelli, Fiorenzo; Tomassetti, Goliardo; Montemiglio, Linda Celeste
2016-01-01
This work shows the effects of exposure to an electromagnetic field at 900 MHz on the catalytic activity of the enzymes lactoperoxidase (LPO) and horseradish peroxidase (HRP). Experimental evidence that irradiation causes conformational changes of the active sites and influences the formation and stability of the intermediate free radicals is documented by measurements of enzyme kinetics, circular dichroism spectroscopy (CD) and cyclic voltammetry.
NASA Astrophysics Data System (ADS)
Rona, P. A.; Guida, V.; Scranton, M. I.; Gong, D.; Haag, S.; Macelloni, L.; Simonetti, A.; James, J.; Diercks, A.; Asper, V. L.
2009-12-01
We investigated Hudson Canyon from where it begins at the seaward edge of the continental shelf (water depth 100 m) to ~30 km seaward (100-700 m) using high-resolution bathymetry (AUV Eagle Ray; ISE Explorer; EM2000 sonar) and standard oceanographic methods. We find features and processes that create varied distinctive habitats in submarine canyons on passive continental margins, as follows: 1)Sediment conduit: The initial 10 km- long section of the canyon head connects with cross-shelf sediment transport and is smoothed by sediment accumulation indicating that it is presently inactive as a sediment conduit, in contrast to its active role during prior intervals of lowered sea level. 2)Circular depressions: A population of circular depressions with diameters from 50 to 400 m, rim-to-floor relief up to 20 m increasing directly with diameter, flat rough floors and steep walls (15-25 degrees) occur in sediment near the base of both walls of the canyon. The number of circular depressions increases with water depth with one at 325 m in the initial 10 km-long NW-SE section of the canyon, two at 350 m in the next 10 km N-S section, and nineteen at 300 to 500 m at the SW wall of the next 10 km NW-SE section. The sharp shape of the depressions suggests that they are actively forming. Larger circular depressions (diameter <800 m) exhibit different characteristics. 3)Methane chemistry: A methane anomaly (50 nmol) ten times background was measured in August 2008 in the near-bottom water column adjacent to one of the two circular depressions in the middle canyon section. In August 2009 water samples were recovered at other circular depressions and are being analyzed to test for methane discharge. We suggest that the circular depressions are gas release-collapse features possibly produced by dissociation of underlying gas hydrates. 4)Fans and ravines: Sediment fans with intervening ravines about 1 km apart extend orthogonal to the canyon axis down the two walls of the canyon in
Environmental issues elimination through circular economy
DOE Office of Scientific and Technical Information (OSTI.GOV)
Špirková, M., E-mail: marta.spirkova@stuba.sk; Pokorná, E.; Šujanová, J.
Environmental efforts of European Union are currently going towards circular economy. Tools like Extended Producer Responsibility and Eco-design were established. The circular economy deals with resources availability issue on one hand and waste management on the other hand. There are few pioneering companies all over the world with some kind of circular economy practice. Generally the concept is not very wide-spread. The paper aims to evaluate possibility of transition towards circular economy in Slovak industrial companies. They need to have an active approach to material treatment of their products after usage stage. Innovation is another important pre-condition for the transition.more » Main problem of current cradle to grave system is landfilling of valuable materials after one cycle of usage. Their potential value for next manufacturing cycles is lost. Companies may do not see connection between waste management and material resource prices and volatility of supplies. Municipalities are responsible for municipal waste collection and treatment in Slovakia. The circular economy operates by cradle to cradle principle. Company manages material flow until the material comes back to the beginning of manufacturing process by itself or by another partners. Stable material supplies with quite low costs are provided this way. It is necessary to deal with environmental problems in phase of product design. Questionnaire survey results show on one hand low involvement of industrial companies in waste management area, however on the other hand they are open to environmental innovations in future.« less
Environmental issues elimination through circular economy
NASA Astrophysics Data System (ADS)
Špirková, M.; Pokorná, E.; Šujanová, J.; Samáková, J.
2016-04-01
Environmental efforts of European Union are currently going towards circular economy. Tools like Extended Producer Responsibility and Eco-design were established. The circular economy deals with resources availability issue on one hand and waste management on the other hand. There are few pioneering companies all over the world with some kind of circular economy practice. Generally the concept is not very wide-spread. The paper aims to evaluate possibility of transition towards circular economy in Slovak industrial companies. They need to have an active approach to material treatment of their products after usage stage. Innovation is another important pre-condition for the transition. Main problem of current cradle to grave system is landfilling of valuable materials after one cycle of usage. Their potential value for next manufacturing cycles is lost. Companies may do not see connection between waste management and material resource prices and volatility of supplies. Municipalities are responsible for municipal waste collection and treatment in Slovakia. The circular economy operates by cradle to cradle principle. Company manages material flow until the material comes back to the beginning of manufacturing process by itself or by another partners. Stable material supplies with quite low costs are provided this way. It is necessary to deal with environmental problems in phase of product design. Questionnaire survey results show on one hand low involvement of industrial companies in waste management area, however on the other hand they are open to environmental innovations in future.
Asgeirsson, Bjarni; Adalbjörnsson, Björn Vidar; Gylfason, Gudjón Andri
2007-06-01
Alkaline phosphatase is an extracellular enzyme that is membrane-bound in eukaryotes but resides in the periplasmic space of bacteria. It normally carries four cysteine residues that form two disulfide bonds, for instance in the APs of Escherichia coli and vertebrates. An AP variant from a Vibrio sp. has only one cysteine residue. This cysteine is second next to the nucleophilic serine in the active site. We have individually modified seven residues to cysteine that are on two loops predicted to be within a 5 A radius. Four of them formed a disulfide bond to the endogenous cysteine. Thermal stability was monitored by circular dichroism and activity measurements. Global stability was similar to the wild-type enzyme. However, a significant increase in heat-stability was observed for the disulfide-containing variants using activity as a measure, together with a large reduction in catalytic rates (k(cat)) and a general decrease in Km values. The results suggest that a high degree of mobility near the active site and in the helix carrying the endogenous cysteine is essential for full catalytic efficiency in the cold-adapted AP.
Linear dichroism and the nature of charge order in underdoped cuprates
Norman, M. R.
2015-04-21
Recent experiments have addressed the nature of the charge order seen in underdoped cuprates. In this paper, I show that x-ray absorption and linear dichroism are excellent probes of such order. Ab initio calculations reveal that a d-wave charge density wave order involving the oxygen ions is a much better description of the data than alternate models.
Soliman, Wael; Wang, Liru; Bhattacharjee, Subir; Kaur, Kamaljit
2011-04-14
Class IIb bacteriocins are ribosomally synthesized antimicrobial peptides comprising two different peptides synergistically acting in equal amounts for optimal potency. In this study, we demonstrate for the first time potent (nanomolar) antimicrobial activity of a representative class IIb bacteriocin, plantaricin S (Pls), against four pathogenic gram-positive bacteria, including Listeria monocytogenes. The structure-activity relationships for Pls were studied using activity assays, circular dichroism (CD), and molecular dynamics (MD) simulations. The two Pls peptides and five Pls derived fragments were synthesized. The CD spectra of the Pls and selected fragments revealed helical conformations in aqueous 2,2,2-trifluoroethanol. The MD simulations showed that when the two Pls peptides are in antiparallel orientation, the helical regions interact and align, mediated by strong attraction between conserved GxxxG/AxxxA motifs. The results strongly correlate with the antimicrobial activity suggesting that helix-helix alignment of the two Pls peptides and interaction between the conserved motifs are crucial for interaction with the target cell membrane.
Daugherty, Ashley B; Horton, John R; Cheng, Xiaodong; Lutz, Stefan
2015-02-06
Circular permutation of the NADPH-dependent oxidoreductase Old Yellow Enzyme from Saccharomyces pastorianus (OYE1) can significantly enhance the enzyme's catalytic performance. Termini relocation into four regions of the protein (sectors I-IV) near the active site has proven effective in altering enzyme function. To better understand the structural consequences and rationalize the observed functional gains in these OYE1 variants, we selected representatives from sectors I-III for further characterization by biophysical methods and X-ray crystallography. These investigations not only show trends in enzyme stability and quaternary structure as a function of termini location, but also provide a possible explanation for the catalytic gains in our top-performing OYE variant (new N-terminus at residue 303; sector III). Crystallographic analysis indicates that termini relocation into sector III affects the loop β6 region (amino acid positions: 290-310) of OYE1 which forms a lid over the active site. Peptide backbone cleavage greatly enhances local flexibility, effectively converting the loop into a tether and consequently increasing the environmental exposure of the active site. Interestingly, such active site remodeling does not negatively impact the enzyme's activity and stereoselectivity, nor does it perturb the conformation of other key active site residues with the exception of Y375. These observations were confirmed in truncation experiments, deleting all residues of the loop β6 region in our OYE variant. Intrigued by the finding that circular permutation leaves most of the key catalytic residues unchanged, we also tested OYE permutants for possible additive or synergistic effects of amino acid substitutions. Distinct functional changes in these OYE variants were detected upon mutations at W116, known in native OYE1 to cause inversion of diastereo-selectivity for ( S )-carvone reduction. Our findings demonstrate the contribution of loop β6 toward determining the
Huang, Rongrong; Zhang, Yuan; Han, Bing; Bai, Ying; Zhou, Rongbin; Gan, Guangming; Chao, Jie; Hu, Gang; Yao, Honghong
2017-10-03
Circular RNAs are a subclass of noncoding RNAs in mammalian cells; however, whether these RNAs are involved in the regulation of astrocyte activation is largely unknown. Here, we have shown that the circular RNA HIPK2 (circHIPK2) functions as an endogenous microRNA-124 (MIR124-2HG) sponge to sequester MIR124-2HG and inhibit its activity, resulting in increased sigma non-opioid intracellular receptor 1 (SIGMAR1/OPRS1) expression. Knockdown of circHIPK2 expression significantly inhibited astrocyte activation via the regulation of autophagy and endoplasmic reticulum (ER) stress through the targeting of MIR124-2HG and SIGMAR1. These findings were confirmed in vivo in mouse models, as microinjection of a circHIPK2 siRNA lentivirus into mouse hippocampi inhibited astrocyte activation induced by methamphetamine or lipopolysaccharide (LPS). These findings provide novel insights regarding the specific contribution of circHIPK2 to astrocyte activation in the context of drug abuse as well as for the treatment of a broad range of neuroinflammatory disorders.
Chemical modification, antioxidant and α-amylase inhibitory activities of corn silk polysaccharides.
Chen, Shuhan; Chen, Haixia; Tian, Jingge; Wang, Yanwei; Xing, Lisha; Wang, Jia
2013-10-15
Water-soluble corn silk polysaccharides (CSPS) were chemically modified to obtain their sulfated, acetylated and carboxymethylated derivatives. Chemical characterization and bioactivities of CSPS and its derivatives were comparatively investigated by chemical methods, gas chromatography, gel filtration chromatography, scanning electron microscope, infrared spectroscopy and circular dichroism spectroscopy, scavenging DPPH free radical assay, scavenging hydroxyl radical assay, ferric reducing power assay, lipid peroxidation inhibition assay and α-amylase activity inhibitory assay, respectively. Among the three derivatives, carboxylmethylated polysaccharide (C-CSPS) demonstrated higher solubility, narrower molecular weight distribution, lower intrinsic viscosity, a hyperbranched conformation, significantly higher antioxidant and α-amylase inhibitory abilities compared with the native polysaccharide and other derivatives. C-CSPS might be used as a novel nutraceutical agent for human consumption. Copyright © 2013 Elsevier Ltd. All rights reserved.
Said, Mohammed El-Amin; Vanloot, Pierre; Bombarda, Isabelle; Naubron, Jean-Valère; Dahmane, El Montassir; Aamouche, Ahmed; Jean, Marion; Vanthuyne, Nicolas; Dupuy, Nathalie; Roussel, Christian
2016-01-15
An unprecedented methodology was developed to simultaneously assign the relative percentages of the major chiral compounds and their prevailing enantiomeric form in crude essential oils (EOs). In a first step the infrared (IR) and vibrational circular dichroism (VCD) spectra of the crude essential oils were recorded and in a second step they were modelized as a linear weighted combination of the IR and VCD spectra of the individual spectra of pure enantiomer of the major chiral compounds present in the EOs. The VCD spectra of enantiomer of known enantiomeric excess shall be recorded if they are not yet available in a library of VCD spectra. For IR, the spectra of pure enantiomer or racemic mixture can be used. The full spectra modelizations were performed using a well known and powerful mathematical model (least square estimation: LSE) which resulted in a weighting of each contributing compound. For VCD modelization, the absolute value of each weighting represented the percentage of the associate compound while the attached sign addressed the correctness of the enantiomeric form used to build the model. As an example, a model built with the non-prevailing enantiomer will show a negative sign of the weighting value. For IR spectra modelization, the absolute value of each weighting represented the percentage of the compounds without of course accounting for the chirality of the prevailing enantiomers. Comparison of the weighting values issuing from IR and VCD spectra modelizations is a valuable source of information: if they are identical, the EOs are composed of nearly pure enantiomers, if they are different the chiral compounds of the EOs are not in an optically pure form. The method was applied on four samples of essential oil of Artemisia herba-alba in which the three major compounds namely (-)-α-thujone, (+)-β-thujone and (-)-camphor were found in different proportions as determined by GC-MS and chiral HPLC using polarimetric detector. In order to validate the
Active Terahertz Chiral Metamaterials Based on Phase Transition of Vanadium Dioxide (VO2).
Wang, Shengxiang; Kang, Lei; Werner, Douglas H
2018-01-09
Compared with natural materials, chiral metamaterials have been demonstrated with orders of magnitude stronger chiroptical response, which provides the basis for applications such as ultracompact polarization components and plasmonic-enhanced biosensing. Terahertz chiral metamaterials that allow dynamic polarization control of terahertz waves are of great practical interest, but remain extremely rare. Here, we show that hybrid metamaterials integrated with vanadium dioxide (VO 2 ) exhibiting phase transition can enable dynamically tunable chiroptical responses at terahertz frequencies. In particular, a circular dichroism of ~40° and a maximum polarization rotation of ~200°/λ are observed around 0.7 THz. Furthermore, our study also reveals that the chiroptical response from the proposed metamaterials is strongly dependent on the phase transition of VO 2 , leading to actively controllable polarization states of the transmitted terahertz waves. This work paves the way for the development of terahertz metadevices capable of enabling active polarization manipulation.
Loret, Erwann P.; Luis, José; Nuccio, Christopher; Villard, Claude; Mansuelle, Pascal; Lebrun, Régine; Villard, Pierre Henri
2018-01-01
Sea anemones are a remarkable source of active principles due to a decentralized venom system. New blood vessel growth or angiogenesis is a very promising target against cancer, but the few available antiangiogenic compounds have limited efficacy. In this study, a protein fraction, purified from tentacles of Anemonia viridis, was able to limit endothelial cells proliferation and angiogenesis at low concentration (14 nM). Protein sequences were determined with Edman degradation and mass spectrometry in source decay and revealed homologies with Blood Depressing Substance (BDS) sea anemones. The presence of a two-turn alpha helix observed with circular dichroism and a trypsin activity inhibition suggested that the active principle could be a Kunitz-type inhibitor, which may interact with an integrin due to an Arginine Glycin Aspartate (RGD) motif. Molecular modeling showed that this RGD motif was well exposed to solvent. This active principle could improve antiangiogenic therapy from existing antiangiogenic compounds binding on the Vascular Endothelial Growth Factor (VEGF). PMID:29671760
Circular Bacteriocins: Biosynthesis and Mode of Action
Brede, Dag A.; Nes, Ingolf F.; Diep, Dzung B.
2014-01-01
Circular bacteriocins are a group of N-to-C-terminally linked antimicrobial peptides, produced by Gram-positive bacteria of the phylum Firmicutes. Circular bacteriocins generally exhibit broad-spectrum antimicrobial activity, including against common food-borne pathogens, such as Clostridium and Listeria spp. These peptides are further known for their high pH and thermal stability, as well as for resistance to many proteolytic enzymes, properties which make this group of bacteriocins highly promising for potential industrial applications and their biosynthesis of particular interest as a possible model system for the synthesis of highly stable bioactive peptides. In this review, we summarize the current knowledge on this group of bacteriocins, with emphasis on the recent progress in understanding circular bacteriocin genetics, biosynthesis, and mode of action; in addition, we highlight the current challenges and future perspectives for the application of these peptides. PMID:25172850
Magnetic x-ray linear dichroism in resonant and non-resonant Gd 4f photoemission
DOE Office of Scientific and Technical Information (OSTI.GOV)
Mishra, S.; Gammon, W.J.; Pappas, D.P.
1997-04-01
The enhancement of the magnetic linear dichroism in resonant 4f photoemission (MLDRPE) is studied from a 50 monolayer film of Gd/Y(0001). The ALS at beamline 7.0.1 provided the source of linearly polarized x-rays used in this study. The polarized light was incident at an angle of 30 degrees relative to the film plane, and the sample magnetization was perpendicular to the photon polarization. The linear dichroism of the 4f core levels is measured as the photon energy is tuned through the 4d-4f resonance. The authors find that the MLDRPE asymmetry is strongest at the resonance. Near the threshold the asymmetrymore » has several features which are out of phase with the fine structure of the total yield.« less
Chang, Le; Baseggio, Oscar; Sementa, Luca; Cheng, Daojian; Fronzoni, Giovanna; Toffoli, Daniele; Aprà, Edoardo; Stener, Mauro; Fortunelli, Alessandro
2018-06-13
We introduce Individual Component Maps of Rotatory Strength (ICM-RS) and Rotatory Strength Density (RSD) plots as analysis tools of chiro-optical linear response spectra deriving from time-dependent density functional theory (TDDFT) simulations. ICM-RS and RSD allow one to visualize the origin of chiro-optical response in momentum or real space, including signed contributions and therefore highlighting cancellation terms that are ubiquitous in chirality phenomena, and should be especially useful in analyzing the spectra of complex systems. As test cases, we use ICM-RS and RSD to analyze circular dichroism spectra of selected (Ag-Au)30(SR)18 monolayer-protected metal nanoclusters, showing the potential of the proposed tools to derive insight and understanding, and eventually rational design, in chiro-optical studies of complex systems.
Tailorable chiroptical activity of metallic nanospiral arrays.
Deng, Junhong; Fu, Junxue; Ng, Jack; Huang, Zhifeng
2016-02-28
The engineering of the chiroptical activity of the emerging chiral metamaterial, metallic nanospirals, is in its infancy. We utilize glancing angle deposition (GLAD) to facilely sculpture the helical structure of silver nanospirals (AgNSs), so that the scope of chiroptical engineering factors is broadened to include the spiral growth of homochiral AgNSs, the combination of left- and right-handed helical chirality to create heterochiral AgNSs, and the coil-axis alignment of the heterochiral AgNSs. It leads to flexible control over the chiroptical activity of AgNS arrays with respect to the sign, resonance wavelength and amplitude of circular dichroism (CD) in the UV and visible regime. The UV chiroptical mode has a distinct response from the visible mode. Finite element simulation together with LC circuit theory illustrates that the UV irradiation is mainly adsorbed in the metal and the visible is preferentially scattered by the AgNSs, accounting for the wavelength-related chiroptical distinction. This work contributes to broadening the horizons in understanding and engineering chiroptical responses, primarily desired for developing a wide range of potential chiroplasmonic applications.
Absolute configuration of (-)-myrtenal by vibrational circular dichroism.
Burgueño-Tapia, Eleuterio; Zepeda, L Gerardo; Joseph-Nathan, Pedro
2010-07-01
The VCD spectrum of the monoterpene (-)-myrtenal (1) was compared with theoretical spectra using ab initio density functional theory (DFT) calculations at the B3LYP/6-31G(d,p), B3LYP/6-31G+(d,p), B3LYP/6-311G+(d,p), B3LYP/DGDZVP, and B3PW91/DGTZVP levels of theory. Conformational analysis of 1 indicated that the lowest energy conformer was s-trans-C2-C10, which contributes more than 98.5% to the total conformational population regardless of the employed level of theory. The use of a recently developed confidence level algorithm demonstrated that VCD spectra calculated for the main conformer, using the indicated hybrid functionals and basis set, gave no significant changes, from where it follows that B3LYP/DGDZVP calculations provide a superior balance between computer cost and VCD spectral accuracy. The DGDZVP basis set demanded around a quarter the time than the 6-311G+(d,p) basis set while providing similar results. The spectral comparison also provided evidence that the levorotatory enantiomer of myrtenal has the 1R absolute configuration. 2010 Elsevier Ltd. All rights reserved.
Generation and electric control of spin-valley-coupled circular photogalvanic current in WSe2
NASA Astrophysics Data System (ADS)
Yuan, Hongtao; Hwang, Harold Y.; Cui, Yi
2015-03-01
Compared to the weak spin-orbit-interaction (SOI) in graphene, layered transitionmetal chalcogenides MX2 have heavy 4d/5d elements with strong atomic SOI, providing a unique way to extend functionalities of novel spintronics and valleytronics devices. Such a valley polarization achieved via valley-selective circular dichroism has been predicted theoretically and demonstrated with optical experiments in MX2 systems. Despite the exciting progresses, the generation of a valley/spin current by valley polarization in MX2 remains elusive and a great challenge. A spin/valley current in MX2 compounds caused by such a valley polarization has never been observed, nor its electric-field control. In this talk, we demonstrated, within an electric-double-layer transistor based on WSe2, the manipulation of a spin-coupled valley photocurrent whose direction and magnitude depend on the degree of circular polarization of the incident radiation and can be further greatly modulated with an external electric field. Such room temperature generation and electric control of valley/spin photocurrent provides a new property of electrons in MX2 systems, thereby enabling new degrees of control for quantum-confined spintronics devices. (In collaboration with S.C. Zhang, Y.L. Chen, Z.X. Shen, B Lian, H.J. Zhang, G Xu, Y Xu, B Zhou, X.Q. Wang, B Shen X.F. Fang) Acknowledge the support from DoE, BES, Division of MSE under contract DE-AC02-76SF00515. Acknowledge the support from DoE, BES, Division of MSE under contract DE-AC02-76SF00515.
Helically assembled π-conjugated polymers with circularly polarized luminescence.
Watanabe, Kazuyoshi; Akagi, Kazuo
2014-08-01
We review the recent progress in the field of helically assembled π -conjugated polymers, focusing on aromatic conjugated polymers with interchain helical π -stacking that exhibit circularly polarized luminescence (CPL). In Part 1, we discuss optically active polymers with white-colored CPL and the amplification of the circular polarization through liquid crystallinity. In Part 2, we focus on the stimuli-responsive CPL that results from changes in the conformation and aggregation state of π -conjugated molecules and polymers. In Part 3, we discuss the self-assembly of achiral cationic π -conjugated polymers into circularly polarized luminescent supramolecular nanostructures with the aid of other chiral molecules.
Lu, Yunjun; Liu, Cencen; Zhao, Mouming; Cui, Chun; Ren, Jiaoyan
2015-11-04
Phytohemagglutin (PHA), purified from red kidney beans (Phaseolus vulgaris) by Affi-Gel blue affinity chromatography, was subjected to ultrahigh-pressure (UHP) treatment (150, 250, 350, and 450 MPa). The purified PHA lost its hemagglutination activity after 450 MPa treatment and showed less pressure tolerance than crude PHA. However, the saccharide specificity and α-glucosidase inhibition activity of the purified PHA did not change much after UHP treatment. Electrophoresis staining by periodic acid-Schiff (PAS) manifested that the glycone structure of purified PHA remained stable even after 450 MPa pressure treatment. However, electrophoresis staining by Coomassie Blue as well as circular dichroism (CD) and differential scanning calorimetry (DSC) assay proved that the protein unit structure of purified PHA unfolded when treated at 0-250 MPa but reaggregates at 250-450 MPa. Therefore, the hemagglutination activity tends to be affected by the protein unit structure, while the stability of the glycone structure contributed to the remaining α-glucosidase inhibition activity.
Inhibition mechanism of lanthanum ion on the activity of horseradish peroxidase in vitro
NASA Astrophysics Data System (ADS)
Guo, Shaofen; Wang, Lihong; Lu, Aihua; Lu, Tianhong; Ding, Xiaolan; Huang, Xiaohua
2010-02-01
In order to understand the inhibition mechanism of lanthanum ion (La 3+) on the activity of horseradish peroxidase (HRP), the effects of La 3+ on the activity, electron transfer and conformation of HRP in vitro were investigated by using cyclic voltammetry (CV), atomic force microscopy (AFM), circular dichroism (CD), high performance liquid chromatography (HPLC), matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy (MALDI-TOF/MS) and inductively coupled plasma mass spectrometry (ICP-MS). It was found that La 3+ can combine with the amide groups of the polypeptide chain in HRP molecule, forming the complex of La 3+ and HRP (La-HRP). The formation of the La-HRP complex causes the destruction of the native structure of HRP molecule, leading to the decrease in the non-planarity of the porphyrin ring in the heme group of HRP molecule, and then in the exposure extent of active center, Fe(III) of the porphyrin ring of HRP molecule. Thus, the direct electrochemical and catalytic activities of HRP are decreased. It is a possible inhibition mechanism of La 3+ on the activity of peroxidase.
Effect of plasma actuator and splitter plate on drag coefficient of a circular cylinder
NASA Astrophysics Data System (ADS)
Akbıyık, Hürrem; Erkan Akansu, Yahya; Yavuz, Hakan; Ertuğrul Bay, Ahmet
2016-03-01
In this paper, an experimental study on flow control around a circular cylinder with splitter plate and plasma actuator is investigated. The study is performed in wind tunnel for Reynolds numbers at 4000 and 8000. The wake region of circular cylinder with a splitter plate is analyzed at different angles between 0 and 180 degrees. In this the study, not only plasma actuators are activated but also splitter plate is placed behind the cylinder. A couple electrodes are mounted on circular cylinder at ±90 degrees. Also, flow visualization is achieved by using smoke wire method. Drag coefficient of the circular cylinder with splitter plate and the plasma actuator are obtained for different angles and compared with the plain circular cylinder. While attack angle is 0 degree, drag coefficient is decreased about 20% by using the splitter plate behind the circular cylinder. However, when the plasma actuators are activated, the improvement of the drag reduction is measured to be 50%.
Circular flow patterns induced by ciliary activity in reconstituted human bronchial epithelium
NASA Astrophysics Data System (ADS)
Viallat, Annie; Khelloufi, Kamel; Gras, Delphine; Chanez, Pascal; Aix Marseille Univ., CNRS, CINaM, Marseille, France Team; Aix Marseille Univ., CNRS, Inserm, LAI, Marseille, France Team
2016-11-01
Mucociliary clearance is the transport at the surface of airways of a complex fluid layer, the mucus, moved by the beats of microscopic cilia present on epithelial ciliated cells. We explored the coupling between the spatial organisation and the activity of cilia and the transport of surface fluids on reconstituted cultures of human bronchial epithelium at air-liquid interface, obtained by human biopsies. We reveal the existence of stable local circular surface flow patterns of mucus or Newtonian fluid at the epithelium surface. We find a power law over more than 3 orders of magnitude showing that the average ciliated cell density controls the size of these flow patterns, and, therefore the distance over which mucus can be transported. We show that these circular flow patterns result from the radial linear increase of the local propelling forces (due to ciliary beats) on each flow domain. This linear increase of local forces is induced by a fine self-regulation of both cilia density and orientation of ciliary beats. Local flow domains grow and merge during ciliogenesis to provide macroscopic mucus transport. This is possible only when the viscoelastic mucus continuously exerts a shear stress on beating cilia, revealing a mechanosensitive function of cilia. M. K. Khelloufi thanks the society MedBioMed for financial support. This work was supported by the ANR MUCOCIL project, Grant ANR-13-BSV5-0015 of the French Agence Nationale de la Recherche.
KiranKumar, Hulihalli N; RohitKumar, Heggodu G; Advirao, Gopal M
2018-01-01
Two new derivatives of pyrimido[4',5';4,5]thieno(2,3-b)quinoline (PTQ), 9-hydroxy-4-(3-diethylaminopropylamino)pyrimido[4',5';4,5]thieno(2,3-b)quinoline (Hydroxy-DPTQ) and 8-methoxy-4-(3-diethylaminopropylamino)pyrimido[4',5';4,5]thieno(2,3-b)quinoline (Methoxy-DPTQ) were synthesized and their DNA binding ability was analyzed using spectroscopy (UV-visible, fluorescence and circular dichroism), ethidium bromide dye displacement assay, melting temperature (T m ) analysis and computational docking studies. The hypochromism in UV-visible spectrum and increased fluorescence emission of Hydroxy-DPTQ and Methoxy-DPTQ in the presence of DNA suggested the molecule-DNA interaction. The association constants calculated from UV-visible and spectral titrations were of the order 10 4 to 10 6 M -1 . Circular dichroism studies corroborated the induced conformational changes in DNA upon addition of molecules. The change in the ellipticity was observed both in negative and positive peak of DNA, thus, suggesting the intercalation of molecules. The observed displacement of ethidium bromide from the DNA and increased T m , upon addition of DNA confirmed the intercalative mode of binding. This was further validated by computational docking, which showed clear intercalation of molecules into the d(GpC)-d(CpG) site of the receptor DNA. Anticancer activities of these molecules are evaluated by using MTT assay. Both molecules showed antiproliferative activity against all the three cancer cells studied, with Hydroxy-DPTQ being more potential molecule among the two. IC 50 value of Hydroxy-DPTQ and Methoxy-DPTQ were in the range of 3-5μM and 130-250μM, respectively. Copyright © 2017 Elsevier B.V. All rights reserved.
3-[(E)-(acridin-9‧-ylmethylidene)amino]-1-substituted thioureas and their biological activity
NASA Astrophysics Data System (ADS)
Bečka, Michal; Vilková, Mária; Salem, Othman; Kašpárková, Jana; Brabec, Viktor; Kožurková, Mária
2017-06-01
This paper describes the synthesis of a novel series of acridine thiosemicarbazones through a two-step reaction between various isothiocyanates and hydrazine followed by treatment with acridin-9-carbaldehyde. The properties of this series of seven new derivatives are studied using NMR and biochemical techniques, and the DNA-binding properties of the compounds are determined using spectrophotometric studies (UV-vis absorption, fluorescence, and circular/linear dichroism) and viscometry. The binding constants K are estimated as being in the range of 2.2 to 7.8 × 104 M- 1 and the percentage of hypochromism was found to be 22.11-49.75% (from UV-vis spectral titration). Electrophoretic experiments prove that the novel compounds demonstrate moderate inhibitory effects against Topo I activity at a concentration of 60 × 10- 6 M.
Activation mechanism of melB tyrosinase from Aspergillus oryzae by acidic treatment.
Fujieda, Nobutaka; Murata, Michiaki; Yabuta, Shintaro; Ikeda, Takuya; Shimokawa, Chizu; Nakamura, Yukihiro; Hata, Yoji; Itoh, Shinobu
2013-01-01
The pro form of recombinant tyrosinase from Aspergillus oryzae (melB) shows no catalytic activity, but acid treatment (around pH 3.5) of protyrosinase activates it to induce tyrosinase activity. Circular dichroism spectra, gel filtration analysis, and colorimetric assay have indicated that acid treatment around pH 3.5 induced the disruption of the conformation of the C-terminal domain covering the enzyme active site. These structural changes induced by the acid treatment may open the entrance to the enzyme active site for substrate incorporation. To compare the mechanism of hydroxylation by the acid-treated tyrosinase with that by trypsin-treated tyrosinase, a detailed steady-state kinetic analysis of the phenolase activity was performed by monitoring the O(2)-consumption rate using a Clark-type oxygen electrode. The results clearly show that the phenolase activity (phenol hydroxylation) of the activated tyrosinase involves an electrophilic aromatic substitution mechanism as in the case of mushroom tyrosinase (Yamazaki and Itoh in J. Am. Chem. Soc. 125:13034-13035, 2003) and activated hemocyanin with urea (Morioka et al. in J. Am. Chem. Soc. 128:6788-6789, 2006).
AGT Activity Towards Intrastrand Crosslinked DNA is Modulated by the Alkylene Linker.
O'Flaherty, Derek K; Wilds, Christopher J
2017-12-05
DNA oligomers containing dimethylene and trimethylene intrastrand crosslinks (IaCLs) between the O4 and O6 atoms of neighboring thymidine (T) and 2'-deoxyguanosine (dG) residues were prepared by solid-phase synthesis. UV thermal denaturation (T m ) experiments revealed that these IaCLs had a destabilizing effect on the DNA duplex relative to the control. Circular dichroism spectroscopy suggested these IaCLs induced minimal structural distortions. Susceptibility to dealkylation by reaction with various O 6 -alkylguanine DNA alkyltransferases (AGTs) from human and Escherichia coli was evaluated. It was revealed that only human AGT displayed activity towards the IaCL DNA, with reduced efficiency as the IaCL shortened (from four to two methylene linkages). Changing the site of attachment of the ethylene linkage at the 5'-end of the IaCL to the N3 atom of T had minimal influence on duplex stability and structure, and was refractory to AGT activity. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Kumar, Santosh; Koh, Joonseok
2012-01-01
This paper describes the physiochemical, optical and biological activity of chitosan-chromone derivative. The chitosan-chromone derivative gels were prepared by reacting chitosan with chromone-3-carbaldehyde, followed by solvent exchange, filtration and drying by evaporation. The identity of Schiff base was confirmed by UV-Vis absorption spectroscopy and Fourier-transform infrared (FTIR) spectroscopy. The chitosan-chromone derivative was evaluated by X-ray diffraction (XRD), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), scanning electron microscopy (SEM), photoluminescence (PL) and circular dichroism (CD). The CD spectrum showed the chitosan-chromone derivative had a secondary helical structure. Microbiological screening results demonstrated the chitosan-chromone derivative had antimicrobial activity against Escherichia coli bacteria. The chitosan-chromone derivative did not have any adverse effect on the cellular proliferation of mouse embryonic fibroblasts (MEF) and did not lead to cellular toxicity in MEFs. These results suggest that the chitosan-chromone derivative gels may open a new perspective in biomedical applications. PMID:22754352
Kuller, L H
1999-11-01
Circular epidemiology can be defined as the continuation of specific types of epidemiologic studies beyond the point of reasonable doubt of the true existence of an important association or the absence of such an association. Circular epidemiology is an extreme example of studies of the consistency of associations. A basic problem for epidemiology is the lack of a systematic approach to acquiring new knowledge to reach a goal of improving public health and preventive medicine. For epidemiologists, research support unfortunately is biased toward the continued study of already proven hypotheses. Circular epidemiology, however, freezes at one point in the evolution of epidemiologic studies, failing to move from descriptive to analytical case-control and longitudinal studies, for example, to experimental, clinical trials. Good epidemiology journals are filled with very well-conducted epidemiologic studies that primarily repeat the obvious or are variations on the theme.
NASA Astrophysics Data System (ADS)
Hamamoto, Satoru; Fujioka, Shuhei; Kanai, Yuina; Yamagami, Kohei; Nakatani, Yasuhiro; Nakagawa, Koya; Fujiwara, Hidenori; Kiss, Takayuki; Higashiya, Atsushi; Yamasaki, Atsushi; Kadono, Toshiharu; Imada, Shin; Tanaka, Arata; Tamasaku, Kenji; Yabashi, Makina; Ishikawa, Tetsuya; Matsumoto, Keisuke T.; Onimaru, Takahiro; Takabatake, Toshiro; Sekiyama, Akira
2017-12-01
We report experimentally observed linear dichroism in angle-resolved core-level photoemission spectra of PrIr2Zn20 and PrB6 with cubic symmetry. The different anisotropic 4f charge distributions between the compounds due to the crystalline-electric-field splitting are responsible for the difference in the linear dichroism, which has been verified by spectral simulations with the full multiplet theory for a single-site Pr3+ ion with cubic symmetry. The observed linear dichroism and polarization-dependent spectra in two different photoelectron directions for PrIr2Zn20 are reproduced by theoretical analysis for the Γ3 ground state, whereas those of the Pr 3d and 4d core levels indicate the Γ5 ground state for PrB6.
Yang, Xiyue; Wang, Jing; Zhou, Zewei; Jiang, Rong; Huang, Jie; Chen, Lulu; Cao, Zhouli; Chu, Han; Han, Bing; Cheng, Yusi; Chao, Jie
2018-06-01
Phagocytosis of silicon dioxide (SiO 2 ) into lung cells causes an inflammatory cascade that results in fibroblast proliferation and migration, followed by fibrosis. Circular RNAs (circRNAs) are a subclass of noncoding RNAs that are present within mammalian cells; however, researchers have not determined whether circRNAs are involved in the pathophysiologic process of silicosis. To elucidate the role of these RNAs in SiO 2 -induced inflammation in pulmonary macrophages, we investigated the upstream molecular mechanisms and functional effects of circRNAs on cell apoptosis, proliferation, and migration. Primary cultures of alveolar macrophages from healthy donors and from patients and the RAW264.7 macrophage cell line were used to explore the functions of circZC3H4 RNA in macrophage activation. The experimental results indicated the following: 1) SiO 2 concomitantly increased circZC3H4 RNA expression and increased ZC3H4 protein levels; 2) circular ZC3H4 (circZC3H4) RNA and ZC3H4 protein participated in SiO 2 -induced macrophage activation; and 3) SiO 2 -activated macrophages promoted fibroblast proliferation and migration via the circZC3H4 RNA/ZC3H4 pathway. The up-regulation of the ZC3H4 protein was confirmed in tissue samples from patients with silicosis. Our study elucidates a link between SiO 2 -induced macrophage activation and the circZC3H4 RNA/ZC3H4 pathway, thereby providing novel insight into the potential use of ZC3H4 to develop novel therapeutic strategies for silicosis.-Yang, X., Wang, J., Zhou, Z., Jiang, R., Huang, J., Chen, L., Cao, Z., Chu, H., Han, B., Cheng, Y., Chao, J. Silica-induced initiation of circular ZC3H4 RNA/ZC3H4 pathway promotes the pulmonary macrophage activation.
Noordermeer, M A; Veldink, G A; Vliegenthart, J F
2001-02-02
Expression of high quantities of alfalfa hydroperoxide lyase in Escherichia coli made it possible to study its active site and structure in more detail. Circular dichroism (CD) spectra showed that hydroperoxide lyase consists for about 75% of alpha-helices. Electron paramagnetic resonance (EPR) spectra confirmed its classification as a cytochrome P450 enzyme. The positive influence of detergents on the enzyme activity is paralleled by a spin state transition of the heme Fe(III) from low to high spin. EPR and CD spectra showed that detergents induce a subtle conformational change, which might result in improved substrate binding. Because hydroperoxide lyase is thought to be a membrane bound protein and detergents mimic a membrane environment, the more active, high spin form likely represents the in vivo conformation. Furthermore, the spin state appeared to be temperature-dependent, with the low spin state favored at low temperature. Point mutants of the highly conserved cysteine in domain D indicated that this residue might be involved in heme binding.
Soil and land management in a circular economy.
Breure, A M; Lijzen, J P A; Maring, L
2018-05-15
This article elaborates the role of soil and land management in a circular economy. The circular economy is highly dependent on the functioning of soils and land for the production of food and other biomass; the storage, filtration and transformation of many substances including water, carbon, and nitrogen; the provision of fresh mineral resources and fossil fuels; and the use of their functions as the platform for nature and human activities. Resource demand is increasing as a result of the growing human population. In addition to the shrinking availability of resources resulting from their unsustainable use in the past, our planet's diminishing potential for resource production, due to a range of reasons, is leading to resource scarcity, especially in the case of depletable resources. As an economic system that focuses on maximizing the reuse of resources and products and minimizing their depreciation, the circular economy greatly influences, and depends on, soil and land management. The concise management of the resources, land and soil is thus necessary, to make a circular economy successful. Copyright © 2017 Elsevier B.V. All rights reserved.
Compact waveguide circular polarizer
Tantawi, Sami G.
2016-08-16
A multi-port waveguide is provided having a rectangular waveguide that includes a Y-shape structure with first top arm having a first rectangular waveguide port, a second top arm with second rectangular waveguide port, and a base arm with a third rectangular waveguide port for supporting a TE.sub.10 mode and a TE.sub.20 mode, where the end of the third rectangular waveguide port includes rounded edges that are parallel to a z-axis of the waveguide, a circular waveguide having a circular waveguide port for supporting a left hand and a right hand circular polarization TE.sub.11 mode and is coupled to a base arm broad wall, and a matching feature disposed on the base arm broad wall opposite of the circular waveguide for terminating the third rectangular waveguide port, where the first rectangular waveguide port, the second rectangular waveguide port and the circular waveguide port are capable of supporting 4-modes of operation.
Huertas Méndez, Nataly De Jesús; Vargas Casanova, Yerly; Gómez Chimbi, Anyelith Katherine; Hernández, Edith; Leal Castro, Aura Lucia; Melo Diaz, Javier Mauricio; Rivera Monroy, Zuly Jenny; García Castañeda, Javier Eduardo
2017-03-12
Linear, dimeric, tetrameric, and cyclic peptides derived from lactoferricin B-containing non-natural amino acids and the RWQWR motif were synthesized, purified, and characterized using RP-HPLC, MALDI-TOF mass spectrometry, and circular dichroism. The antibacterial activity of peptides against Escherichia coli ATCC 11775, Stenotrophomonas maltophilia ATCC 13636, and Salmonella enteritidis ATCC 13076 was evaluated. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were determined. The synthetic bovine lactoferricin exhibited antibacterial activity against E. coli ATCC 11775 and S. enteritidis ATCC 13076. The dimeric peptide (RRWQWR)₂K-Ahx exhibited the highest antibacterial activity against the tested bacterial strain. The monomeric, cyclic, tetrameric, and palindromic peptides containing the RWQWR motif exhibited high and specific activity against E. coli ATCC 11775. The results suggest that short peptides derived from lactoferricin B could be considered as potential candidates for the development of antibacterial agents against infections caused by E. coli .
[Circular migration in Indonesia].
Mantra, I B
1979-12-01
The author examines circular migration in Indonesia, with primary focus on the 1970s. It is found that circular, or repeated return migration, generally occurs over short distances and for short periods and is more frequent than lifetime migration. The relationships between improvements in the national transport system, access to labor force opportunities in both the formal and informal sectors of the economy, and circular migration are discussed.
Daugherty, Ashley B.; Horton, John R.; Cheng, Xiaodong; ...
2014-12-09
Circular permutation of the NADPH-dependent oxidoreductase Old Yellow Enzyme from Saccharomyces pastorianus (OYE1) can significantly enhance the enzyme’s catalytic performance. Termini relocation into four regions of the protein (sectors I–IV) near the active site has proven effective in altering enzyme function. To better understand the structural consequences and rationalize the observed functional gains in these OYE1 variants, we selected representatives from sectors I–III for further characterization by biophysical methods and X-ray crystallography. These investigations not only show trends in enzyme stability and quaternary structure as a function of termini location but also provide a possible explanation for the catalytic gainsmore » in our top-performing OYE variant (new N-terminus at residue 303; sector III). Crystallographic analysis indicates that termini relocation into sector III affects the loop β6 region (amino acid positions: 290–310) of OYE1, which forms a lid over the active site. Peptide backbone cleavage greatly enhances local flexibility, effectively converting the loop into a tether and consequently increasing the environmental exposure of the active site. Interestingly, such an active site remodeling does not negatively impact the enzyme’s activity and stereoselectivity; neither does it perturb the conformation of other key active site residues with the exception of Y375. These observations were confirmed in truncation experiments, deleting all residues of the loop β6 region in our OYE variant. Intrigued by the finding that circular permutation leaves most of the key catalytic residues unchanged, we also tested OYE permutants for possible additive or synergistic effects of amino acid substitutions. Distinct functional changes in these OYE variants were detected upon mutations at W116, known in native OYE1 to cause inversion of diastereoselectivity for (S)-carvone reduction. In conclusion, our findings demonstrate the
Femtosecond characterization of vibrational optical activity of chiral molecules.
Rhee, Hanju; June, Young-Gun; Lee, Jang-Soo; Lee, Kyung-Koo; Ha, Jeong-Hyon; Kim, Zee Hwan; Jeon, Seung-Joon; Cho, Minhaeng
2009-03-19
Optical activity is the result of chiral molecules interacting differently with left versus right circularly polarized light. Because of this intrinsic link to molecular structure, the determination of optical activity through circular dichroism (CD) spectroscopy has long served as a routine method for obtaining structural information about chemical and biological systems in condensed phases. A recent development is time-resolved CD spectroscopy, which can in principle map the structural changes associated with biomolecular function and thus lead to mechanistic insights into fundamental biological processes. But implementing time-resolved CD measurements is experimentally challenging because CD is a notoriously weak effect (a factor of 10(-4)-10(-6) smaller than absorption). In fact, this problem has so far prevented time-resolved vibrational CD experiments. Here we show that vibrational CD spectroscopy with femtosecond time resolution can be realized when using heterodyned spectral interferometry to detect the phase and amplitude of the infrared optical activity free-induction-decay field in time (much like in a pulsed NMR experiment). We show that we can detect extremely weak signals in the presence of large achiral background contributions, by simultaneously measuring with a femtosecond laser pulse the vibrational CD and optical rotatory dispersion spectra of dissolved chiral limonene molecules. We have so far only targeted molecules in equilibrium, but it would be straightforward to extend the method for the observation of ultrafast structural changes such as those occurring during protein folding or asymmetric chemical reactions. That is, we should now be in a position to produce 'molecular motion pictures' of fundamental molecular processes from a chiral perspective.
Induction of tumor apoptosis through a circular RNA enhancing Foxo3 activity.
Du, William W; Fang, Ling; Yang, Weining; Wu, Nan; Awan, Faryal Mehwish; Yang, Zhenguo; Yang, Burton B
2017-02-01
Circular RNAs are a class of non-coding RNAs that are receiving extensive attention. Despite reports showing circular RNAs acting as microRNA sponges, the biological functions of circular RNAs remain largely unknown. We show that in patient tumor samples and in a panel of cancer cells, circ-Foxo3 was minimally expressed. Interestingly, during cancer cell apoptosis, the expression of circ-Foxo3 was found to be significantly increased. We found that silencing endogenous circ-Foxo3 enhanced cell viability, whereas ectopic expression of circ-Foxo3 triggered stress-induced apoptosis and inhibited the growth of tumor xenografts. Also, expression of circ-Foxo3 increased Foxo3 protein levels but repressed p53 levels. By binding to both, circ-Foxo3 promoted MDM2-induced p53 ubiquitination and subsequent degradation, resulting in an overall decrease of p53. With low binding affinity to Foxo3 protein, circ-Foxo3 prevented MDM2 from inducing Foxo3 ubiquitination and degradation, resulting in increased levels of Foxo3 protein. As a result, cell apoptosis was induced by upregulation of the Foxo3 downstream target PUMA.
2017-08-08
Another area of the design that needs to be experimentally tested is the SMPS connectors used to attach the two beamforming stages together. In...AFRL-RY-WP-TR-2017-0104 ELECTROMAGNETIC SCATTERING AND ANTENNA TECHNOLOGY (EMSAT) Task Order 0003: Design of a Circularly Polarized, 20-60...Order 0003: Design of a Circularly Polarized, 20-60 GHZ Active Phased Array for Wide Angle Scanning 5a. CONTRACT NUMBER FA8650-14-D-1714-0003 5b
A Helicene Nanoribbon with Greatly Amplified Chirality.
Schuster, Nathaniel J; Hernández Sánchez, Raúl; Bukharina, Daria; Kotov, Nicholas A; Berova, Nina; Ng, Fay; Steigerwald, Michael L; Nuckolls, Colin
2018-05-14
We report the synthesis and characterization of a chiral, shape-persistent, perylene-diimide-based nanoribbon. Specifically, the fusion of three perylene-diimide monomers with intervening naphthalene subunits resulted in a helical superstructure with two [6]helicene subcomponents. This π-helix-of-helicenes exhibits very intense electronic circular dichroism, including one of the largest Cotton effects ever observed in the visible range. It also displays more than an order of magnitude increase in circular dichroism for select wavelengths relative to its smaller homologue. These impressive chiroptical properties underscore the potential of this new nanoribbon architecture in the context of chiral electronic materials.
DOE Office of Scientific and Technical Information (OSTI.GOV)
Takeichi, Yasuo, E-mail: yasuo.takeichi@kek.jp; Inami, Nobuhito; Ono, Kanta
We report the stability and recent performances of a new type of scanning transmission X-ray microscopy. The optics and compact design of the microscope realized mobility and robust performance. Detailed consideration to the vibration control will be described. The insertion device upgraded to elliptical polarization undulator enabled linear dichroism and circular dichroism experiments.
A Wideband Circularly Polarized Antenna with a Multiple-Circular-Sector Dielectric Resonator.
Trinh-Van, Son; Yang, Youngoo; Lee, Kang-Yoon; Hwang, Keum Cheol
2016-11-03
This paper presents the design of a wideband circularly polarized antenna using a multiple-circular-sector dielectric resonator (DR). The DR is composed of twelve circular-sector DRs with identical central angles of 30 ∘ but with different radii. A genetic algorithm is utilized to optimize the radii of the twelve circular-sector DRs to realize wideband circular polarization. The proposed antenna is excited using an aperture-coupled feeding technique through a narrow rectangular slot etched onto the ground plane. An antenna prototype is experimentally verified. The measured -10 dB reflection and 3 dB axial ratio (AR) bandwidths are 31.39% (1.88-2.58 GHz) and 19.30% (2.06-2.50 GHz), respectively, covering the operating bands of the following systems: UMTS-2100 (2.145 GHz), WiMAX (2.3 GHz), and Wi-Fi (2.445 GHz). A measured peak gain of 7.65 dBic at 2.225 GHz and gain variation of less than 2.70 dBic within the measured 3 dB AR bandwidth are achieved. In addition, the radiation patterns of the proposed antenna are presented and discussed.
A Wideband Circularly Polarized Antenna with a Multiple-Circular-Sector Dielectric Resonator
Trinh-Van, Son; Yang, Youngoo; Lee, Kang-Yoon; Hwang, Keum Cheol
2016-01-01
This paper presents the design of a wideband circularly polarized antenna using a multiple-circular-sector dielectric resonator (DR). The DR is composed of twelve circular-sector DRs with identical central angles of 30∘ but with different radii. A genetic algorithm is utilized to optimize the radii of the twelve circular-sector DRs to realize wideband circular polarization. The proposed antenna is excited using an aperture-coupled feeding technique through a narrow rectangular slot etched onto the ground plane. An antenna prototype is experimentally verified. The measured −10 dB reflection and 3 dB axial ratio (AR) bandwidths are 31.39% (1.88–2.58 GHz) and 19.30% (2.06–2.50 GHz), respectively, covering the operating bands of the following systems: UMTS-2100 (2.145 GHz), WiMAX (2.3 GHz), and Wi-Fi (2.445 GHz). A measured peak gain of 7.65 dBic at 2.225 GHz and gain variation of less than 2.70 dBic within the measured 3 dB AR bandwidth are achieved. In addition, the radiation patterns of the proposed antenna are presented and discussed. PMID:27827881
Investigation on chlorosomal antenna geometries: tube, lamella and spiral-type self-aggregates.
Linnanto, Juha M; Korppi-Tommola, Jouko E I
2008-06-01
Molecular mechanics calculations and exciton theory have been used to study pigment organization in chlorosomes of green bacteria. Single and double rod, multiple concentric rod, lamella, and Archimedean spiral macrostructures of bacteriochlorophyll c molecules were created and their spectral properties evaluated. The effects of length, width, diameter, and curvature of the macrostructures as well as orientations of monomeric transition dipole moment vectors on the spectral properties of the aggregates were studied. Calculated absorption, linear dichroism, and polarization dependent fluorescence-excitation spectra of the studied long macrostructures were practically identical, but circular dichroism spectra turned out to be very sensitive to geometry and monomeric transition dipole moment orientations of the aggregates. The simulations for long multiple rod and spiral-type macrostructures, observed in recent high-resolution electron microscopy images (Oostergetel et al., FEBS Lett 581:5435-5439, 2007) gave shapes of circular dichroism spectra observed experimentally for chlorosomes. It was shown that the ratio of total circular dichroism intensity to integrated absorption of the Q(y) transition is a good measure of degree of tubular structures in the chlorosomes. Calculations suggest that the broad Q(y) line width of chlorosomes of sulfur bacteria could be due to (1) different orientations of the transition moment vectors in multi-walled rod structures or (2) a variety of Bchl-aggregate structures in the chlorosomes.
Circular RNAs are abundant, conserved, and associated with ALU repeats
Jeck, William R.; Sorrentino, Jessica A.; Wang, Kai; Slevin, Michael K.; Burd, Christin E.; Liu, Jinze; Marzluff, William F.; Sharpless, Norman E.
2013-01-01
Circular RNAs composed of exonic sequence have been described in a small number of genes. Thought to result from splicing errors, circular RNA species possess no known function. To delineate the universe of endogenous circular RNAs, we performed high-throughput sequencing (RNA-seq) of libraries prepared from ribosome-depleted RNA with or without digestion with the RNA exonuclease, RNase R. We identified >25,000 distinct RNA species in human fibroblasts that contained non-colinear exons (a “backsplice”) and were reproducibly enriched by exonuclease degradation of linear RNA. These RNAs were validated as circular RNA (ecircRNA), rather than linear RNA, and were more stable than associated linear mRNAs in vivo. In some cases, the abundance of circular molecules exceeded that of associated linear mRNA by >10-fold. By conservative estimate, we identified ecircRNAs from 14.4% of actively transcribed genes in human fibroblasts. Application of this method to murine testis RNA identified 69 ecircRNAs in precisely orthologous locations to human circular RNAs. Of note, paralogous kinases HIPK2 and HIPK3 produce abundant ecircRNA from their second exon in both humans and mice. Though HIPK3 circular RNAs contain an AUG translation start, it and other ecircRNAs were not bound to ribosomes. Circular RNAs could be degraded by siRNAs and, therefore, may act as competing endogenous RNAs. Bioinformatic analysis revealed shared features of circularized exons, including long bordering introns that contained complementary ALU repeats. These data show that ecircRNAs are abundant, stable, conserved and nonrandom products of RNA splicing that could be involved in control of gene expression. PMID:23249747
Takeoka, Yuko; Saito, Fumihiko; Rikukawa, Masahiro
2013-07-09
Regioregular polythiophenes containing an optically active substituent in the third position of the thiophene ring, head-to-tail poly(3-[2-((S)-1-methyloctyloxy)ethyl]thiophene)s (HT-P(S)MOETs), were synthesized using highly reactive zinc. For comparison, HT-P(R)MOET and achiral HT-P(±)MOET also were synthesized from R-type monomers and racemic monomers, respectively. The HT-PMOET possessed greater than 95% head-to-tail coupling with a weight-average molecular weight (Mw) between 1.96 × 10(4) and 2.94 × 10(4). The polymers were characterized using (1)H and (13)C NMR, optical rotatory power measurements, circular dichroism (CD), and UV-vis spectroscopy. X-ray diffraction patterns of the cast films demonstrated that regioregular HT-PMOET possessed a strong tendency to self-assemble into highly ordered, crystalline structures. The HT-P(S)MOET and HT-P(R)MOET showed strong Cotton effects, while HT-P(±)MOET showed very weak Cotton effects. The presence of a circular dichroism effect indicated that the side chain chirality induced optical activity in poly(thiophene) main chains. The monolayer formation of HT-PMOET spread on the water surface was characterized using a pressure-area (π-A) isotherm. The molecular areas of HT-P(S)MOET and HT-P(R)MOET molecules on the water surface were 33.5 and 32.9 Å(2), respectively, at 10 °C, which were larger than that of HT-P(±)MOET (27.9 Å(2)), suggesting that optically active HT-PMOET expanded because of the chiral repulsion between side chains. Multilayer films of HT-PMOET were prepared by repeating horizontal deposition of the monolayer on the water surface. The multilayer films of optically active HT-PMOET obtained showed stronger Cotton effects than did the cast films. In addition, electrical conductivities of HT-PMOET multilayer films were superior to those of spin-coated films. Head-to-tail poly(3-[2-((S)-1-methylpropyloxy)ethyl]thiophene) (HT-P(S)MPET), which contained shorter side chain lengths compared to HT
NASA Astrophysics Data System (ADS)
Sharma, Bhagwati; Mandani, Sonam; Sarma, Tridib K.
2015-01-01
Pepsin, a digestive protease enzyme, could function as a reducing as well as stabilizing agent for the synthesis of Au nanostructures of various size and shape under different reaction conditions. The simple tuning of the pH of the reaction medium led to the formation of spherical Au nanoparticles, anisotropic Au nanostructures such as triangles, hexagons, etc., as well as ultra small fluorescent Au nanoclusters. The activity of the enzyme was significantly inhibited after its participation in the formation of Au nanoparticles due to conformational changes in the native structure of the enzyme which was studied by fluorescence, circular dichroism (CD), and infra red spectroscopy. However, the Au nanoparticle-enzyme composites served as excellent catalyst for the reduction of p-nitrophenol and resazurin, with the catalytic activity varying with size and shape of the nanoparticles. The presence of pepsin as the surface stabilizer played a crucial role in the activity of the Au nanoparticles as reduction catalysts, as the approach of the reacting molecules to the nanoparticle surface was actively controlled by the stabilizing enzyme.
Srinivasan, Anandi; Cortijo, Miguel; Bulicanu, Vladimir; Naim, Ahmad; Clérac, Rodolphe; Rogalev, Andrei; Wilhelm, Fabrice; Rosa, Patrick
2017-01-01
A simple procedure based on anion exchange was employed for the enantiomeric resolution of the extended metal atom chain (EMAC) [Co3(dpa)4(MeCN)2]2+. Use of the chiral salt (NBu4)2[As2(tartrate)2], (Λ-1 or Δ-1), resulted in the selective crystallization of the EMAC enantiomers as [Δ-Co3(dpa)4(MeCN)2](NBu4)2[Λ-As2(tartarte)2]2, (Δ-2) and [Λ-Co3(dpa)4(MeCN)2](NBu4)2[Δ-As2(tartrate)2]2 (Λ-2), respectively, in the P4212 space group, whereas a racemic mixture of 1 yielded [Co3(dpa)4(MeCN)2][As2(tartrate)2]·2MeCN (rac-3), which crystallized in the C2/c space group. The local electronic and magnetic structure of the EMAC enantiomers was studied, exploiting a variety of dichroisms in single crystals. A strong linear dichroism at the Co K-edge was observed in the orthoaxial configuration, whereas it vanished in the axial orientation, thus spectroscopically confirming the D4 crystal symmetry. Compounds Δ-2 and Λ-2 are shown to be enantiopure materials as evidenced by mirror-image natural circular dichroism spectra in the UV/vis in solution and in the X-ray range at the Co K-edge in single crystals. The surprising absence of detectable X-ray magnetic circular dichroism or X-ray magnetochiral dichroism signals at the Co K-edge, even at low temperature (3 K) and a high magnetic field (17 T), is ascribed to a strongly delocalized spin density on the tricobalt core. PMID:29675158
NASA Astrophysics Data System (ADS)
Hu, Linzhen; Zhu, Hucheng; Li, Lei; Huang, Jinfeng; Sun, Weiguang; Liu, Junjun; Li, Hua; Luo, Zengwei; Wang, Jianping; Xue, Yongbo; Zhang, Yu; Zhang, Yonghui
2016-06-01
Two pairs of new enantiomers with unusual 5,5-spiroketal cores, termed (±)-japonones A and B [(±)-1 and (±)-2], were obtained from Hypericum japonicum Thunb. The absolute configurations of (±)-1 and (±)-2 were characterized by extensive analyses of spectroscopic data and calculated electronic circular dichroism (ECD) spectra, the application of modified Mosher’s methods, and the assistance of quantum chemical predictions (QCP) of 13C NMR chemical shifts. Among these metabolites, (+)-1 exhibited some inhibitory activity on Kaposi’s sarcoma associated herpesvirus (KSHV). Virtual screening of (±)-1 and (±)-2 were conducted using the Surflex-Dock module in the Sybyl software, and (+)-1 exhibited ability to bind with ERK to form key interactions with residues Lys52, Pro56, Ile101, Asp165, Gly167 and Val99.
NASA Astrophysics Data System (ADS)
Maji, Anukul; Beg, Maidul; Mandal, Amit Kumar; Das, Somnath; Jha, Pradeep K.; Kumar, Anoop; Sarwar, Shamila; Hossain, Maidul; Chakrabarti, Pinak
2017-08-01
This study looks into a safe, proficient and low-cost way for the preparation of novel silver nanoparticles by using 5% aqueous leaves extract of a medicinal plant, Marsilea quadrifolia (family: Marsileaceae) without using any external reducing and stabilizing agents. The synthesized AgNPs showed maximum UV-Vis absorbance at 435 nm due to surface plasmon resonance (SPR). The average diameter (∼22.5 nm) of AgNPs was measured from TEM analysis and was also supported by FE-SEM. The existence of a silver signal in EDX spectra supported the AgNPs formation and negative zeta potential value (-18.7 mV) which suggested its stability. FT-IR spectroscopic analysis showed that the functional groups like sbnd Osbnd H, sbnd Nsbnd H and sbnd Cdbnd O were responsible for the synthesis of AgNPs. The antibacterial activity of the AgNPs was tested against E. coli ATCC 25922. The anticancer potential of AgNPs was also assessed using two different cell lines, such as MCF-7 and HeLa. The interaction study of AgNPs with human serum albumin (HSA) and human hemoglobin (Hb) was performed by means of UV-Vis, fluorescence spectroscopy, Circular dichroism (CD) and zeta potential measurement. More negative zeta potential values of AgNPs-HSA/Hb (-21.1/-19.5 mV) complexes than AgNPs (-18.7 mV) indicated corresponding stability of bio-conjugates. The basic structure of HSA/Hb remained unchanged and its secondary structure was slightly changed upon interaction with the AgNPs concluded from Circular dichroism. So, it can be predicted that this AgNPs may be applied in the medical field.
Li, Jing; Zhong, Yi-sheng; Yuan, Jie; Zhu, Xun; Lu, Yong-jun; Lin, Yong-cheng; Liu, Lan
2015-09-01
A new benzodiazepine alkaloid containing terminal cyano group has been isolated from a mangrove endophytic fungus, Penicillium 299#. Structure elucidation was determined by 1D and 2D NMR spectroscopy and the absolute configuration was determined by electronic circular dichroism (ECD). The new compound showed no cytotoxic activities in vitro against human cancer lines MDA-MB-435, HepG2, HCT-116, and Calu-3.
FUCHS-towards full circular RNA characterization using RNAseq.
Metge, Franziska; Czaja-Hasse, Lisa F; Reinhardt, Richard; Dieterich, Chistoph
2017-01-01
Circular RNAs (circRNAs) belong to a recently re-discovered species of RNA that emerge during RNA maturation through a process called back-splicing. A downstream 5' splice site is linked to an upstream 3' splice site to form a circular transcript instead of a canonical linear transcript. Recent advances in next-generation sequencing (NGS) have brought circRNAs back into the focus of many scientists. Since then, several studies reported that circRNAs are differentially expressed across tissue types and developmental stages, implying that they are actively regulated and not merely a by-product of splicing. Though functional studies have shown that some circRNAs could act as miRNA-sponges, the function of most circRNAs remains unknown. To expand our understanding of possible roles of circular RNAs, we propose a new pipeline that could fully characterizes candidate circRNA structure from RNAseq data-FUCHS: FU ll CH aracterization of circular RNA using RNA- S equencing. Currently, most computational prediction pipelines use back-spliced reads to identify circular RNAs. FUCHS extends this concept by considering all RNA-seq information from long reads (typically >150 bp) to learn more about the exon coverage, the number of double break point fragments, the different circular isoforms arising from one host-gene, and the alternatively spliced exons within the same circRNA boundaries. This new knowledge will enable the user to carry out differential motif enrichment and miRNA seed analysis to determine potential regulators during circRNA biogenesis. FUCHS is an easy-to-use Python based pipeline that contributes a new aspect to the circRNA research.
Circular states of atomic hydrogen
DOE Office of Scientific and Technical Information (OSTI.GOV)
Lutwak, R.; Holley, J.; Chang, P.P.
1997-08-01
We describe the creation of circular states of hydrogen by adiabatic transfer of a Rydberg state in crossed electric and magnetic fields, and also by adiabatic passage in a rotating microwave field. The latter method permits rapid switching between the two circular states of a given n manifold. The two methods are demonstrated experimentally, and results are presented of an analysis of the field ionization properties of the circular states. An application for the circular states is illustrated by millimeter-wave resonance in hydrogen of the n=29{r_arrow}n=30 transition. {copyright} {ital 1997} {ital The American Physical Society}
NASA Astrophysics Data System (ADS)
Gelikonov, V. M.; Romashov, V. N.; Shabanov, D. V.; Ksenofontov, S. Yu.; Terpelov, D. A.; Shilyagin, P. A.; Gelikonov, G. V.; Vitkin, I. A.
2018-05-01
We consider a cross-polarization optical coherence tomography system with a common path for the sounding and reference waves and active maintenance of the circular polarization of a sounding wave. The system is based on the formation of birefringent characteristics of the total optical path, which are equivalent to a quarter-wave plate with a 45° orientation of its optical axes with respect to the linearly polarized reference wave. Conditions under which any light-polarization state can be obtained using a two-element phase controller are obtained. The dependence of the local cross-scattering coefficient of light in a model medium and biological tissue on the sounding-wave polarization state is demonstrated. The necessity of active maintenance of the circular polarization of a sounding wave in this common path system (including a flexible probe) is shown to realize uniform optimal conditions for cross-polarization studies of biological tissue.
Circular chemiresistors for microchemical sensors
Ho, Clifford K [Albuquerque, NM
2007-03-13
A circular chemiresistor for use in microchemical sensors. A pair of electrodes is fabricated on an electrically insulating substrate. The pattern of electrodes is arranged in a circle-filling geometry, such as a concentric, dual-track spiral design, or a circular interdigitated design. A drop of a chemically sensitive polymer (i.e., chemiresistive ink) is deposited on the insulating substrate on the electrodes, which spreads out into a thin, circular disk contacting the pair of electrodes. This circularly-shaped electrode geometry maximizes the contact area between the pair of electrodes and the polymer deposit, which provides a lower and more stable baseline resistance than with linear-trace designs. The circularly-shaped electrode pattern also serves to minimize batch-to-batch variations in the baseline resistance due to non-uniform distributions of conductive particles in the chemiresistive polymer film.
Circular polarization of twilight.
NASA Technical Reports Server (NTRS)
Angel, J. R. P.; Illing, R.; Martin, P. G.
1972-01-01
Review of observations of circular polarization of twilight performed with a polarimeter which uses an electronically switched Pockels cell operated as a reversible quarter-wave plate to convert circular into linear polarization. The latter was then analyzed by a Wollaston prism followed by two gallium-arsenide photomultipliers. The discovery of a definite natural circular polarization at twilight does suggest that, with increased observation precision, measurements of the small daylight component are possible. These could give useful information about particles in the atmosphere and be valuable in studies of meteorology and air pollution.
NASA Astrophysics Data System (ADS)
Petronijevic, E.; Leahu, G.; Belardini, A.; Centini, M.; Li Voti, R.; Hakkarainen, T.; Koivusalo, E.; Rizzo Piton, M.; Suomalainen, S.; Guina, M.; Sibilia, C.
2018-04-01
We report on the extrinsic chirality behavior of GaAs-based NWs asymmetrically hybridized with Au. The samples are fabricated by a recently developed, lithography-free self-organized GaAs growth, with the addition of AlGaAs shell and GaAs supershell. The angled Au flux is then used to cover three-out-of-six sidewalls with a thin layer of Au. Oblique incidence and proper sample orientation can lead to circular dichroism. We characterize this chiral behavior at 532 {nm} and 980 {nm} by means of photo-acoustic spectroscopy, which directly measures the difference in absorption for the circularly polarized light of the opposite headedness. For the first time to our knowledge, circular dichroism is observed in both the amplitude and the phase of the photo-acoustic signal. We strongly believe that such samples can be used for chiral applications, spanning from circularly polarized light emission, to the enantioselectivity applications.
Belardini, Alessandro; Centini, Marco; Leahu, Grigore; Hooper, David C.; Li Voti, Roberto; Fazio, Eugenio; Haus, Joseph W.; Sarangan, Andrew; Valev, Ventsislav K.; Sibilia, Concita
2016-01-01
Extrinsic or pseudo-chiral (meta)surfaces have an achiral structure, yet they can give rise to circular dichroism when the experiment itself becomes chiral. Although these surfaces are known to yield differences in reflected and transmitted circularly polarized light, the exact mechanism of the interaction has never been directly demonstrated. Here we present a comprehensive linear and nonlinear optical investigation of a metasurface composed of tilted gold nanowires. In the linear regime, we directly demonstrate the selective absorption of circularly polarised light depending on the orientation of the metasurface. In the nonlinear regime, we demonstrate for the first time how second harmonic generation circular dichroism in such extrinsic/pseudo-chiral materials can be understood in terms of effective nonlinear susceptibility tensor elements that switch sign depending on the orientation of the metasurface. By providing fundamental understanding of the chiroptical interactions in achiral metasurfaces, our work opens up new perspectives for the optimisation of their properties. PMID:27553888
Circularly Polarized Luminescence from Simple Organic Molecules.
Sánchez-Carnerero, Esther M; Agarrabeitia, Antonia R; Moreno, Florencio; Maroto, Beatriz L; Muller, Gilles; Ortiz, María J; de la Moya, Santiago
2015-09-21
This article aims to show the identity of "circularly polarized luminescent active simple organic molecules" as a new concept in organic chemistry due to the potential interest of these molecules, as availed by the exponentially growing number of research articles related to them. In particular, it describes and highlights the interest and difficulty in developing chiral simple (small and non-aggregated) organic molecules able to emit left- or right-circularly polarized light efficiently, the efforts realized up to now to reach this challenging objective, and the most significant milestones achieved to date. General guidelines for the preparation of these interesting molecules are also presented. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Kudryashova, Elena V; Artemova, Tatiana M; Vinogradov, Alexei A; Gladilin, Alexander K; Mozhaev, Vadim V; Levashov, Andrey V
2003-04-01
Formation of enzyme-oligoamine complexes was suggested as an approach to obtain biocatalysts with enhanced resistance towards inactivation in water-organic media. Complex formation results in broadening (by 20-40% v/v ethanol) of the range of cosolvent concentrations where the enzyme retains its catalytic activity (stabilization effect). At moderate cosolvent concentrations (20-40% v/v) complex formation activates the enzyme (by 3-6 times). The magnitude of activation and stabilization effects increases with the number of possible electrostatic contacts between the protein surface and the molecules of oligoamines (OA). Circular dichroism spectra in the far-UV region show that complex formation stabilizes protein conformation and prevents aggregation in water-organic solvent mixtures. Two populations of the complexes with different thermodynamic stabilities were found in alpha-chymotrypsin (CT)-OA systems depending on the CT/OA ratio. The average dissociation constants and stoichiometries of both low- and high-affinity populations of the complexes were estimated. It appears that it is the low-affinity sites on the CT surface that are responsible for the activation effect.
Chionis, Kostas; Krikorian, Dimitrios; Koukkou, Anna-Irini; Sakarellos-Daitsiotis, Maria; Panou-Pomonis, Eugenia
2016-11-01
Anoplin is a short natural cationic antimicrobial peptide which is derived from the venom sac of the solitary wasp, Anoplius samariensis. Due to its short sequence G 1 LLKR 5 IKT 8 LL-NH 2 , it is ideal for research tests. In this study, novel analogs of anoplin were prepared and examined for their antimicrobial, hemolytic activity, and proteolytic stability. Specific substitutions were introduced in amino acids Gly 1 , Arg 5 , and Thr 8 and lipophilic groups with different lengths in the N-terminus in order to investigate how these modifications affect their antimicrobial activity. These cationic analogs exhibited higher antimicrobial activity than the native peptide; they are also nontoxic at their minimum inhibitory concentration (MIC) values and resistant to enzymatic degradation. The substituted peptide GLLKF 5 IKK 8 LL-NH 2 exhibited high activity against Gram-negative bacterium Zymomonas mobilis (MIC = 7 µg/ml), and the insertion of octanoic, decanoic, and dodecanoic acid residues in its N-terminus increased the antimicrobial activity against Gram-positive and Gram-negative bacteria (MIC = 5 µg/ml). The conformational characteristics of the peptide analogs were studied by circular dichroism. Structure activity studies revealed that the substitution of specific amino acids and the incorporation of lipophilic groups enhanced the amphipathic α-helical conformation inducing better antimicrobial effects. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.
Inhibition of cathelicidin activity by bacterial exopolysaccharides.
Foschiatti, Michela; Cescutti, Paola; Tossi, Alessandro; Rizzo, Roberto
2009-06-01
The interaction of bacterial exopolysaccharides, produced by opportunistic lung pathogens, with antimicrobial peptides of the innate primate immune system was investigated. The exopolysaccharides were produced by Pseudomonas aeruginosa, Inquilinus limosus and clinical isolates of the Burkholderia cepacia complex, bacteria that are all involved in lung infections of cystic fibrosis patients. The effects of the biological activities of three orthologous cathelicidins from Homo sapiens sapiens, Pongo pygmaeus (orangutan) and Presbitys obscurus (dusky leaf monkey) were examined. Inhibition of the antimicrobial activity of peptides was assessed using minimum inhibitory concentration assays on a reference Escherichia coli strain in the presence and absence of exopolysaccharides, whereas complex formation between peptides and exopolysaccharides was investigated by means of circular dichroism, fluorescence spectroscopy and atomic force microscopy. Biological assays revealed that the higher the negative charge of exopolysaccharides the stronger was their inhibiting effect. Spectroscopic studies indicated the formation of molecular complexes of varying stability between peptides and exopolysaccharides, explaining the inhibition. Atomic force microscopy provided a direct visualization of the molecular complexes. A model is proposed where peptides with an alpha-helical conformation interact with exopolysaccharides through electrostatic and other non-covalent interactions.
Palermo, Nicholas Y; Thomas, Peter; Murphy, Richard F; Lovas, Sándor
2012-04-01
Colorectal cancers with metastatic potential secrete the glycoprotein carcinoembryonic antigen (CEA). CEA has been implicated in colorectal cancer metastasis by inducing Kupffer cells to produce inflammatory cytokines which, in turn, make the hepatic micro-environment ideal for tumor cell implantation. CEA binds to the heterogeneous ribonucleoprotein M (hnRNP M) which acts as a cell surface receptor in Kupffer cells. The amino acid sequence in CEA, which binds the hnRNP M receptor, is Tyr-Pro-Glu-Leu-Pro-Lys. In this study, the structure of Ac-Tyr-Pro-Glu-Leu-Pro-Lys-NH₂ (YPELPK) was investigated using electronic circular dichroism, vibrational circular dichroism, and molecular dynamics simulations. The binding of the peptide to hnRNP M was also investigated using molecular docking calculations. The biological activity of YPELPK was studied using differentiated human THP-1 cells, which express hnRNP M on their surface and secrete IL-6 when stimulated by CEA. YPELPK forms a stable polyproline-II helix and stimulates IL-6 production of THP-1 cells at micromolar concentrations. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.
de Melo, Edinara Targino; Estrela, Andréia Bergamo; Santos, Elizabeth Cristina Gomes; Machado, Paula Renata Lima; Farias, Kleber Juvenal Silva; Torres, Taffarel Melo; Carvalho, Enéas; Lima, João Paulo Matos Santos; Silva-Júnior, Arnóbio Antonio; Barbosa, Euzébio Guimarães; Fernandes-Pedrosa, Matheus de Freitas
2015-06-01
A new antimicrobial peptide, herein named Stigmurin, was selected based on a transcriptomic analysis of the Brazilian yellow scorpion Tityus stigmurus venom gland, an underexplored source for toxic peptides with possible biotechnological applications. Stigmurin was investigated in silico, by circular dichroism (CD) spectroscopy, and in vitro. The CD spectra suggested that this peptide interacts with membranes, changing its conformation in the presence of an amphipathic environment, with predominance of random coil and beta-sheet structures. Stigmurin exhibited antibacterial and antifungal activity, with minimal inhibitory concentrations ranging from 8.7 to 69.5μM. It was also showed that Stigmurin is toxic against SiHa and Vero E6 cell lines. The results suggest that Stigmurin can be considered a potential anti-infective drug. Copyright © 2015 Elsevier Inc. All rights reserved.
Ali, Abid; Azam, Mohd W; Khan, Asad U
2018-06-01
New Delhi metallo β-lactamase-1 is one of the carbapenemases, causing hydrolysis of almost all β-lactamase antibiotics. Seventeen different NDM variants have been reported so far, they varied in their sequences either by single or multiple amino acid substitutions. Hence, it is important to understand its structural and functional relation. In the earlier studies role of active site residues has been studied but non-active site residues has not studied in detail. Therefore, we have initiated to further comprehend its structure and function relation by mutating some of its non-active site residues. A laboratory mutant of NDM-1 was generated by PCR-based site-directed mutagenesis, replacing Q to A at 123 position. The MICs of imipenem and meropenem for NDM-1 Q123A were found increased by 2 fold as compare to wild type and so the hydrolytic activity was enhanced (Kcat/Km) as compared to NDM-1 wild type. GOLD fitness scores were also found in favour of kinetics data. Secondary structure for α-helical content was determined by Far-UV circular dichroism (CD), which showed significant conformational changes. We conclude a noteworthy role of non-active-site amino acid residues in the catalytic activity of NDM-1. This study also provides an insight of emergence of new variants through natural evolution. Copyright © 2018 Elsevier B.V. All rights reserved.
Activity Enhancement of G-Quadruplex/Hemin DNAzyme by Flanking d(CCC).
Chang, Tianjun; Gong, Hongmei; Ding, Pi; Liu, Xiangjun; Li, Weiguo; Bing, Tao; Cao, Zehui; Shangguan, Dihua
2016-03-14
G-quadruplex (G4)/hemin DNAzymes have been extensively applied in bioanalysis and molecular devices. However, their catalytic activity is still much lower than that of proteinous enzymes. The G4/hemin DNAzyme activity is correlated with the G4 conformations and the solution conditions. However, little is known about the effect of the flanking sequences on the activity, though they are important parts of G4s. Here, we report sequences containing d(CCC), flanked on both ends of the G4-core sequences remarkably enhance their DNAzyme activity. By using circular dichroism and UV-visible spectroscopy, the d(CCC) flanking sequences were demonstrated to improve the hemin binding affinity to G4s instead of increasing the parallel G4 formation, which might explain the enhanced DNAzyme activity. Meanwhile, the increased hemin binding ability promoted the degradation of hemin within the DNAzyme by H2O2. Furthermore, the DNAzyme with d(CCC) flanking sequences showed strong tolerance to pH value changes, which makes it more suitable for applications requiring wide pH conditions. The results highlight the influence of the flanking sequences on the DNAzyme activity and provide insightful information for the design of highly active DNAzymes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Zhang, Wei; Zhang, Jing; Fang, Leiping; Zhou, Ling; Wang, Shuai; Xiang, Zhijun; Li, Yuan; Wisely, Bruce; Zhang, Guifeng; An, Gang; Wang, Yonghui; Leung, Stewart; Zhong, Zhong
2012-10-01
In a screen for small-molecule inhibitors of retinoid acid-related orphan receptor γ (RORγ), we fortuitously discovered that a class of aryl amide compounds behaved as functional activators of the interleukin 17 (IL-17) reporter in Jurkat cells. Three of these compounds were selected for further analysis and found to activate the IL-17 reporter with potencies of ∼0.1 μM measured by EC₅₀. These compounds were shown to directly bind to RORγ by circular dichroism-based thermal stability experiments. Furthermore, they can enhance an in vitro Th17 differentiation process in human primary T cells. As RORγ remains an orphan nuclear receptor, discovery of these aryl amide compounds as functional agonists will now provide pharmacological tools for us to dissect functions of RORγ and facilitate drug discovery efforts for immune-modulating therapies.
Knee arthrodesis with circular external fixation.
Garberina, M J; Fitch, R D; Hoffmann, E D; Hardaker, W T; Vail, T P; Scully, S P
2001-01-01
Knee arthrodesis can enable limb salvage in patients with disability secondary to trauma, infected total knee arthroplasty, pyarthrosis, and other complications. Historically, intramedullary nailing has resulted in the highest overall knee fusion rates. However, intramedullary nailing is relatively contraindicated in the presence of active infection. Nineteen patients who underwent knee arthrodesis with circular external fixation were studied retrospectively. Postoperative radiographs were evaluated for evidence of bony fusion, which was defined as trabecular bridging between the femur and tibia. Patients were interviewed and graded using the functional assessment portion of the Knee Society clinical rating system. Fusion was successful in 13 of 19 (68%) patients. Overall, patients spent an average of 4 months 8 days wearing the circular external fixator. Average time to radiographic and clinical evidence of arthrodesis (defined as lack of motion across the fusion site) was 4 months 18 days. No patient with successful fusion considered himself or herself housebound. All but one of these patients require some form of assistive device for ambulation. Complications occurred in 16 of 19 (84%) patients overall. Superficial pin tract infection (55%) and nonunion (32%) were the most common. Circular external fixation is an effective method for obtaining knee arthrodesis in patients who are not good candidates for intramedullary nailing.
Zhou, Le; Wang, Jie; Guo, Rui; Lin, Bin; Wang, Xiao-Bo; Huang, Xiao-Xiao; Song, Shao-Jiang
2018-05-30
Four new dihydrobenzofuran neolignans 1a/1b and 2a/2b were isolated from the fruit of Rubus ideaus. 1a/1b and 2a/2b as two pairs of enantiomers were separated on a chiral chromatographic column. Their structures were determined using a suite of techniques including 1D and 2D NMR, HRESIMS, together with theoretical electronic circular dichroism (ECD) calculation. All compounds were evaluated for their inhibition of self-induced Aβ 1-42 aggregation. Compounds 1b and 2a exhibited optimal Aβ 1-42 aggregation inhibition capability, with an inhibition potency of 81.6% and 83.4% at 20 μM, respectively. Additionally, molecular docking was performed to identify the possible factor responsible for the enantioselectivity in the anti-Aβ 1-42 aggregation activity. Copyright © 2018 Elsevier Inc. All rights reserved.
5 CFR 1310.3 - Availability of circulars.
Code of Federal Regulations, 2010 CFR
2010-01-01
... 5 Administrative Personnel 3 2010-01-01 2010-01-01 false Availability of circulars. 1310.3 Section 1310.3 Administrative Personnel OFFICE OF MANAGEMENT AND BUDGET OMB DIRECTIVES OMB CIRCULARS § 1310.3 Availability of circulars. Copies of individual circulars are available at OMB's Internet home page; you may...
Chen, Tuo; He, Sailing
2014-08-11
Manipulating the circular polarization of light is of great importance in chemistry and biology, as chiral molecules exhibit different physiological properties when exposed to different circularly polarized waves. Here we suggest a graphene/dielectric-stacked structure, which has both the properties of an epsilon-near-zero material and the high Hall conductivity of graphene. The proposed sub-wavelength structure demonstrates efficient manipulation of circular polarization properties of light. In a quite broad frequency range and at a large oblique incidence angle, the present magnetically active structure is transparent for one circularly polarized wave, and opaque for another. Such an effect can be further tuned by changing the magnitude of the applied magnetic field and chemical potential of graphene.
21 CFR 606.122 - Instruction circular.
Code of Federal Regulations, 2010 CFR
2010-04-01
... instruction circular shall contain: (1) Instructions to administer a suitable plasma volume expander if Red... circular shall contain: (1) The approximate volume of plasma from which a sample unit of Platelets is... entering the container. (m) For Plasma, the instruction circular shall contain: (1) A warning against...
21 CFR 606.122 - Instruction circular.
Code of Federal Regulations, 2011 CFR
2011-04-01
... instruction circular shall contain: (1) Instructions to administer a suitable plasma volume expander if Red... circular shall contain: (1) The approximate volume of plasma from which a sample unit of Platelets is... entering the container. (m) For Plasma, the instruction circular shall contain: (1) A warning against...
Choong, Oi Kuan; Tejo, Bimo Ario; Omar, Abdul Rahman
2014-01-01
Feline Infectious Peritonitis (FIP) is a severe fatal immune-augmented disease in cat population. It is caused by FIP virus (FIPV), a virulent mutant strain of Feline Enteric Coronavirus (FECV). Current treatments and prophylactics are not effective. The in vitro antiviral properties of five circular Triple-Helix Forming Oligonucleotide (TFO) RNAs (TFO1 to TFO5), which target the different regions of virulent feline coronavirus (FCoV) strain FIPV WSU 79-1146 genome, were tested in FIPV-infected Crandell-Rees Feline Kidney (CRFK) cells. RT-qPCR results showed that the circular TFO RNAs, except TFO2, inhibit FIPV replication, where the viral genome copy numbers decreased significantly by 5-fold log10 from 1014 in the virus-inoculated cells to 109 in the circular TFO RNAs-transfected cells. Furthermore, the binding of the circular TFO RNA with the targeted viral genome segment was also confirmed using electrophoretic mobility shift assay. The strength of binding kinetics between the TFO RNAs and their target regions was demonstrated by NanoITC assay. In conclusion, the circular TFOs have the potential to be further developed as antiviral agents against FIPV infection. PMID:24707494
Amylocyclicin, a Novel Circular Bacteriocin Produced by Bacillus amyloliquefaciens FZB42
Scholz, Romy; Vater, Joachim; Budiharjo, Anto; Wang, Zhiyuan; He, Yueqiu; Dietel, Kristin; Schwecke, Torsten; Herfort, Stefanie; Lasch, Peter
2014-01-01
Bacillus amyloliquefaciens FZB42 is a Gram-positive plant growth-promoting bacterium with an impressive capacity to synthesize nonribosomal secondary metabolites with antimicrobial activity. Here we report on a novel circular bacteriocin which is ribosomally synthesized by FZB42. The compound displayed high antibacterial activity against closely related Gram-positive bacteria. Transposon mutagenesis and subsequent site-specific mutagenesis combined with matrix-assisted laser desorption ionization–time of flight mass spectroscopy revealed that a cluster of six genes covering 4,490 bp was responsible for the production, modification, and export of and immunity to an antibacterial compound, here designated amylocyclicin, with a molecular mass of 6,381 Da. Peptide sequencing of the fragments obtained after tryptic digestion of the purified peptide revealed posttranslational cleavage of an N-terminal extension and head-to-tail circularization of the novel bacteriocin. Homology to other putative circular bacteriocins in related bacteria let us assume that this type of peptide is widespread among the Bacillus/Paenibacillus taxon. PMID:24610713
High-throughput sequencing reveals circular substrates for an archaeal RNA ligase
Becker, Hubert F.; Héliou, Alice; Djaout, Kamel; Lestini, Roxane; Regnier, Mireille; Myllykallio, Hannu
2017-01-01
ABSTRACT It is only recently that the abundant presence of circular RNAs (circRNAs) in all kingdoms of Life, including the hyperthermophilic archaeon Pyrococcus abyssi, has emerged. This led us to investigate the physiologic significance of a previously observed weak intramolecular ligation activity of Pab1020 RNA ligase. Here we demonstrate that this enzyme, despite sharing significant sequence similarity with DNA ligases, is indeed an RNA-specific polynucleotide ligase efficiently acting on physiologically significant substrates. Using a combination of RNA immunoprecipitation assays and RNA-seq, our genome-wide studies revealed 133 individual circRNA loci in P. abyssi. The large majority of these loci interacted with Pab1020 in cells and circularization of selected C/D Box and 5S rRNA transcripts was confirmed biochemically. Altogether these studies revealed that Pab1020 is required for RNA circularization. Our results further suggest the functional speciation of an ancestral NTase domain and/or DNA ligase toward RNA ligase activity and prompt for further characterization of the widespread functions of circular RNAs in prokaryotes. Detailed insight into the cellular substrates of Pab1020 may facilitate the development of new biotechnological applications e.g. in ligation of preadenylated adaptors to RNA molecules. PMID:28277897
Optically active bis(β-diketonate) complexes of titanium.
Kongprakaiwoot, Natcharee; Armstrong, Jack B; Noll, Bruce C; Brown, Seth N
2010-11-14
The 2,2'-bis(methylene)biphenyl bridged bis(diketonate) (Tol(2)Bob)Ti(IV) fragment is resolved by reaction of the isopropoxide complex with (R)-1,1'-bi-2-naphthol, which selectively forms (S,Δ)-(Tol(2)Bob)Ti(R-BINOL). The binaphtholate ligand can be cleaved from titanium by careful treatment with trifluoromethanesulfonic acid to give (S,Δ)-(Tol(2)Bob)Ti(OTf)(2), which has a half-life toward racemization of at least 34 h at 51 °C. Racemization of the (Tol(2)Bob)Ti(IV) fragment is strongly accelerated under protic conditions, probably due to protonolysis of one of the diketonate ligands. Analogous optically active titanium bis(diketonates) can also be prepared by using an optically active 2,2'-bis(methylene)-1,1'-binaphthyl bridged bis(diketonate) ligand, Tol(2)Bobbinap, prepared from (R)-BINOLH2. Complexation of (R)-Tol(2)BobbinapH(2) with Ti(OiPr)(4) gives only a single diastereomer with the Λ configuration at titanium. The bis(diketonate)titanium(IV) fragment gives rise to characteristic signals in circular dichroism spectra which can be used to identify the configuration at the metal centre.
NASA Astrophysics Data System (ADS)
Fujimaki, Nobuhiro; Nishiya, Ken; Miura, Takashi; Nakabayashi, Takakazu
2016-11-01
The acquisition of pro-oxidant activity of the mutated form of human Cu, Zn-superoxide dismutase (SOD1) has been investigated to clarify the relationship between mutations in SOD1 and the pathogenesis of amyotrophic lateral sclerosis (ALS). Ala4 → Val (A4V) and Gly93 → Ala (G93A) mutants, which are representative ALS-linked SOD1 mutants, have been found to exhibit both the denaturation and the gain of pro-oxidant activity after incubation in the apo-form at a physiological condition of 37 °C and pH 7.4 and the rebinding of Cu2+. These characteristics are similar to those previously reported for the His43 → Arg (H43R) mutant. UV-resonance Raman spectra indicated that the coordination structure of the Cu-binding site catalyzing the oxidation reaction is the same among the denatured A4V, G93A, and H43R. Since wild-type SOD1 does not exhibit the denaturation in its apo-form at 37 °C and pH 7.4, the instability of the protein structure due to mutation can be considered as a significant factor that induces the denaturation and the subsequent pro-oxidant activity.
Unusual structural transition of antimicrobial VP1 peptide.
Shanmugam, Ganesh; Phambu, Nsoki; Polavarapu, Prasad L
2011-05-01
VP1 peptide, an active domain of m-calpain enzyme with antimicrobial activity is found to undergo an unusual conformational transition in trifluoroethanol (TFE) solvent. The nature of, and time dependent variations in, circular dichroism associated with the amide I vibrations, suggest that VP1 undergoes self-aggregation forming anti-parallel β-sheet structure in TFE. Transmission electron micrograph (TEM) images revealed that β-sheet aggregates formed by VP1 possess fibril-like assemblies. Copyright © 2011 Elsevier B.V. All rights reserved.
NASA Astrophysics Data System (ADS)
Abbasi, Shahryar; Khani, Hamzeh
2017-11-01
Herein, we demonstrated a simple and efficient method to detect Cu2 + based on amplified optical activity in the chiral nanoassemblies of gold nanorods (Au NRs). L-Cysteine can induce side-by-side or end-to-end assembly of Au NRs with an evident plasmonic circular dichroism (PCD) response due to coupling between surface plasmon resonances (SPR) of Au NRs and the chiral signal of L-Cys. Because of the obvious stronger plasmonic circular dichrosim (CD) response of the side-by-side assembly compared with the end-to-end assemblies, SS assembled Au NRs was selected as a sensitive platform and used for Cu2 + detection. In the presence of Cu2 +, Cu2 + can catalyze O2 oxidation of cysteine to cystine. With an increase in Cu2 + concentration, the L-Cysteine-mediated assembly of Au NRs decreased because of decrease in the free cysteine thiol groups, and the PCD signal decreased. Taking advantage of this method, Cu2 + could be detected in the concentration range of 20 pM-5 nM. Under optimal conditions, the calculated detection limit was found to be 7 pM.
Abbasi, Shahryar; Khani, Hamzeh
2017-11-05
Herein, we demonstrated a simple and efficient method to detect Cu 2+ based on amplified optical activity in the chiral nanoassemblies of gold nanorods (Au NRs). L-Cysteine can induce side-by-side or end-to-end assembly of Au NRs with an evident plasmonic circular dichroism (PCD) response due to coupling between surface plasmon resonances (SPR) of Au NRs and the chiral signal of L-Cys. Because of the obvious stronger plasmonic circular dichrosim (CD) response of the side-by-side assembly compared with the end-to-end assemblies, SS assembled Au NRs was selected as a sensitive platform and used for Cu 2+ detection. In the presence of Cu 2+ , Cu 2+ can catalyze O 2 oxidation of cysteine to cystine. With an increase in Cu 2+ concentration, the L-Cysteine-mediated assembly of Au NRs decreased because of decrease in the free cysteine thiol groups, and the PCD signal decreased. Taking advantage of this method, Cu 2+ could be detected in the concentration range of 20pM-5nM. Under optimal conditions, the calculated detection limit was found to be 7pM. Copyright © 2017 Elsevier B.V. All rights reserved.
Fujiki, Michiya; Kawagoe, Yoshifumi; Nakano, Yoko; Nakao, Ayako
2013-06-17
Solvent chirality transfer of (S)-/(R)-limonenes allows the instant generation of optically active PF8P2 aggregates with distinct circular dichroism (CD)/circularly polarized luminescence (CPL) amplitudes with a high quantum yield of 16-20%. The present paper also reports subtle mirror-symmetry-breaking effects in CD-/CPL-amplitude and sign, CD/UV-vis spectral wavelengths, and photodynamics of the aggregates, though the reasons for the anomaly are unsolved. However, these photophysical properties depend on (i) the chemical natures of chiral and achiral molecules when used in solvent quantity, (ii) clockwise and counterclockwise stirring operations, and (iii) the order of addition of limonene and methanol to the chloroform solution.
Qi, Qiu-Yue; Li, Er-Wei; Han, Jun-Jie; Pei, Yun-Fei; Ma, Ke; Bao, Li; Huang, Ying; Zhao, Feng; Liu, Hong-Wei
2015-05-19
Four new ambuic acid derivatives (1-4), and four known derivatives (5-8), were isolated from the solid culture of a plant pathogenic fungus Pestalotiopsis neglecta. Their structures were elucidated by extensive NMR experiments. The absolute configuration of the C-16 secondary alcohol in 1 was deduced via the CD data of the in situ formed [Rh2(OCOCF3)4] complex with the acetonide derivative of 1. The absolute configuration in 3 was assigned by comparison of the experimental and simulated electronic circular dichroism (ECD) spectrum. The NMR data of compound 5 was reported for the first time. In the nitric oxide (NO) inhibition assay, compounds 4, 6 and 7 showed inhibitory activity against the NO production in the lipopolysaccharide (LPS)-induced macrophage with IC50 values of 88.66, 11.20, and 20.80 µM, respectively.
Instrumentation | Center for Cancer Research
Instrumentation [accordion collapsed] Circular Dichroism (CD) Spectroscopy Instrument: J-1500 CD Spectrophotometer (Jasco) Applications: Conformational analysis of biomolecules Protein thermal stability Binding studies Major Specifications:
Wang, Dong-Mei; Zhang, Cheng-Chen; Zhang, Qiang; Shafiq, Nusrat; Pescitelli, Gennaro; Li, Deng-Wu; Gao, Jin-Ming
2014-07-16
Five new sesquiterpene polyol esters with a dihydro-β-agarofuran skeleton, designated as wightianines A-E (1-5), besides two known compounds, were isolated from the methanolic extract of the whole plant of the traditional herbal medicine Parnassia wightiana Wall. The structures of the isolated compounds were elucidated on the basis of spectroscopic analyses, including two-dimensional nuclear magnetic resonance techniques (correlation spectroscopy, heteronuclear multiple-quantum coherence, nuclear Overhauser effect spectrometry, and heteronuclear multiple-bond correlation) and electronic circular dichroism studies. The antifungal and insecticidal activities of five compounds were evaluated against several plant pathogenic fungi and armyworm larvae (Mythimna separata Walker). Among the test metabolites, compounds 2 and 7 both exhibited potent antifungal activity against the phytopathogenic fungus Cytospora sp. with minimum inhibitory concentration values of 0.78 μg/mL, which are equal to the two positive controls, hymexazol and carbendazim. However, no insecticidal activity of the test compounds was observed in the present study. Compounds 2 and 7 could be promising leads for developing new fungicides against agriculturally important fungus Cytospora sp.
Cell-type specific features of circular RNA expression.
Salzman, Julia; Chen, Raymond E; Olsen, Mari N; Wang, Peter L; Brown, Patrick O
2013-01-01
Thousands of loci in the human and mouse genomes give rise to circular RNA transcripts; at many of these loci, the predominant RNA isoform is a circle. Using an improved computational approach for circular RNA identification, we found widespread circular RNA expression in Drosophila melanogaster and estimate that in humans, circular RNA may account for 1% as many molecules as poly(A) RNA. Analysis of data from the ENCODE consortium revealed that the repertoire of genes expressing circular RNA, the ratio of circular to linear transcripts for each gene, and even the pattern of splice isoforms of circular RNAs from each gene were cell-type specific. These results suggest that biogenesis of circular RNA is an integral, conserved, and regulated feature of the gene expression program.
Zhu, Zhen-Yuan; Dong, Fengying; Liu, Xiaocui; Lv, Qian; YingYang; Liu, Fei; Chen, Ling; Wang, Tiantian; Wang, Zheng; Zhang, Yongmin
2016-04-20
This study was to investigate the effects of different extraction methods on the yield, chemical structure and antitumor activity of polysaccharides from Cordyceps gunnii (C. gunnii) mycelia. Five extraction methods were used to extract crude polysaccharides (CPS), which include room-temperature water extraction (RWE), hot-water extraction (HWE), microwave-assisted extraction (MAE), ultrasound-assisted extraction (UAE) and cellulase-assisted extraction (CAE). Then Sephadex G-100 was used for purification of CPS. As a result, the antitumor activities of CPS and PPS on S180 cells were evaluated. Five CPS and purified polysaccharides (PPS) were obtained. The yield of CPS by microwave-assisted extraction (CPSMAE) was the highest and its anti-tumor activity was the best and its macromolecular polysaccharide (3000-1000kDa) ratio was the largest. The PPS had the same monosaccharide composition, but their obvious difference was in the antitumor activity and the physicochemical characteristics, such as intrinsic viscosity, specific rotation, scanning electron microscopy and circular dichroism spectra. Copyright © 2015 Elsevier Ltd. All rights reserved.
Finding the Speed of a Bicycle in Circular Motion by Measuring the Lean Angle of the Bicycle
ERIC Educational Resources Information Center
Ben-Abu, Yuval; Wolfson, Ira; Yizhaq, Hezi
2018-01-01
We suggest an activity for measuring the speed of a bicycle going in circular motion by measuring the bicycle's lean angle. In this activity students will be able to feel the strength that is being activated on their bodies while they are moving in circular motion. They will also understand that it is impossible to ride in a circle without the…
Cell-Type Specific Features of Circular RNA Expression
Salzman, Julia; Chen, Raymond E.; Olsen, Mari N.; Wang, Peter L.; Brown, Patrick O.
2013-01-01
Thousands of loci in the human and mouse genomes give rise to circular RNA transcripts; at many of these loci, the predominant RNA isoform is a circle. Using an improved computational approach for circular RNA identification, we found widespread circular RNA expression in Drosophila melanogaster and estimate that in humans, circular RNA may account for 1% as many molecules as poly(A) RNA. Analysis of data from the ENCODE consortium revealed that the repertoire of genes expressing circular RNA, the ratio of circular to linear transcripts for each gene, and even the pattern of splice isoforms of circular RNAs from each gene were cell-type specific. These results suggest that biogenesis of circular RNA is an integral, conserved, and regulated feature of the gene expression program. PMID:24039610
Asymptotic theory of circular polarization memory.
Dark, Julia P; Kim, Arnold D
2017-09-01
We establish a quantitative theory of circular polarization memory, which is the unexpected persistence of the incident circular polarization state in a strongly scattering medium. Using an asymptotic analysis of the three-dimensional vector radiative transfer equation (VRTE) in the limit of strong scattering, we find that circular polarization memory must occur in a boundary layer near the portion of the boundary on which polarized light is incident. The boundary layer solution satisfies a one-dimensional conservative scattering VRTE. Through a spectral analysis of this boundary layer problem, we introduce the dominant mode, which is the slowest-decaying mode in the boundary layer. To observe circular polarization memory for a particular set of optical parameters, we find that this dominant mode must pass three tests: (1) this dominant mode is given by the largest, discrete eigenvalue of a reduced problem that corresponds to Fourier mode k=0 in the azimuthal angle, and depends only on Stokes parameters U and V; (2) the polarization state of this dominant mode is largely circular polarized so that |V|≫|U|; and (3) the circular polarization of this dominant mode is maintained for all directions so that V is sign-definite. By applying these three tests to numerical calculations for monodisperse distributions of Mie scatterers, we determine the values of the size and relative refractive index when circular polarization memory occurs. In addition, we identify a reduced, scalar-like problem that provides an accurate approximation for the dominant mode when circular polarization memory occurs.
Interaction of firefly luciferase and silver nanoparticles and its impact on enzyme activity
NASA Astrophysics Data System (ADS)
Käkinen, Aleksandr; Ding, Feng; Chen, Pengyu; Mortimer, Monika; Kahru, Anne; Ke, Pu Chun
2013-08-01
We report on the dose-dependent inhibition of firefly luciferase activity induced by exposure of the enzyme to 20 nm citrate-coated silver nanoparticles (AgNPs). The inhibition mechanism was examined by characterizing the physicochemical properties and biophysical interactions of the enzyme and the AgNPs. Consistently, binding of the enzyme induced an increase in zeta potential from -22 to 6 mV for the AgNPs, triggered a red-shift of 44 nm in the absorbance peak of the AgNPs, and rendered a ‘protein corona’ of 20 nm in thickness on the nanoparticle surfaces. However, the secondary structures of the enzyme were only marginally affected upon formation of the protein corona, as verified by circular dichroism spectroscopy measurement and multiscale discrete molecular dynamics simulations. Rather, inductively coupled plasma mass spectrometry measurement revealed a significant ion release from the AgNPs. The released silver ions could readily react with the cysteine residues and N-groups of the enzyme to alter the physicochemical environment of their neighboring catalytic site and subsequently impair the enzymatic activity.
Thermal preparation of lysozyme-imprinted microspheres by using ionic liquid as a stabilizer.
Qian, Li-Wei; Hu, Xiao-Ling; Guan, Ping; Gao, Bo; Wang, Dan; Wang, Chao-Li; Li, Ji; Du, Chun-Bao; Song, Wen-Qi
2014-11-01
Thermal preparation of lysozyme-imprinted microspheres was firstly investigated by using biocompatible ionic liquid (IL) as a thermal stabilizer. The imprinted microspheres made with IL could obtain the good recognition ability to template protein, whereas the imprinted polymer synthesized in the absence of it had a similar adsorption capacity to the non-imprinted one. Furthermore, the preparation conditions of imprinted polymers (MIPs) including the content of IL, temperature of polymerization, and types of functional monomers and crosslinkers were systematically analyzed via circular dichroism spectrum and activity assay. The results illustrated that using hydroxyethyl acrylate as the functional monomer, ethylene glycol dimethacrylate as the crosslinker, 5 % IL as the stabilizer, and 75 °C as the reaction temperature could retain the structure of template protein as much as possible. The obtained MIPs showed excellent recognition ability to the template protein with the separation factor and selectivity factor value of 4.30 and 2.21, respectively. Consequently, it is an effective way to accurately imprint and separate template protein by cooperatively using circular dichroism spectroscopy and activity assay during the preparation of protein MIPs. The method of utilizing IL to stabilizing protein at high temperature would offer a good opportunity for various technologies to improve the development of macromolecules imprinting.
DOE Office of Scientific and Technical Information (OSTI.GOV)
Ovchinnikova, E. N.; Rogalev, A.; Wilhelm, F.
The local electronic structure of copper ions in a copper metaborate CuB{sub 2}O{sub 4} crystal is studied on the ESRF synchrotron using X-ray absorption polarization-dependent spectroscopy. The X-ray natural circular dichroism near the K absorption edge of copper is measured in the direction that is perpendicular to crystal axis c. The data obtained indicate the presence of hybridized p–d electronic states of copper. Theoretical calculations are used to separate the contributions of the two crystallographically nonequivalent positions of copper atoms in the unit cell of CuB{sub 2}O{sub 4} to the absorption and X-ray circular dichroism spectra of the crystal.
Polavarapu, Prasad L.; Donahue, Emily A.; Shanmugam, Ganesh; Scalmani, Giovanni; Hawkins, Edward K.; Rizzo, Carmelo; Ibnusaud, Ibrahim; Thomas, Grace; Habel, Deenamma; Sebastian, Dellamol
2013-01-01
Electronic circular dichroism (ECD), optical rotatory dispersion (ORD), and vibrational circular dichroism (VCD) spectra of hibiscus acid dimethyl ester have been measured and analyzed in combination with quantum chemical calculations of corresponding spectra. These results, along with those reported previously for garcinia acid dimethyl ester, reveal that none of these three (ECD, ORD, or VCD) spectroscopic methods, in isolation, can unequivocally establish the absolute configurations of diastereomers. This deficiency is eliminated when a combined spectral analysis of either ECD and VCD or ORD and VCD methods is used. It is also found that the ambiguities in the assignment of absolute configurations of diastereomers may also be overcome when unpolarized vibrational absorption is included in the spectral analysis. PMID:21568330
DNA/RNA binding and anticancer/antimicrobial activities of polymer-copper(II) complexes
NASA Astrophysics Data System (ADS)
Lakshmipraba, Jagadeesan; Arunachalam, Sankaralingam; Riyasdeen, Anvarbatcha; Dhivya, Rajakumar; Vignesh, Sivanandham; Akbarsha, Mohammad Abdulkader; James, Rathinam Arthur
2013-05-01
Water soluble polymer-copper(II) complexes with various degrees of coordination in the polymer chain were synthesized and characterized by elemental analysis, IR, UV-visible and EPR spectra. The DNA/RNA binding behavior of these polymer-copper(II) complexes was examined by UV-visible absorption, emission and circular dichroism spectroscopic methods, and cyclic voltammetry techniques. The binding of the polymer-copper(II) complexes with DNA/RNA was mainly through intercalation but some amount of electrostatic interaction was also observed. This binding capacity increased with the degree of coordination of the complexes. The polymer-copper(II) complex having the highest degree of coordination was subjected to analysis of cytotoxic and antimicrobial properties. The cytotoxicity study indicated that the polymer-copper(II) complexes affected the viability of MCF-7 mammary carcinoma cells, and the cells responded to the treatment with mostly through apoptosis although a few cells succumbed to necrosis. The antimicrobial screening showed activity against some human pathogens.
Diterpenes from buds of Wikstroemia chamaedaphne showing anti-hepatitis B virus activities.
Li, Shi-Fei; Jiao, Ying-Ying; Zhang, Zhi-Qiang; Chao, Jian-Bin; Jia, Jie; Shi, Xun-Long; Zhang, Li-Wei
2018-07-01
Phytochemical study of the buds of Wikstroemia chamaedaphne Meisn. led to the isolation of seven previously undescribed diterpenes, including one tigliane diterpene (wikstchalide A), two daphnane diterpenes (wikstroelides W-X), and four lathyrane diterpenes (laurifoliosides A-B and 2-epi-laurifoliosides A-B), along with four known diterpenes. The structures of these compounds were established by extensive spectroscopic evidence and electronic circular dichroism (ECD) calculations. Wikstchalide A possesses a 5,6-epoxy ring in the tigliane skeleton. Two compounds exhibited potential anti-hepatitis B virus activities, with IC 50 values of 46.5 and 88.3 μg/mL against hepatitis B virus (HBV) surface antigen (HBsAg), and six compounds showed certain inhibitory effects on HBV-DNA replication with the inhibition ratios ranging from 2.0% to 33.0% at the concentrations ranging from 0.39 to 6.25 μg/mL. Copyright © 2018 Elsevier Ltd. All rights reserved.
Blahó, Miklós; Egri, Adám; Hegedüs, Ramón; Jósvai, Júlia; Tóth, Miklós; Kertész, Krisztián; Biró, László Péter; Kriska, György; Horváth, Gábor
2012-02-28
The strongest known circular polarization of biotic origin is the left-circularly polarized (LCP) light reflected from the metallic shiny exocuticle of certain beetles of the family Scarabaeidae. This phenomenon has been discovered by Michelson in 1911. Although since 1955 it has been known that the human eye perceives a visual illusion when stimulated by circularly polarized (CP) light, it was discovered only recently that a stomatopod shrimp is able to perceive circular polarization. It is pertinent to suppose that scarab beetles reflecting LCP light in an optical environment (vegetation) being deficient in CP signals may also perceive circular polarization and use it to find each other (mate/conspecifics) as until now it has been believed. We tested this hypothesis in six choice experiments with several hundred individuals of four scarab species: Anomala dubia, Anomala vitis (Coleoptera, Scarabaeidae, Rutelinae), and Cetonia aurata, Potosia cuprea (Coleoptera, Scarabaeidae, Cetoniinae), all possessing left-circularly polarizing exocuticle. From the results of our experiments we conclude that the studied four scarab species are not attracted to CP light when feeding or looking for mate or conspecifics. We demonstrated that the light reflected by host plants of the investigated scarabs is circularly unpolarized. Our results finally solve a puzzle raised over one hundred years ago, when Michaelson discovered that scarab beetles reflect circularly polarized light. Copyright © 2011 Elsevier Inc. All rights reserved.
All-dielectric planar chiral metasurface with gradient geometric phase.
Ma, Zhijie; Li, Yi; Li, Yang; Gong, Yandong; Maier, Stefan A; Hong, Minghui
2018-03-05
Planar optical chirality of a metasurface measures its differential response between left and right circularly polarized (CP) lights and governs the asymmetric transmission of CP lights. In 2D ultra-thin plasmonic structures the circular dichroism is limited to 25% in theory and it requires high absorption loss. Here we propose and numerically demonstrate a planar chiral all-dielectric metasurface that exhibits giant circular dichroism and transmission asymmetry over 0.8 for circularly polarized lights with negligible loss, without bringing in bianisotropy or violating reciprocity. The metasurface consists of arrays of high refractive index germanium Z-shape resonators that break the in-plane mirror symmetry and induce cross-polarization conversion. Furthermore, at the transmission peak of one handedness, the transmitted light is efficiently converted into the opposite circular polarization state, with a designated geometric phase depending on the orientation angle of the optical element. In this way, the optical component sets before and after the metasurface to filter the light of certain circular polarization states are not needed and the metasurface can function under any linear polarization, in contrast to the conventional setup for geometry phase based metasurfaces. Anomalous transmission and two-dimensional holography based on the geometric phase chiral metasurface are numerically demonstrate as proofs of concept.
Chang, B S; Beauvais, R M; Arakawa, T; Narhi, L O; Dong, A; Aparisio, D I; Carpenter, J F
1996-01-01
The degradation products of recombinant human interleukin-1 receptor antagonist (rhIL-1ra) formed during storage at 30 degrees C in aqueous solution were characterized. Cationic exchange chromatography of the stored sample showed two major, new peaks eluting before (P1) and after (L2) the native protein, which were interconvertible. Size-exclusion chromatography and electrophoresis documented that both the P1 and L2 fractions were irreversible dimers, formed by noncovalent interactions. A competition assay with interleukin-1 indicated that on a per monomer basis the P1 and L2 dimers retained about two-thirds of the activity of the native monomer. Infrared and far-UV circular dichroism spectroscopies showed that only minor alterations in secondary structure arose upon the formation of the P1 dimer. However, alteration in the near-UV circular dichroism spectrum suggested the presence of disulfide bonds in the P1 dimer, which are absent in the native protein. Mass spectroscopy and tryptic mapping, before and after carboxymethylation, demonstrated that the P1 dimer contained an intramolecular disulfide bond between Cys-66 and Cys-69. Although conversion of native protein to the P1 dimer was irreversible in buffer alone, the native monomer could be regained by denaturing the P1 dimer with guanidine hydrochloride and renaturing it by dialysis, suggesting that the intramolecular disulfide bond does not interfere with refolding. Analysis of the time course of P1 formation during storage at 30 degrees C indicated that the process followed first-order, and not second-order, kinetics, suggesting that the rate-limiting step was not dimerization. It is proposed that a conformational change in the monomer is the rate-limiting step in the formation of the P1 dimer degradation product. Sucrose stabilized the native monomer against this process. This result can be explained by the general stabilization mechanism for this additive, which is due to its preferential exclusion from the
Engineering of the institutionalization of the circular economy at the level of casting production
NASA Astrophysics Data System (ADS)
Vescan, M. M.; Soporan, V. F.; Crișan, D. M.; Lehene, T. R.; Pădurețu, S.; Samuila, V.
2017-06-01
This paper is motivated by the necessity of introducing the principles of circular economy at the level of different social - economic activities, and from this point of view one of the fields with a special potential is that of the manufacture of castings. Objective: to connect to the organizing and application of the methodology of the circular economy principles. The proposed method is an innovating one, being connected to the use of institutionalization engineering. Formulating the subject: The subject formulated to be solved aims at the introduction of new approaches, defined through institutionalization engineering, which proposes to set the correlation of actions between the specifics of the circular economy and the specific elements of the manufacture of castings. Research method: An institutional structuring operation was imposed for the optimization of the research method, in which different versions interact at the following levels: the level of public policies, the level of the regulatory framework, the level of technical solutions and the level of financing solutions and financial instruments. The determination of the optimal solution established in a dynamic context, favorable for the requirements of the different actors present within the process, appeals to the elements of critical thinking, specific for the engineer’s actions. Achievement of the research activity: The research activity structures a methodology of quantifying the contributions of each stage of the manufacturing process for castings at the fulfilling of the specific conditions of the circular economy, indicating the critical areas of action for more efficient actions of the circular economy, according to the market economy requirements, where there is a potential of implementing the technical solutions by quantizing the financial solutions and the opportunity of using the financial instruments. The major contribution of the research: The proposed methodology, with examples at the
Song, Xiaomin; Wang, Jing; Wu, Fang; Li, Xu; Teng, Maikun; Gong, Weimin
2005-01-01
SPE10 is an antifungal protein isolated from the seeds of Pachyrrhizus erosus. cDNA encoding a 47 amino acid peptide was cloned by RT-PCR and the gene sequence proved SPE10 to be a new member of plant defensin family. The synthetic cDNA with codons preferred in yeast was cloned into the pPIC9 plasmid directly in-frame with the secretion signal alpha-mating factor, and highly expressed in methylotrophic Pichia pastoris. Activity assays showed the recombinant SPE10 inhibited specifically the growth of several pathogenic fungi as native SPE10. Circular dichroism and fluorescence spectroscopy analysis indicated that the native and recombinant protein should have same folding, though there are eight cystein residues in the sequence. Several evidence suggested SPE10 should be the first dimeric plant defensin reported so far.