The Experts below are selected from a list of 1929 Experts worldwide ranked by ideXlab platform
Petr Bouř - One of the best experts on this subject based on the ideXlab platform.
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α synuclein conformations followed by Vibrational Optical Activity simulation and understanding of the spectra
Physical Chemistry Chemical Physics, 2021Co-Authors: Josef Kapitan, Jiři Kessler, Andrii Kurochka, Jiři Průsa, Petr BouřAbstract:α-Synuclein is a neuronal protein which adopts multiple conformations. These can be conveniently studied by the spectroscopy of Vibrational Optical Activity (VOA). However, the interpretation of VOA spectra based on quantum-chemical simulations is difficult. To overcome the hampering of the computations by the protein size, we used the Cartesian tensor transfer technique to investigate links between the spectral shapes and protein structure. Vibrational circular dichroism (VCD) and Raman Optical Activity (ROA) spectra of α-synuclein in disordered, α-helical and β-sheet (fibril) forms were measured and analyzed on the basis of molecular dynamics and density functional theory computations. For the disordered and α-helical conformers, a high fidelity of the simulated spectra with a reasonable computational cost was achieved. Most experimental spectral features could be assigned to the structure. So far unreported ROA marker bands of the secondary structure were found for the lower-frequency and CH stretching vibrations. Fibril VCD spectra were simulated with a rigid periodic model of the geometry and the results are consistent with previous studies based on cryogenic electron microscopy. The fibrils also give a specific ROA signal, but unlike VCD it is currently not fully explicable by the simulations. In connection with the computational modeling the VOA spectroscopy thus appears as an extremely useful tool for monitoring α-synuclein and other proteins in solutions.
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pressure dependence of Vibrational Optical Activity of model biomolecules a computational study
Chirality, 2020Co-Authors: Lubos Plamitzer, Petr BouřAbstract:Change of molecular properties with pressure is an attracting means to regulate molecular reActivity or biological Activity. However, the effect is usually small and so far explored rather scarcely. To obtain a deeper insight and estimate the sensitivity of Vibrational Optical Activity spectra to pressure-induced conformational changes, we investigate small model molecules. The Ala-Ala dipeptide, isomaltose disaccharide and adenine-uracil dinucleotide were chosen to represent three different biomolecular classes. The pressure effects were modeled by molecular dynamics and density functional theory simulations. The dinucleotide was found to be the most sensitive to the pressure, whereas for the disaccharide the smallest changes are predicted. Pressure-induced relative intensity changes in Vibrational circular dichroism and Raman Optical Activity spectra are predicted to be 2-3-times larger than for non-polarized IR and Raman techniques.
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recent trends in chirOptical spectroscopy theory and applications of Vibrational circular dichroism and raman Optical Activity
ChemPlusChem, 2020Co-Authors: Monika Krupova, Jiři Kessler, Petr BouřAbstract:ChirOptical spectroscopy exploring the interaction of matter with polarized light provides many tools for molecular structure and interaction studies. Here, some recent discoveries are reviewed, primarily in the field of Vibrational Optical Activity. Technological advances results in the development of more sensitive Vibrational circular dichroism (VCD), Raman Optical Activity (ROA) or circular polarized luminescence (CPL) spectrometers. Significant contributions to the field also come from the light scattering and electronic structure theories, and their implementation in computer systems. Finally, new chirOptical phenomena have been observed, such as enhanced circular dichroism of biopolymers (protein fibrils, nucleic acids), plasmonic and resonance chirality-transfer ROA experiments. Some of them are not yet understood or attributed to instrumental artifacts so far. Nevertheless, these unknown territories also indicate the vast potential of the chirOptical spectroscopy, and their investigation is even more challenging.
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interpretation of Vibrational Optical Activity spectra of proteins
2020Co-Authors: Jana Hudecova, Petr BouřAbstract:Abstract Methods of Vibrational Optical Activity (VOA) traditionally include Raman Optical Activity and Vibrational circular dichroism. They combine structural sensitivity of chirOptical spectroscopy with the richness of Vibrational spectra. Different peptide and protein conformations usually provide quite distinct VOA patterns. For spectra interpretation, it is desirable to understand the underlying physical principles. Quantum-chemical simulations of spectral shapes can also be very helpful. At present, they are implemented in common software, usually within the density functional theory. However, simulations of VOA spectra of even small molecules may be complicated by interactions with the solvent and molecular flexibility. For large molecules, direct quantum-chemical methods can be combined with or replaced by molecular dynamic simulations or semiempirical approaches. We present several examples of calculations used for small and large systems, with a bias to our previous results. Nevertheless, we tried to document general possibilities of contemporary computational chemistry.
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Vibrational Optical Activity of intermolecular overtone and combination bands 2 chloropropionitrile and α pinene
Journal of Physical Chemistry B, 2019Co-Authors: Pavel Michal, Michal Dudka, Karthick Thangavel, Radek Celechovský, Josef Kapitan, Milan Vůjtek, Marie Beresova, Jaroslav Sebestik, Petr BouřAbstract:Spectroscopy of Vibrational Optical Activity has been established as a powerful tool to study molecular structures and interactions. In most cases, only fundamental molecular transitions are analyz...
Minhaeng Cho - One of the best experts on this subject based on the ideXlab platform.
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terahertz chirOptical spectroscopy of an α helical polypeptide a molecular dynamics simulation study
Journal of Physical Chemistry B, 2014Co-Authors: Jun Ho Choi, Minhaeng ChoAbstract:Vibrational spectroscopy has provided incisive information on the structure of biological molecules. Here, using a molecular dynamics simulation method, infrared Vibrational circular dichroism and Vibrational Optical rotatory dispersion spectra of a right-handed α-helix in the terahertz (THz) frequency range are calculated. Both the autocorrelation function of an electric dipole moment and the cross-correlation function of electric and magnetic dipole moments of the α-helix are calculated and Fourier-transformed to obtain THz absorption and Optical Activity spectra, which reveal characteristic features of the helical polypeptide structure. The anharmonicity and delocalized nature of the low-frequency modes in the THz frequency domain are taken into account to obtain statistically convergent results on the THz Optical Activity spectra. In addition, the magnitude of the THz Vibrational Optical Activity signal of the α-helix is directly compared with those of typical, previously studied mid- and near-infrare...
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terahertz chirOptical spectroscopy of an α helical polypeptide a molecular dynamics simulation study b
The Journal of Physical Chemistry, 2014Co-Authors: Jun Ho Choi, Minhaeng ChoAbstract:Vibrational spectroscopy has provided incisive information on the structure of biological molecules. Here, using a molecular dynamics simulation method, infrared Vibrational circular dichroism and Vibrational Optical rotatory dispersion spectra of a right-handed α-helix in the terahertz (THz) frequency range are calculated. Both the autocorrelation function of an electric dipole moment and the cross-correlation function of electric and magnetic dipole moments of the α-helix are calculated and Fourier-transformed to obtain THz absorption and Optical Activity spectra, which reveal characteristic features of the helical polypeptide structure. The anharmonicity and delocalized nature of the low-frequency modes in the THz frequency domain are taken into account to obtain statistically convergent results on the THz Optical Activity spectra. In addition, the magnitude of the THz Vibrational Optical Activity signal of the α-helix is directly compared with those of typical, previously studied mid- and near-infrared chiral molecules. We anticipate that THz chirOptical spectroscopy that has not yet been demonstrated experimentally would provide highly important and complementary information on protein structure and dynamics.
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direct calculations of mid and near ir absorption and circular dichroism spectra of chiral molecules using qm mm molecular dynamics simulation method
Journal of Chemical Theory and Computation, 2011Co-Authors: Jun Ho Choi, Minhaeng ChoAbstract:The infrared (IR) and Vibrational circular dichroism (VCD) spectra of (1S)-(-)-β-pinene in the mid- and near- IR frequency regions are numerically simulated by using a time-correlation function theory and mixed quantum/classical simulation method. Anharmonic Vibrational dynamics and fluctuating atomic partial charges of the chiral pinene were obtained by carrying out quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations. Thus obtained time-correlation functions of electric and magnetic dipole moments are used to calculate the IR absorption and VCD spectra, and they are directly compared with experimental results. Not only the fundamental transition bands but also first overtone and combination bands in the near-IR frequency region are successfully simulated. It is shown that the polarizable nature of the solute is particularly important in quantitatively reproducing the near-IR spectra, whereas such polarization effects on dipole and rotational strengths of lower-frequency and large-amplitude vibrations are less critical. We anticipate that the present QM/MM MD method in combination with mixed quantum/classical time-correlation function theory to calculate both mid- and near-IR absorption and VCD spectra will be of critical use in interpreting Vibrational Optical Activity properties of even conformationally flexible chiral molecules, such as proteins.
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calculations of Vibrationally resonant sum and difference frequency generation spectra of chiral molecules in solutions three wave mixing Vibrational Optical Activity
Journal of Chemical Physics, 2010Co-Authors: Jun Ho Choi, Sangheon Cheon, Minhaeng ChoAbstract:Determining absolute configuration of chiral molecule can be achieved by using Vibrational Optical Activity (VOA) measurement methods, such as Vibrational circular dichroism and Raman Optical Activity (ROA). Recently, Vibrationally resonant sum frequency generation and difference frequency generation utilizing circularly polarized beams were theoretically studied and shown that they can be alternative and complementary VOA measurement techniques [S. Cheon and M. Cho, Phys. Rev. A 71, 013808 (2005); J. Phys. Chem. A 113, 2438 (2009)]. Even for randomly oriented chiral molecules in solutions, the sum- and difference-frequency-generation signals induced by linearly polarized incident beams with mutually perpendicular polarization directions can be nonzero and are determined by the Optical Activity hyperpolarizability given by a product of antisymmetric Raman tensor and Vibrational transition dipole. If one of the beams involved in the three-wave-mixing processes is circularly polarized and if the difference signal is measured, not only the same Optical Activity hyperpolarizability but also that including electric quadrupole-ROA tensor are required to determine the signals. Here, we carried out quantum chemistry calculations to obtain these quantities for a representative chiral molecule, (S)-methyl lactate, and numerically simulated the corresponding spectra. It is shown that the circular polarization three-wave-mixing signal intensities are quantitatively similar to those of the linear polarization three-wave-mixing signals, respectively, and that they are sensitive to the absolute configuration of chiral molecule. The calculation results thus suggest that these two novel techniques will be of use in studying molecular chirality even in time domain, once polarization-modulated ultrashort pulses are used to carry out circular polarization three-wave-mixing experiments.
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phase sensitive detection of Vibrational Optical Activity free induction decay Vibrational cd and ord
Journal of The Optical Society of America B-optical Physics, 2009Co-Authors: Hanju Rhee, Young Gun June, Zee Hwan Kim, Seung Joon Jeon, Minhaeng ChoAbstract:Optical Activity is manifested by chiral molecules including natural products and drugs, so that circular dichroism (CD) and Optical rotatory dispersion (ORD) measurements can provide invaluable information on their chiro-Optical properties and structures. It is experimentally demonstrated that heterodyne-detected Fourier-transform spectral interferometry with a femtosecond infrared pulse can be used to fully characterize the phase and amplitude of Vibrational Optical Activity free-induction-decay field. The measured spectral interferograms are then converted to the linear Optical Activity susceptibility whose imaginary and real parts correspond to Vibrational CD and ORD spectra. Unlike the conventional differential measurement technique, the present method based on a heterodyned interferometry is shown to be quite robust and stable. We anticipate that the present Vibrational Optical Activity measurement technique will be of critical use in elucidating chiro-Optical properties and structural changes in biomolecules.
Laurence A Nafie - One of the best experts on this subject based on the ideXlab platform.
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Vibrational Optical Activity from discovery and development to future challenges
Chirality, 2020Co-Authors: Laurence A NafieAbstract:Vibrational Optical Activity (VOA) consisting of infrared Vibrational circular dichroism (VCD) and Vibrational Raman Optical Activity (ROA) was predicted, discovered, and confirmed between 1971 and 1975. My path to VOA was mentored by three pioneers of chirality and Vibrational spectroscopy: Professors Albert Moscowitz, Warner L. Peticolas, and Philip J. Stephens, and while they are no longer alive today, the Chirality Medal, my award address, and this paper are dedicated to each of them. Since the discovery of VOA, a number of key advances have made possible the current era of widespread applications. The principal instrumental advances were Fourier-transform VCD (FT-VCD) and multichannel charge coupled detector (CCD) ROA. Computational advances include the first complete quantum chemistry formulation of VCD leading to the magnetic field perturbation (MFP) and the nuclear velocity perturbation (NVP) theories. The strength of VOA is the comparison between measured and calculated spectra that enables the determination of absolute configuration and solution-state conformations. More recently, VCD has uncovered supramolecular chirality in amyloid fibrils and ROA to high-order protein structure. Future challenges for VOA include describing the effects of weak intermolecular interactions, transfer of chirality, solvent effects, supramolecular chirality, and the generation of nuclear velocity electron current density.
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Vibrational Optical Activity from small chiral molecules to protein pharmaceuticals and beyond
2018Co-Authors: Laurence A NafieAbstract:Abstract Vibrational Optical Activity, consisting of infrared Vibrational circular dichroism (VCD) and Vibrational Raman Optical Activity (ROA), is an area of Vibrational spectroscopy of growing importance as chemists gain greater control of chirality in molecular structure in both synthetic and molecules of biological origin. Discovered in the early-to-mid 1970s, both VCD and ROA have emerged in recent decades to greater worldwide usage, spurred by the availability of commercial instruments and software for the measurement and calculation of VOA spectra. The principal applications of VCD involve determination of absolute configuration of synthetic molecules, pharmaceutical active ingredients, and natural products, while ROA is finding its primary impact in the conformations of large biological molecules and biopharmaceuticals. This chapter highlights the frontier areas of VCD and ROA from small chiral molecules to biopharmaceuticals and describes how these two chirOptical techniques are providing new information at the forefront of molecular science.
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a confidence level algorithm for the determination of absolute configuration using Vibrational circular dichroism or raman Optical Activity
ChemPhysChem, 2011Co-Authors: Elke Debie, Rina K. Dukor, Laurence A Nafie, Ewoud De Gussem, Wouter A Herrebout, Patrick BultinckAbstract:Spectral comparison is an important part of the assignment of the absolute configuration (AC) by Vibrational circular dichroism (VCD), or equally by Raman Optical Activity (ROA). In order to avoid bias caused by personal interpretation, numerical methods have been developed to compare measured and calculated spectra. Using a neighbourhood similarity measure, the agreement between a computed and measured VCD or ROA spectrum is expressed numerically to introduce a novel confidence level measure. This allows users of Vibrational Optical Activity (VOA) techniques (VCD and ROA) to assess the reliability of their assignment of the AC of a compound. To that end, a database of successful AC determinations is compiled along with neighbourhood similarity values between the experimental spectrum and computed spectra for both enantiomers. For any new AC determination, the neighbourhood similarities between the experimental spectrum and the computed spectra for both enantiomers are projected on the database allowing an interpretation of the reliability of their assignment.
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Determination of absolute configuration of chiral molecules using Vibrational Optical Activity: A review
Applied Spectroscopy, 2011Co-Authors: Yanan He, Rina K. Dukor, Bo Wang, Laurence A NafieAbstract:Determination of the absolute handedness, known as absolute configuration (AC), of chiral molecules is an important step in any field related to chirality, especially in the pharmaceutical industry. Vibrational Optical Activity (VOA) has become a powerful tool for the determination of the AC of chiral molecules in the solution state after nearly forty years of evolution. VOA offers a novel alternative, or supplement, to X-ray crystallography, permitting AC determinations on neat liquid, oil, and solution samples without the need to grow single crystals of the pure chiral sample molecules as required for X-ray analysis. By comparing the sign and intensity of the measured VOA spectrum with the corresponding ab initio density functional theory (DFT) calculated VOA spectrum of a chosen configuration, one can unambiguously assign the AC of a chiral molecule. Comparing measured VOA spectra with calculated VOA spectra of all the conformers can also provide solution-state conformational populations. VOA consists of infrared Vibrational circular dichroism (VCD) and Vibrational Raman Optical Activity (ROA). Currently, VCD is used routinely by researchers in a variety of backgrounds, including molecular chirality, asymmetric synthesis, chiral catalysis, drug screening, pharmacology, and natural products. Although the application of ROA in AC determination lags behind that of VCD, with the recent implementation of ROA subroutines in commercial quantum chemistry software, ROA will in the future complement VCD for AC determination. In this review, the basic principles of the application of VCD to the determination of absolute configuration in chiral molecules are described. The steps required for VCD spectral measurement and calculation are outlined, followed by brief descriptions of recently published papers reporting the determination of AC in small organic, pharmaceutical, and natural product molecules.
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observation and calculation of Vibrational circular birefringence a new form of Vibrational Optical Activity
Chirality, 2009Co-Authors: Rosina Lombardi, Laurence A NafieAbstract:We report the first mid-infrared observation of Vibrational circular birefringence (VCB) arising from individual chiral molecules. VCB can also be called Vibrational Optical rotatory dispersion (VORD) and is the Kramers-Kronig transform of Vibrational circular dichroism (VCD). The method of measurement involves a simple change in the Optical set-up and electronic processing of a VCD spectrometer such that the VCB spectrum appears at twice the polarization modulation frequency as a pseudo Vibrational linear dichroism (VLD) spectrum. VCB spectra are also calculated with density function theory (DFT) for the first time using a commercially available program for rotational strengths where the calculated intensities are convolved with the real, dispersive part of a normalized complex Lorentzian lineshape rather than the imaginary, absorptive part, normally used for IR and VCD intensity calculations. Comparison of themeasured and calculated VCB, VCD, and IR spectra of (+)-R-limonene and (−)-S-α-pinene show close agreement and confirm the validity of the new VCB measurements. Chirality 21:E277–E286, 2009. © 2009 Wiley-Liss, Inc.
Xiangtian Kong - One of the best experts on this subject based on the ideXlab platform.
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mid infrared plasmonic circular dichroism generated by graphene nanodisk assemblies
Nano Letters, 2017Co-Authors: Xiangtian Kong, Runbo Zhao, Zhiming Wang, Alexander O GovorovAbstract: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.
Alexander O Govorov - One of the best experts on this subject based on the ideXlab platform.
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mid infrared plasmonic circular dichroism generated by graphene nanodisk assemblies
Nano Letters, 2017Co-Authors: Xiangtian Kong, Runbo Zhao, Zhiming Wang, Alexander O GovorovAbstract: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.
