Measurement and comparison of absolute value of soft X-ray natural circular dichroism of serine and alanine

Izumi, Yudai; Imazu, Akiko; Mimoto, Aki; Tanaka, Masafumi; Nakagawa, Kazumichi; Tanaka, Masahito; Agui, Akane; Matsuki, Takayuki

doi:10.1088/1742-6596/190/1/012209

Cited by 10 publications

(10 citation statements)

References 15 publications

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“…Natural circular dichroism (CD), which is the difference between the absorptions for left and right circular polarizations, has been commonly used as a tool in the structural analysis of chiral molecules such as proteins, because CD is highly sensitive to the conformations of these molecules. – In recent years, the wavelength coverage of CD measurements has extended to the vacuum ultraviolet (VUV) and X-ray regions, using a combination of synchrotron radiation techniques. – Attempts to analyze the protein secondary structures precisely have resulted in vigorous development worldwide of CD systems in the VUV region. – CD measurements in the VUV region can be used to obtain structural information on molecules devoid of chromophores, such as saturated carbon hydrides and alcohols, as well as information on proteins and aromatic organic compounds. Theoretical methods for CD prediction, based on quantum-chemical calculations, have also progressed in recent years. – The establishment of an experimental and theoretical understanding of CD in the VUV region will yield nonempirical conformational analyses of many chiral substances in the future.…”

Section: Introductionmentioning

confidence: 99%

“…In addition, amino acids are key molecules in studying the origin of biomolecular homochirality, as well as being the building blocks of proteins. As a result, a large number of experimental and theoretical studies of the optical properties of amino acids in solution and in the solid state have been reported. ,,– ,– Recently, we have developed a system for CD measurements in the VUV, and even the extreme ultraviolet (EUV) regions, using the polarizing undulator at the beamline BL5 at TERAS, Japan as a polarized light source. – This CD system has also been successfully used to measure the CD spectra of some amino acids films in the VUV region , and to observe CD spectra in the EUV region up to 30 eV for the first time. , …”

Section: Introductionmentioning

confidence: 99%

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Chiroptical Study of α-Aliphatic Amino Acid Films in the Vacuum Ultraviolet Region

et al. 2010

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A series of natural circular dichroism (CD) and absorption spectra for films of α-aliphatic amino acids--such as alanine, aminobutyric acid, norvaline, norleucine, valine, leucine, and isoleucine--in the vacuum ultraviolet (VUV) region were observed with the absolute values of optical constants at the undulator-based CD beamline TERAS BL5. Preliminary predictions of some CD spectra were also performed, based on quantum-chemical calculations using the crystal structure. Although the absorption spectra show similar features to each other, significant differences between the CD spectra were found, especially in the 7-8 eV region. The CD spectra of aliphatic amino acids with branched alkyl groups in the side-chain--such as valine, leucine, and isoleucine--exhibit strong negative CD peaks in this energy region. In contrast, the corresponding CD peaks were weak or absent in the spectra of amino acids with straight alkyl groups. Our simple calculation, and the absorption spectra of alkanes, suggest that this difference partly originates from the contribution of the alkyl group. Clear discrepancies between the CD spectra of these amino acids in solutions and those in the solid state were also observed; this is probably caused by the different molecular structures in each state. Our results clearly indicated that CD spectra in the VUV region were very sensitive to the conformations of chiral molecules.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Chiroptical Study of α-Aliphatic Amino Acid Films in the Vacuum Ultraviolet Region

et al. 2010

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“…Since the oscillator strength distributions are uncharacterized in this region, it is also an important future work to determine them experimentally although they can be roughly estimated from the number of atoms comprising the molecules [25]. In such experiments, the method described in this work is applicable by replacing the collodion films for silicon nitride [26,27] or silicon carbide films [28]. By combining such future works, more precise estimations of the interaction between DNA bases and IRs or photons can be achieved.…”

Section: Resultsmentioning

confidence: 99%

Optical Absorption Cross-Section of DNA Bases—Thymine and Guanine—in the Energy Region from 3.1 to 250 eV (5–400 nm)

Koswattage

Izumi

Nakagawa

2020

QuBS

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(1) Background: Optical absorption cross-section—the absolute absorption intensity specific to each molecule—of nucleic acid bases enables us to estimate the reaction yields of DNA lesions induced by the exposure to not only photons but also ionizing radiations. However, it was unknown in the energy region exceeding ~10 eV (wavelength < ~120 nm). (2) Methods: Thin films of DNA bases—thymine and guanine—were prepared using a vacuum sublimation technique. Absorption spectra of these films were measured in the energy region from 3.1 to 250 eV (5–400 nm) at the synchrotron radiation facility UVSOR. (3) Results: The absorption spectra of both bases exhibited prominent absorption peaks around 20 eV and smaller peaks in the energy region below 10 eV. The determined optical oscillator strength distribution was verified to be reasonable based on the Thomas–Reiche–Kuhn oscillator strength sum rule. (4) Conclusion: Most of the oscillator strength distribution was positioned in the measured energy region, and therefore the absorption spectra significantly contributed to the quantitative study for the photo and radiation-chemical reactions of DNA.

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“…Although early authors seem to have followed Kuhn’s terminology, the same quantity is alternatively referred to as the “dissymmetry factor” in the more recent literature. − One major property of the anisotropy factor is that it does not depend on the amount of sample molecules, so, neither upon the molecule concentration nor upon the thickness of the sample. Moreover, when comparing experimental and theoretical spectra, the anisotropy spectra have been found to be “a more discerning tool” than the corresponding ECD spectra. , Experiments using synchrotron radiation have extended the ECD spectra deep into the vacuum ultraviolet (VUV) region, − reporting the anisotropy spectra of several amino acids . The derivation of the anisotropy spectra from experimental absorption and ECD spectra usually depends on the segmentation of the latter into slices of somewhat arbitrary finite sizes to compute their ratio.…”

Section: Introductionmentioning

confidence: 99%

Theoretical Study of the Anisotropy Spectra of the Valine Zwitterion and Glyceraldehyde

Suo

Cassam-Chenaı̈

2020

J. Phys. Chem. A

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The electronic absorption (EA), circular dichroism (ECD), and anisotropy spectra of the l-valine zwitterion and d-glyceraldehyde are calculated by time-dependent density functional theory (TDDFT) with the M06-2X and B3LYP functionals. It is found that the absorption and ECD spectra from TDDFT/M06-2X agree well with experimental results measured from the amorphous film of l-valine. Moreover, the calculations reproduce all three major peaks observed in the experimental anisotropy spectra. For d-glyceraldehyde, the TDDFT/M06-2X calculations indicate that the excitation wavelengths of the first excited state of 32 stable conformers distribute from 288 to 322 nm, giving rise to two ECD peaks with opposite signs centered at 288 and 322 nm. The very weak absorption of the first excited state (S1) induces two high peaks in the anisotropy spectra of d-glyceraldehyde, which should be seen in future experimental studies.

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Measurement and comparison of absolute value of soft X-ray natural circular dichroism of serine and alanine

Cited by 10 publications

References 15 publications

Chiroptical Study of α-Aliphatic Amino Acid Films in the Vacuum Ultraviolet Region

Chiroptical Study of α-Aliphatic Amino Acid Films in the Vacuum Ultraviolet Region

Optical Absorption Cross-Section of DNA Bases—Thymine and Guanine—in the Energy Region from 3.1 to 250 eV (5–400 nm)

Theoretical Study of the Anisotropy Spectra of the Valine Zwitterion and Glyceraldehyde

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