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8 pages, 1107 KiB

Open AccessArticle

Measurement of Circular Dichroism Spectra without Control of a Phase Modulator using Retardation Domain Analysis

by Hiroshi Satozono

Molecules 2019, 24(7), 1418; https://doi.org/10.3390/molecules24071418 - 10 Apr 2019

Cited by 2 | Viewed by 3521

Abstract

This study investigated the measurement of circular dichroism (CD) spectra without controlling a phase modulator. In a conventional CD system, the peak retardation of the phase modulator must remain constant over the observed wavelength range. Thus, the phase modulator must be controlled to [...] Read more.

This study investigated the measurement of circular dichroism (CD) spectra without controlling a phase modulator. In a conventional CD system, the peak retardation of the phase modulator must remain constant over the observed wavelength range. Thus, the phase modulator must be controlled to maintain an appropriate modulation degree at an observed wavelength. In contrast, CD obtained using retardation domain analysis is not affected by peak retardation. Consequently, CD spectra can be measured without control of the phase modulator, which was experimentally demonstrated in this study. Additionally, linear dichroism spectra were obtained using retardation domain analysis. Full article

(This article belongs to the Special Issue Recent Advances in Chiroptical Spectroscopy)

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17 pages, 2774 KiB

Open AccessArticle

Chiroptical Symmetry Analysis: Exciton Chirality-Based Formulae to Understand the Chiroptical Responses of C_n and D_n Symmetric Systems

by Silvia Castro-Fernández, Ángeles Peña-Gallego, Ricardo A. Mosquera and José Lorenzo Alonso-Gómez

Molecules 2019, 24(1), 141; https://doi.org/10.3390/molecules24010141 - 1 Jan 2019

Cited by 6 | Viewed by 4080

Abstract

The high sensitivity of chiroptical responses to conformational changes and supramolecular interactions has prompted an increasing interest in the development of chiroptical applications. However, prediction of and understanding the chiroptical responses of the necessary large systems may not be affordable for calculations at [...] Read more.

The high sensitivity of chiroptical responses to conformational changes and supramolecular interactions has prompted an increasing interest in the development of chiroptical applications. However, prediction of and understanding the chiroptical responses of the necessary large systems may not be affordable for calculations at high levels of theory. In order to facilitate the development of chiroptical applications, methodologies capable of evaluating the chiroptical responses of large systems are necessary. The exciton chirality method has been extensively used for the interaction between two independent chromophores through the Davydov model. For systems presenting C₂ or D₂ symmetry, one can get the same results by applying the selection rules. In the present article, the analysis of the selection rules for systems with symmetries C_n and D_n with n = 3 and 4 is used to uncover the origin of their chiroptical responses. We foresee that the use of the Chiroptical Symmetry Analysis (CSA) for systems presenting the symmetries explored herein, as well as for systems presenting higher symmetries will serve as a useful tool for the development of chiroptical applications. Full article

(This article belongs to the Special Issue Recent Advances in Chiroptical Spectroscopy)

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12 pages, 3541 KiB

Open AccessArticle

Sample Volume Reduction Using the Schwarzschild Objective for a Circular Dichroism Spectrophotometer and an Application to the Structural Analysis of Lysine-36 Trimethylated Histone H3 Protein

by Yudai Izumi and Koichi Matsuo

Molecules 2018, 23(11), 2865; https://doi.org/10.3390/molecules23112865 - 2 Nov 2018

Cited by 4 | Viewed by 3713

Abstract

With the increasing interest in scarce proteins, reducing the sample volume for circular dichroism (CD) spectroscopy has become desirable. Demagnification of the incident beam size is required to reduce the sample volume for CD spectroscopy detecting transmitted light passed through the sample. In [...] Read more.

With the increasing interest in scarce proteins, reducing the sample volume for circular dichroism (CD) spectroscopy has become desirable. Demagnification of the incident beam size is required to reduce the sample volume for CD spectroscopy detecting transmitted light passed through the sample. In this study, the beam size was demagnified using a focal mirror, and small-capacity sample cells were developed in an attempt to reduce the sample volume. The original beam size was 6 × 6 mm²; we successfully converged it to a size of 25 × 25 μm² using the Schwarzschild objective (SO). The new sample cell and SO allowed the required sample volume to be reduced to 1/10 (15 → 1.5 μL), when using a 15 μm path length cell. By adopting a smaller sample cell, further sample reduction could be achieved. By using the SO system, the secondary structural contents of the lysine-36 trimethylated histone H3 protein were analyzed. The trimethylation induced the increment of helix structures and decrement of unordered structures. These structural alterations may play a role in regulating cellular function(s), such as DNA damage repair processes. Full article

(This article belongs to the Special Issue Recent Advances in Chiroptical Spectroscopy)

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36 pages, 9318 KiB

Open AccessFeature PaperArticle

Questions of Mirror Symmetry at the Photoexcited and Ground States of Non-Rigid Luminophores Raised by Circularly Polarized Luminescence and Circular Dichroism Spectroscopy: Part 1. Oligofluorenes, Oligophenylenes, Binaphthyls and Fused Aromatics

by Michiya Fujiki, Julian R. Koe, Takashi Mori and Yoshihiro Kimura

Molecules 2018, 23(10), 2606; https://doi.org/10.3390/molecules23102606 - 11 Oct 2018

Cited by 13 | Viewed by 6532 | Correction

Abstract

We report experimental tests of whether non-rigid, π-conjugated luminophores in the photoexcited (S₁) and ground (S₀) states dissolved in achiral liquids are mirror symmetrical by means of circularly polarized luminescence (CPL) and circular dichroism (CD) spectroscopy. [...] Read more.

We report experimental tests of whether non-rigid, π-conjugated luminophores in the photoexcited (S₁) and ground (S₀) states dissolved in achiral liquids are mirror symmetrical by means of circularly polarized luminescence (CPL) and circular dichroism (CD) spectroscopy. Herein, we chose ten oligofluorenes, eleven linear/cyclic oligo-p-arylenes, three binaphthyls and five fused aromatics, substituted with alkyl, alkoxy, phenyl and phenylethynyl groups and also with no substituents. Without exception, all these non-rigid luminophores showed negative-sign CPL signals in the UV-visible region, suggesting temporal generation of energetically non-equivalent non-mirror image structures as far-from equilibrium open-flow systems at the S₁ state. For comparison, unsubstituted naphthalene, anthracene, tetracene and pyrene, which are achiral, rigid, planar luminophores, did not obviously show CPL/CD signals. However, camphor, which is a rigid chiral luminophore, showed mirror-image CPL/CD signals. The dissymmetry ratio of CPL (g_lum) for the oligofluorenes increased discontinuously, ranging from ≈ −(0.2 to 2.0) × 10⁻³, when the viscosity of the liquids increased. When the fluorene ring number increased, the g_lum value extrapolated at [η] = 0 reached −0.8 × 10⁻³ at 420 nm, leading to (–)-CPL signals predicted in the vacuum state. Our comprehensive CPL and CD study should provide a possible answer to the molecular parity violation hypothesis arising due to the weak neutral current mediated by the Z⁰-boson. Full article

(This article belongs to the Special Issue Recent Advances in Chiroptical Spectroscopy)

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9 pages, 1724 KiB

Open AccessArticle

Circular Dichroism in Fluorescence Emission Following the C 1s→π* Excitation and Resonant Auger Decay of Carbon Monoxide

by Martin Pitzer, Philipp Schmidt, Christian Ozga, Andreas Hans, Philipp Reiß, Ivan D. Petrov, Anton N. Artemyev, Arno Ehresmann, André Knie and Philipp V. Demekhin

Molecules 2018, 23(7), 1534; https://doi.org/10.3390/molecules23071534 - 26 Jun 2018

Viewed by 4617

Abstract

Dichroism in angle-resolved spectra of circularly polarized fluorescence from freely-rotating CO molecules was studied experimentally and theoretically. For this purpose, carbon monoxide in the gas phase was exposed to circularly polarized soft X-ray synchrotron radiation. The photon energy was tuned across the C [...] Read more.

Dichroism in angle-resolved spectra of circularly polarized fluorescence from freely-rotating CO molecules was studied experimentally and theoretically. For this purpose, carbon monoxide in the gas phase was exposed to circularly polarized soft X-ray synchrotron radiation. The photon energy was tuned across the C 1s→π* resonant excitation, which decayed via the participator Auger transition into the CO⁺ A ²Π state. The dichroic parameter β1 of the subsequent CO⁺ (A ²Π → X ²Σ⁺) visible fluorescence was measured by photon-induced fluorescence spectroscopy. Present experimental results are explained with the ab initio electronic structure and dynamics calculations performed by the single center method. Our results confirm the possibility to perform partial wave analysis of the emitted photoelectrons in closed-shell molecules. Full article

(This article belongs to the Special Issue Recent Advances in Chiroptical Spectroscopy)

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9 pages, 20067 KiB

Open AccessArticle

Long-Time Relaxation of Stress-Induced Birefringence of Microcrystalline Alkali Halide Crystals

by Hiroki Ueno, Ryoga Arakane, Yoshihisa Matsumoto, Tomoki Tsumura, Akihito Kitazaki, Toru Takahashi, Shotaro Hirao, Yasushi Ohga and Takunori Harada

Molecules 2018, 23(4), 757; https://doi.org/10.3390/molecules23040757 - 25 Mar 2018

Cited by 3 | Viewed by 4940

Abstract

Alkali halide single crystals are most commonly used as the diluent matrix in the tablet method or disk technique for spectroscopic measurements. However, stress-induced birefringence (SIB) of alkali halides as well as intrinsic birefringence manifest during the disk formation process. Thus, the true [...] Read more.

Alkali halide single crystals are most commonly used as the diluent matrix in the tablet method or disk technique for spectroscopic measurements. However, stress-induced birefringence (SIB) of alkali halides as well as intrinsic birefringence manifest during the disk formation process. Thus, the true chiroptical measurement is disturbed by optical anisotropies (OA) containing SIB and intrinsic birefringence, except in the case of optical homogeneity. SIB is generally larger than intrinsic birefringence and has a value of several thousand millidegrees in the ultraviolet-visible wavelength range, although this varies with disk type. Here, to investigate the SIB origin, alkali halide crystals were examined using polarized light, X-ray diffraction, Fourier-transform infrared, and electron backscattering diffraction spectroscopic measurements. It was found that, after stress release, the SIB exhibited nonlinear long-time relaxation, which roughly converged within several hours, with the only time-invariant intrinsic birefringence remaining being due to OA. This behavior was strongly related to an increase in the quasi-amorphous domain and the generation of an air gap between the crystallite boundaries and their pellets. Further, a straightforward correlation was found between amorphization and an increase in the disk water content caused by deliquescence. Thus, the OA of alkali halide single crystals was found to have two different origins yielding intrinsic birefringence and SIB. Full article

(This article belongs to the Special Issue Recent Advances in Chiroptical Spectroscopy)

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10 pages, 1069 KiB

Open AccessArticle

Chiral and Molecular Recognition through Protonation between Aromatic Amino Acids and Tripeptides Probed by Collision-Activated Dissociation in the Gas Phase

by Akimasa Fujihara, Hikaru Inoue, Masanobu Sogi, Michiko Tajiri and Yoshinao Wada

Molecules 2018, 23(1), 162; https://doi.org/10.3390/molecules23010162 - 13 Jan 2018

Cited by 6 | Viewed by 4572

Abstract

Chiral and molecular recognition through protonation was investigated through the collision-activated dissociation (CAD) of protonated noncovalent complexes of aromatic amino acid enantiomers with l-alanine- and l-serine-containing tripeptides using a linear ion trap mass spectrometer. In the case of l-alanine-tripeptide (AAA), [...] Read more.

Chiral and molecular recognition through protonation was investigated through the collision-activated dissociation (CAD) of protonated noncovalent complexes of aromatic amino acid enantiomers with l-alanine- and l-serine-containing tripeptides using a linear ion trap mass spectrometer. In the case of l-alanine-tripeptide (AAA), NH₃ loss was observed in the CAD of heterochiral H⁺(d-Trp)AAA, while H₂O loss was the main dissociation pathways for l-Trp, d-Phe, and l-Phe. The protonation site of heterochiral H⁺(d-Trp)AAA was the amino group of d-Trp, and the NH₃ loss occurred from H⁺(d-Trp). The H₂O loss indicated that the proton was attached to the l-alanine tripeptide in the noncovalent complexes. With the substitution of a central residue of l-alanine tripeptide to l-Ser, ASA recognized l-Phe by protonation to the amino group of l-Phe in homochiral H⁺(l-Phe)ASA. For the protonated noncovalent complexes of His enantiomers with tripeptides (AAA, SAA, ASA, and AAS), protonated His was observed in the spectra, except for those of heterochiral H⁺(d-His)SAA and H⁺(d-His)AAS, indicating that d-His did not accept protons from the SAA and AAS in the noncovalent complexes. The amino-acid sequences of the tripeptides required for the recognition of aromatic amino acids were determined by analyses of the CAD spectra. Full article

(This article belongs to the Special Issue Recent Advances in Chiroptical Spectroscopy)

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Review

Jump to: Research, Other

22 pages, 619 KiB

Open AccessFeature PaperReview

Instrumentation for Vibrational Circular Dichroism Spectroscopy: Method Comparison and Newer Developments

by Timothy A. Keiderling

Molecules 2018, 23(9), 2404; https://doi.org/10.3390/molecules23092404 - 19 Sep 2018

Cited by 23 | Viewed by 9736

Abstract

Vibrational circular dichroism (VCD) is a widely used standard method for determination of absolute stereochemistry, and somewhat less so for biomolecule characterization and following dynamic processes. Over the last few decades, different VCD instrument designs have developed for various purposes, and reliable commercial [...] Read more.

Vibrational circular dichroism (VCD) is a widely used standard method for determination of absolute stereochemistry, and somewhat less so for biomolecule characterization and following dynamic processes. Over the last few decades, different VCD instrument designs have developed for various purposes, and reliable commercial instrumentation is now available. This review will briefly survey historical and currently used instrument designs and describe some aspects of more recently reported developments. An important factor in applying VCD to conformational studies is theoretical modeling of spectra for various structures, techniques for which are briefly surveyed. Full article

(This article belongs to the Special Issue Recent Advances in Chiroptical Spectroscopy)

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11 pages, 2216 KiB

Open AccessReview

UV-Denaturation Assay to Assess Protein Photostability and Ligand-Binding Interactions Using the High Photon Flux of Diamond B23 Beamline for SRCD

by Rohanah Hussain, Edoardo Longo and Giuliano Siligardi

Molecules 2018, 23(8), 1906; https://doi.org/10.3390/molecules23081906 - 31 Jul 2018

Cited by 13 | Viewed by 5178

Abstract

Light irradiation with high photon flux in the vacuum and far-UV region is known to denature the conformation of biopolymers. Measures are in place at Diamond Light Source B23 beamline for Synchrotron Radiation Circular Dichroism (SRCD) to control and make this effect negligible. [...] Read more.

Light irradiation with high photon flux in the vacuum and far-UV region is known to denature the conformation of biopolymers. Measures are in place at Diamond Light Source B23 beamline for Synchrotron Radiation Circular Dichroism (SRCD) to control and make this effect negligible. However, UV denaturation of proteins can also be exploited as a novel method for assessing biopolymer photostability as well as ligand-binding interactions. Usually, host–ligand binding interactions can be assessed monitoring CD changes of the host biopolymer upon ligand addition. The novel method of identifying ligand binding monitoring the change of relative rate of UV denaturation using SRCD is especially important when there are very little or insignificant secondary structure changes of the host protein upon ligand binding. The temperature study, another method used to determine molecular interactions, can often be inconclusive when the thermal effect associated with the displacement of the bound solvent molecules by the ligand is also small, making the determination of the binding interaction inconclusive. Herein we present a review on the UV-denaturation assay as a novel method to determine the relative photostability of protein formulations as well as the screening of ligand-binding interactions using the high photon flux Diamond B23 beamline for SRCD. Full article

(This article belongs to the Special Issue Recent Advances in Chiroptical Spectroscopy)

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