Analysis of Molecular Configuration and Conformation by (Electronic and) Vibrational Circular Dichroism: Theoretical Calculation and Exciton Chirality Method

Taniguchi, Tohru

doi:10.1246/bcsj.20170113

Cited by 20 publications

(7 citation statements)

References 91 publications

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“…Although cyber-space-related technologies such as information technology and artificial intelligence have made substantial recent progress, science and technology in physical space remain important for the development of human activities. By analogy with computational optimizations of efficiency and function of novel cyber technologies such as machine learning [1][2][3][4][5], the optimization of structure, combination, and organization of materials towards advanced functionality based on accumulated knowledge, theories, facts, experiences, and intuitions must continue [6][7][8][9]. Current societal demands including materials synthesis and production [10][11][12][13][14], energy storage and conversion [15][16][17][18][19][20][21][22], analyte sensing and detection [23][24][25][26], environmental remediation [27][28][29][30], and biological and biomedical applications [31][32][33][34][35][36] are currently being met through developments in the science and technology of advanced materials.…”

Section: Introductionmentioning

confidence: 99%

Self-assembly as a key player for materials nanoarchitectonics

Ariga

Nishikawa

Mori

et al. 2019

Science and Technology of Advanced Materials

364

255

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The development of science and technology of advanced materials using nanoscale units can be conducted by a novel concept involving combination of nanotechnology methodology with various research disciplines, especially supramolecular chemistry. The novel concept is called 'nanoarchitectonics' where self-assembly processes are crucial in many cases involving a wide range of component materials. This review of self-assembly processes reexamines recent progress in materials nanoarchitectonics. It is composed of three main sections: (1) the first short section describes typical examples of self-assembly research to outline the matters discussed in this review; (2) the second section summarizes self-assemblies at interfaces from general viewpoints; and (3) the final section is focused on self-assembly processes at interfaces. The examples presented demonstrate the strikingly wide range of possibilities and future potential of self-assembly processes and their important contribution to materials nanoarchitectonics. The research examples described in this review cover variously structured objects including molecular machines, molecular receptors, molecular pliers, molecular rotors, nanoparticles, nanosheets, nanotubes, nanowires, nanoflakes, nanocubes, nanodisks, nanoring, block copolymers, hyperbranched polymers, supramolecular polymers, supramolecular gels, liquid crystals, Langmuir monolayers, Langmuir-Blodgett films, self-assembled monolayers, thin films, layer-by-layer structures, breath figure motif structures, two-dimensional molecular patterns, fullerene crystals, metal-organic frameworks, coordination polymers, coordination capsules, porous carbon spheres, mesoporous materials, polynuclear catalysts, DNA origamis, transmembrane channels, peptide conjugates, and vesicles, as well as functional materials for sensing, surface-enhanced Raman spectroscopy, photovoltaics, charge transport, excitation energy transfer, lightharvesting, photocatalysts, field effect transistors, logic gates, organic semiconductors, thin-film-based devices, drug delivery, cell culture, supramolecular differentiation, molecular recognition, molecular tuning, and hand-operating (hand-operated) nanotechnology.

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Section: Introductionmentioning

confidence: 99%

Self-assembly as a key player for materials nanoarchitectonics

Ariga

Nishikawa

Mori

et al. 2019

Science and Technology of Advanced Materials

364

255

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“…Geometry optimization was carried out to reduce the calculation period for the conformer distribution population. Thereafter, the calculation was calculated in the protocol of Monte Carlo to reduce the computational effort in the conformational analysis [5,[16][17][18].…”

Section: Ecm-ecd Analysis Of 1-5mentioning

confidence: 99%

Conformational Analysis of Diterpene Lactone Andrographolide towards Reestablishment of Its Absolute Configuration via Theoretical and Experimental ECD and VCD Methods

et al. 2020

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Andrographolide, the major constituent from the terrestrial plant Andrographis paniculata is a much-studied bioactive ent-labdane diterpene lactone and has become an important medicinal intermediate. Its structure as determined by X-ray crystallography has been applied in molecular docking studies to explain biological activities. Nevertheless, recently there has been a number of conflicting reports concerning the stereochemistry at the C-14 and C-10 positions affecting the absolute configuration (AC) of the compound. Since a lack of information on the molecular flexibility of the molecule can lead to misleading conclusions on biological activity, a conformational analysis of the molecule in the solution state was necessary. The conformational analysis was performed by the Spartan14 package using the Merck Molecular Force Field (MMFF). The exciton chirality method in electronic circular dichroism spectroscopy (ECM-ECD) and vibrational circular dichroism (VCD) techniques were then jointly employed to re-establish the AC of andrographolide. Theoretical calculations were performed using TD-DFT methods by using the hybrid functionals B3LYP and CAM-B3LYP combined with 6-31G(d,p) basis set. Long-range exciton coupling of 2-naphthoyl chromophores at C-14 and C-19 led to the establishment of the AC to be 3R, 4R, 5S, 9R, 10R and 14S. Comparison between the theoretical VCD data of 14-S and 14-R stereoisomer confirmed a configuration of S at C-14 position instead of R.

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“…[37] The wise combinationo ft wo chiroptical methods (ECD-ORD, ECD-VCD; ORD = optical rotatory dispersion) may solve this problem because it seems that conformer types, relative weights, and spectralp roperties (VCD and ECD) are calculated at an acceptable similarity. [38][39][40][41]…”

Section: Conformers Shifted By Steric Repulsionmentioning

confidence: 99%

Assignment of Vibrational Circular Dichroism Cross‐Referenced Electronic Circular Dichroism Spectra of Flexible Foldamer Building Blocks: Towards Assigning Pure Chiroptical Properties of Foldamers

Farkas

Nagy

Menyhárd

et al. 2019

Chemistry A European J

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Assignment of the most established electronic circular dichroism (ECD) spectra of polypeptides and foldamers is either “evidence based” or relies on the 3D structures of longer oligomers of limited internal dynamics, which are derived from NMR spectroscopy (or X‐ray) data. Critics warn that the use of NMR spectroscopy and ECD side by side has severe limitations for flexible molecules because explicit knowledge of conformational ensembles is a challenge. Herein, an old–new method of comparing ab initio computed and measured vibrational circular dichroism (VCD) data is presented to validate both the structures (conf(i)) and their relative weights (c(i)) that make up the conformational ensemble. Based on the array of {conf(i), c(i)}, the pure ECD spectra, g(i)conf(i), can be ab initio calculated. The reconstructed spectrum Σc(i)g(i)conf(i) can thus help to assign any experimental ECD counterparts. Herein, such a protocol is successfully applied to flexible foldamer building blocks of sugar β‐amino acid diamides. The epimeric pair of the model system was selected because these molecules were conformationally tunable by simple chemical modification, and thus, the robustness of the current approach could be probed. The initial hydrogen bond (NH⋅⋅⋅O) eliminated by N‐methylation reorients the amide plain, which influences the chiroptical properties of the foldamer building block; this structural change is successfully monitored by changes to the VCD and ECD transitions, which are now assigned to pure conformers. The current method seems to be general and effective without requiring extensive CPU and spectroscopic resources.

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Analysis of Molecular Configuration and Conformation by (Electronic and) Vibrational Circular Dichroism: Theoretical Calculation and Exciton Chirality Method

Cited by 20 publications

References 91 publications

Self-assembly as a key player for materials nanoarchitectonics

Self-assembly as a key player for materials nanoarchitectonics

Conformational Analysis of Diterpene Lactone Andrographolide towards Reestablishment of Its Absolute Configuration via Theoretical and Experimental ECD and VCD Methods

Assignment of Vibrational Circular Dichroism Cross‐Referenced Electronic Circular Dichroism Spectra of Flexible Foldamer Building Blocks: Towards Assigning Pure Chiroptical Properties of Foldamers

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