Vibrational circular dichroism spectroscopy in the C-D, XY, and XYZ stretching region

Vibrational circular dichroism (VCD) spectroscopy is a powerful technique for structural analysis of chiral molecules, but information available from VCD spectra of large molecular systems can be limited by severe overlap of vibrational bands. While common chiral molecules do not absorb in the 1900-2400 cm-1 region, observation of VCD signals in this spectrally-isolated region is possible for molecules containing C-D, XY, and XYZ chromophores. Thus, a strategic introduction of these chromophores to a target molecule may produce VCD signals informative for molecular structures. VCD spectroscopy in the 1900-2400 cm-1 region is a rather unexplored research field and its basic properties remain to be investigated. This perspective article discusses insight obtained so far on the usefulness and physicochemical aspects of VCD spectroscopy in this region with briefly summarizing previous experimental VCD studies including classic examples as well as our recent results. We show that anharmonic effects such as overtones and combination bands often complicate VCD patterns. On the other hand, some molecules exhibit characteristic VCD signals that can be well interpreted by harmonic DFT spectral calculations for structural analysis. This article also discusses several examples of the use of this region for studying solute-solvent interactions and for VCD signal augmentation.

Supramolecular Chirogenesis in a Sterically Hindered Porphyrin: A Critical Theoretical Analysis

The determination of molecular stereochemistry and absolute configuration is an important part of modern chemistry, pharmacology, and biology. Electronic circular dichroism (ECD) spectroscopy is a widely used tool for chirality assignment, especially with porphyrin macrocycles employed as reporter chromophores. However, the mechanisms of induced ECD in porphyrin complexes are yet to be comprehensively rationalized. In this work, the ECD spectra of a sterically hindered hexa-cationic porphyrin with two camphorsulfonic acids in dichloromethane and chloroform were experimentally measured and computationally analyzed. The influence of geometric factors such as the position of chiral guest molecules, distortion of the porphyrin macrocycle, and orientation of aromatic and non-aromatic peripheral substituents on the ECD spectra was theoretically studied. Various potential pitfalls, such as a lack of significant conformations and accidental agreement of experimental and simulated spectra, are considered and discussed.

Scope and limitations of absolute configuration determination of allenic natural products using the CCC stretching VCD signal

The allene functional group in natural products isolated so far exists in a non-racemic form, but its axial chirality is difficult to elucidate. Allenes exhibit a characteristic antisymmetric CCC stretching mode at around 1950 cm^-1, and their VCD properties have not been studied in detail. This work, for the first time, applied VCD spectroscopy to allenic natural products and allenic molecules with other asymmetric centers focusing on the antisymmetric CCC stretching mode. This vibrational mode yielded a negligibly weak VCD signal for several molecules, but in the presence of electron-withdrawing and/or conjugating substituents, it generated a stronger one. Its sign was found to be influenced by the nature of substituents. These findings should deepen the understanding of the VCD properties of the allene functional group and should be useful for future studies of chiral allenes.

Anonazepine, a new alkaloid from the leaves of Annona muricata (Annonaceae)

From the CHCl3-soluble extract of Annona muricata L. (Annonaceae) leaves, one new 3-benzazepine-type alkaloid, anonazepine (1), and four known aporphine-type alkaloids, (+)-laurotetanine (2), (+)-norglaucine (3), (−)-xylopine (4), and lanuginosine (5), were isolated. Except for (−)-xylopine (4), these remaining known alkaloids were first reported in A. muricata. The structures of the isolated alkaloids were established by 1D and 2D NMR spectroscopy and MS, as well as comparison with literature data. The new 3-benzazepine-type alkaloid existed in an inseparable mixture of two equilibrium conformers. Its absolute configuration was determined based on comparing their experimental and calculated ECD data. The anti-inflammatory activity of the isolated alkaloids was investigated, but none of the alkaloids showed a significant result.

Deuterium labelling to extract local stereochemical information by VCD spectroscopy in the C-D stretching region: a case study of sugars

Stereochemical elucidation of molecules with multiple chiral centers is difficult. Even with VCD spectroscopy, excluding all but one diastereomeric structural candidate is challenging because the stereochemical inversion of one chiral center among many centers does not always result in noticeable differences in their VCD spectra. This work demonstrates that the introduction of a suitable VCD chromophore with absorption in the 2300-1900 cm^-1 region can be used for extracting local stereochemical information and for the stereochemical assignment of the C-1 position of various sugars as a case study. Through studies on a series of epimeric pairs of monosaccharides and their derivatives, we found that the introduction of one -OCD₃ group to each C-1 position produced almost mirror-image VCD patterns in the 2300-1900 cm^-1 region depending on the C-1 stereochemistry irrespective of the other molecular moieties. This work also shows that comparison of the observed VCD signals and the calculated ones enables the stereochemical assignment of a chiral center in the vicinity of the chromophore. This study provides a proof of concept that the use of a VCD chromophore in the 2300-1900 cm^-1 region enables the analysis of selected stereochemistry of suitable molecular systems. Further studies on this concept should lead to the development of a method useful for the structural elucidation of other types of complex molecules.

Exploration of chromophores for a VCD couplet in a spectrally transparent infrared region for biomolecules

Interactions of two chromophores such as carbonyl groups yield a strong VCD couplet that reflects the molecular structures. The use of VCD couplets for biomacromolecular structural studies has been hampered by severe signal overlap caused by numerous functional groups that originally exist in biomacromolecules. Nitrile, isonitrile, alkyne, and azido groups show characteristic IR absorption in the 2300-2000 cm^-1 region, where biomolecules do not strongly absorb. We herein examined the usefulness of these functional groups as chromophores to observe a strong VCD couplet that can be readily interpreted using theoretical calculations. Studies on a chiral binaphthyl scaffold possessing two identical chromophores showed that nitrile and isonitrile groups generate moderately-strong but complex VCD signals due to anharmonic contributions. The nature of their anharmonic VCD patterns is discussed by comparison with the VCD spectrum of a mono-chromophoric molecule and by anharmonic DFT calculations. On the other hand, through studies on diazido binaphthyl and diazido monosaccharide, we demonstrated that the azido group is more promising for structural analysis of larger molecules due to its simple, strong VCD couplet whose spectral patterns are readily predicted by harmonic DFT calculations.

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

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.

Self-assembly as a key player for materials nanoarchitectonics

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 re-examines 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, light-harvesting, 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.

Preparation of Carbodiimides with One-Handed Axial Chirality

The axial chirality of carbodiimide was proposed in 1932, but the synthesis of carbodiimide with one-handed axial chirality has not been achieved because of the low barrier of racemization. This work presents a strategy to use a conformationally restrained cyclic structure for creating carbodiimides whose biases of the axial chirality (labeled as S_NCN/ R_NCN) are higher than 100:1, as determined by vibrational circular dichroism spectroscopy and density functional theory calculations.

Nanoarchitectonic-Based Material Platforms for Environmental and Bioprocessing Applications

The challenges of pollution, environmental science, and energy consumption have become global issues of broad societal importance. In order to address these challenges, novel functional systems and advanced materials are needed to achieve high efficiency, low emission, and environmentally friendly performance. A promising approach involves nanostructure-level controls of functional material design through a novel concept, nanoarchitectonics. In this account article, we summarize nanoarchitectonic approaches to create nanoscale platform structures that are potentially useful for environmentally green and bioprocessing applications. The introduced platforms are roughly classified into (i) membrane platforms and (ii) nanostructured platforms. The examples are discussed together with the relevant chemical processes, environmental sensing, bio-related interaction analyses, materials for environmental remediation, non-precious metal catalysts, and facile separation for biomedical uses.

Nanoparticle-based Chemiluminescence for Chiral Discrimination of Thiol-Containing Amino Acids

The ability to recognize the molecular chirality of enantiomers is extremely important owing to their critical role in drug development and biochemistry. Convenient discrimination of enantiomers has remained a challenge due to lack of unsophisticated methods. In this work, we have reported a simple strategy for chiral recognition of thiol-containing amino acids including penicillamine (PA), and cysteine (Cys). We have successfully designed a nanoparticle-based chemiluminescence (CL) system based on the reaction between cadmium telluride quantum dots (CdTe QDs) and the enantiomers. The different interactions of CdTe QDs with PA enantiomers or Cys enantiomers led to different CL intensities, resulting in the chiral recognition of these enantiomers. The developed method showed the ability for determination of enantiomeric excess of PA and Cys. It has also obtained an enantioselective concentration range from 1.15 to 9.2 mM for PA. To demonstrate the potential application of this method, the designed platform was applied for the quantification of PA in urine and tablet samples. For the first time, we presented a novel practical application of nanoparticle-based CL system for chiral discrimination.

Stereochemistry (and Conformation) of Nucleosides and Their Synthetic Precursors by Vibrational Circular Dichroism

The chemistry of artificial nucleosides is associated with the difficulties in the characterization of the stereochemistry and conformation of their furanose ring moiety. This unit describes how to use vibrational circular dichroism (VCD) spectroscopy to identify the three-dimensional structure of nucleosides. The experimental part of this protocol is dedicated to obtain a VCD spectrum of a sample with high S/N ratio. The computational part generally starts with a conformational search using molecular mechanics and the following structural optimization by density functional theory calculation. Then, theoretical VCD spectra of stable conformers are calculated and averaged on the basis of their Boltzmann population. Finally, the obtained experimental and theoretical VCD spectra are compared qualitatively or quantitatively. The agreement between these spectra leads to determination of the stereochemistry of the studied molecule. This protocol may also be useful for analyzing the conformation of nucleosides. © 2018 by John Wiley & Sons, Inc.