New description of molecular chirality and its application to the prediction of the preferred enantiomer in stereoselective reactions

A new representation of molecular chirality as a fixed-length code is introduced. This code describes chiral carbon atoms using atomic properties and geometrical features independent of conformation and is able to distinguish between enantiomers. It was used as input to counterpropagation (CPG) neural networks in two different applications. In the case of a catalytic enantioselective reaction the CPG network established a correlation between the chirality codes of the catalysts and the major enantiomer obtained by the reaction. In the second application-enantioselective reduction of ketones by DIP-chloride-the series of major and minor enantiomers produced from different substrates were clustered by the CPG neural network into separate regions, one characteristic of the minor products and the other characteristic of the major products.     

Large-Scale Chirality Measures and General Symmetry Deficiency Measures for Functional Group Polyhedra of Proteins

Functional Group Polyhedra provide a simplified representation of the most essential spatial features of macromolecules, especially, of globular proteins. Since the functional group polyhedron model focuses on large scale features, the chirality and other symmetry deficiency measures of these molecules, when adapted to these polyhedra, should also be based on the characterization of large scale shape features. Two new approaches for the evaluation of such symmetry deficiency and chirality measures are presented.     

Mechanism of diastereoisomer-induced chirality of BiOBr

Chiral molecule-driven asymmetric structures are known to be elusive because of the intriguing chirality transfer from chiral molecules to achiral species. Here, we found that the chiral assembly of BiOBr is independent of the chirality of the organic molecular inducer but dependent on geometric structural matching between the inducer and inorganic species. Diastereoisomeric sugar alcohols (DSAs) with identical numbers of carbon chiral centers and functional groups but with different R/S configurations and optical activities (OAs) were chosen as symmetry-breaking agents for inducing chiral mesostructured BiOBr films (CMBFs) under hydrothermal conditions. Multiple levels of chirality with different handedness were identified in the CMBFs. Density functional theory (DFT) calculations and molecular dynamics (MD) simulations suggest that asymmetric defects in the Br–Bi tetragonal cone caused by physically adsorbed DSAs on the surfaces of the BiOBr crystals are the geometric basis for triggering the chiral twist in the BiOBr monolayer. Our findings provide new insights for understanding the origin of chirality and the chiral transfer mechanism underlying the assembly of achiral species.

The chirality transfer is dependent on geometrical matching between the chiral inducer and inorganic species.     

Theoretical investigation of Raman optical activity signatures of Tröger's base

The Raman and VROA spectra of (S,S)-Tr?ger's base are simulated. We mainly discuss the peaks in the 1140-1400 cm(-1) wavenumber range where an intense VROA signature is found. In this range, nearly all of the Raman-active bands belong to the irreducible representation A (C(2) point group), whereas no such observation is made for the VROA spectrum. The vibrational normal modes associated with the peaks in this range mainly consist of wagging and twisting motions of the hydrogen atoms. From the atomic contribution patterns (ACPs) and the group coupling matrices (GCMs), one finds that the VROA backward-scattering intensities mainly arise from hydrogen and carbon atoms in the vicinity of the two chiral nitrogen atoms. The VROA signatures in the 1140-1400 cm(-1) range are therefore a fingerprint of the local chirality around the two chiral nitrogen centers.     

Size-dependent exciton chirality in (R)-(+)-1,1'-bi-2-naphthol dimethyl ether nanoparticles

Organic nanoparticles from a chiral auxiliary, (R)-(+)-1,1'-bi-2-naphthol dimethyl ether (BNDE), with a range of particle sizes from 25 to 100 nm were fabricated through the reprecipitation method. It is found that BNDE nanoparticles exhibit positive exciton chirality in 200-260 nm region in circular dichroism (CD) spectra, which are completely opposite to CD spectra of the dilute solution. The exciton chirality of the particles displays size-dependent behavior; that is, the exciton chirality peaks evolve to the low-energy side with increase in particles size. CD spectra accompanied with UV, fluorescence spectra, lifetime measurements of the excited states, and quantum mechanical calculations reveal that the chirality inversion results from intermolecular exciton coupling between two adjacent BNDE molecules in the nanoparticles, and the bathochromic shift of the peaks is attributed to the increased intermolecular interaction with increasing particle size.     

Experimental tests of chirality algebra

Most chiral molecules can be dissected into a collection of ligands attached to an underlying skeleton. Application of permutation group theory and group representation theory to such a model can lead to chirality functions which can be used to approximate pseudoscalar measurements such as optical rotation or circular dichroism. Such chirality functions have been tested experimentally for the following skeletons: (1) The polarized triangle of phosphines and phosphine oxides; (2) the tetrahedron of methane derivatives; (3) the disphenoid of allene and 2, 2-spirobiindane derivatives; (4) the polarized rectangle of [2, 2]-metacyclophanes; (5) the polarized pentagon of heterodisubstituted ferrocenes. The success of this method is fair to good for the polarized triangle, tetrahedron, and disphenoid skeletons but deteriorates rapidly for the polarized rectangle and polarized pentagon skeletons, in accord with the greater group-theoretical complexity of the latter skeletons.     

Inclusion Complexes of Dyes and Cyclodextrins: Modeling Supermolecules by Rigorous Quantum Mechanics

The results of structure optimization and molecular dynamics simulationof host-guest -cyclodextrin-pinacyanol dye inclusion complexesare obtained by applying a density functional based tight-binding code.The results attempt to correlate UV/Vis and circular dichroism spectraldata with calculated aggregate structures of the sandwich dimer, withthe monomers twisted slightly against each other. The sense of twist ispredetermined by the chirality of the complexing host. The UV/Vis-spectralare interpreted using the exciton model. Within this model, each excitedstate of the monomer generates two excitonic states in the dimer. Theinteraction between the two monomers results then in a Davydov splittingof the two dimer states. The opposite signs of the two dimer states can beattributed to the twist of the monomers when they interact.     

Is There a “Most Chiral Tetrahedron”?

A degree of chirality is a function that purports to measure the amount of chirality of an object: it is equal for enantiomers, vanishes only for achiral or degenerate objects and is similarity invariant, dimensionless and normalisable to the interval [0,1]. For a tetrahedron of non-zero three-dimensional volume, achirality is synonymous with the presence of a mirror plane containing one edge and bisecting its opposite, and hence it is easy to design degree-of-chirality functions based on edge length that incorporate all constraints. It is shown that such functions can have largest maxima at widely different points in the tetrahedral shape space, and by incorporation of appropriate factors, the maxima can be pushed to any point in the space. Thus the phrase "most chiral tetrahedron" has no general meaning: any chiral tetrahedron is the most chiral for some legitimate choice of degree of chirality.     

Theoretical study of the 13C NMR spectroscopy of single-walled carbon nanotubes

The 13C NMR spectroscopy of armchair and zigzag single-walled carbon nanotubes has been investigated theoretically. Spectra for (4,4), (5,5), (6,6), (6,0), (9,0), and (10,0) nanotubes have been simulated based on ab initio calculations of model systems. The calculations predict a dominant band arising from the carbon atoms in the "tube" with smaller peaks at higher chemical shifts arising from the carbon atoms of the caps. The dominant band lies in the range of 128 and 138 ppm. Its position depends weakly on the length, width, and chirality of the tubes. The calculations demonstrate how structural information may be gleaned from relatively low-resolution nanotube 13C NMR spectra.     

Chirality polynomials

Chirality algebra uses ideas from permutation group theory and group representation theory to derive chirality polynomials having appropriate transformation properties for estimation of the magnitude and sign of a given pseudoscalar property (e.g. optical rotation, circular dichroism) for a given skeleton using parameters which depend only upon the ligands located at the specific sites of the skeleton, the particular skeleton, and the particular pseudoscalar property. For all but the simplest skeletons, a qualitatively complete chirality polynomial describing all chirality phenomena associated with the skeleton contains more than one component and thus requires more than one set of ligand parameters. Qualitatively complete chirality polynomials are reviewed for the most important transitive skeletons (i.e. skeletons in which all sites are equivalent), including the polarized triangle, tetrahedron, disphenoid (allene), polarized square, polarized rectangle, polarized pentagon, octahedron, trigonal prism (cyclopropane), and polarized heptagon skeletons.     

Influence of point defects on the structural and electronic properties of SiC nanotubes

We have performed studies of the structural and electronic properties of functionalized single wall silicon carbide nanotubes (SW-SiCNTs) with chirality (5,5). Our first principles studies are done using density functional theory. The exchange-correlation energies are modeled according to the Hamprecht-Cohen-Tozer-Handy functional in the generalized gradient approximation (HCTH-GGA) and the DNP basis function with double polarization is applied. To determine the most stable geometry, we have applied the minimum energy criterion considering several initial configurations of the hydroxyl (OH) functional group interacting with the single wall SiCNT. In particular, we tested different orientations of the OH adsorbed on the nanotube surface (oriented towards the Si or C atoms) and at the end of the nanotube. Results indicate that the most favorable geometry corresponds to OH adsorption (chemisorption) at the end of the nanotube. The polarity increases yielding better conditions for solubility and dispersion. The work function of the SW-SiCNT-OH is reduced, which in turn favors conditions for field emission properties (FEPs). Finally, the presence of silicon or carbon mono-vacancies in the functionalized nanotubes suggests this may be a good structure to fabricate semiconductor devices      

Can Raman Optical Activity Separate Axial from Local Chirality? A Theoretical Study of Helical Deca‐Alanine

Motivated by experimental work on the distinction of protein secondary structure motifs by Raman optical activity (ROA) spectroscopy, we demonstrate using density functional theory that axial chirality in structures with different local chirality can be filtered out by ROA spectroscopy. To this purpose, two diastereomers of right-handed helical deca-alanine, the (all-S) and the (R,S,R,S,R,S,R,S,R,S) form, are compared. Furthermore, we suggest to interpret calculated ROA spectra of large molecules in terms of vibrational bands rather than individual peaks. This is due to the non-homogeneous effect of the harmonic approximation as well as of the chosen electronic structure method onto the vibrational frequencies, which in a dense region of many vibrations will strongly determine the shape of the spectrum. In addition, the calculated ROA spectrum of (all-S)-deca-alanine is compared to the experimental spectrum of poly-(L)-alanine in solution.     

Simple One-electron Invariants of Molecular Chirality

Pseudoscalar measures of electronic chirality for molecular systems are derived using the spectral moment theory applied to the frequency-dependent rotational susceptibility. In this scheme a one-electron chirality operator naturally emerges as a quantum counterpart of the triple scalar product, involving velocity, acceleration and second acceleration. Averaging over an electronic state vector gives rise to an additive chirality invariant (κ-index), considered as a quantitative measure of chirality. A simple computational technique for quick calculation of the κ-index is developed and various structural classes (cyclic hydrocarbons, cage-shaped systems, etc.) are studied. Reasonable behaviour of the chirality index is demonstrated. The chirality changes during the β-turn formation in Leu-Enkephalin is presented as a useful example of the chirality analysis for conformational transitions.     

Chiral molecular nanosilicas

Molecular nanoparticles including polyoxometalates, proteins, fullerenes and polyhedral oligosiloxane (POSS) are nanosized objects with atomic precision, among which POSS derivatives are the smallest nanosilicas. Incorporation of molecular nanoparticles into chiral aggregates either by chiral matrices or self-assembly allows for the transfer of supramolecular chirality, yet the construction of intrinsic chirality with atomic precision in discrete molecules remains a great challenge. In this work, we present a molecular folding strategy to construct giant POSS molecules with inherent chirality. Ferrocenyl diamino acids are conjugated by two or four POSS segments. Hydrogen bonding-driven folding of diamino acid arms into parallel β-sheets facilitates the chirality transfer from amino acids to ferrocene and POSS respectively, disregarding the flexible alkyl spacers. Single crystal X-ray structures, density functional theory (DFT) calculations, circular dichroism and vibrational circular dichroism spectroscopy clearly verify the preferential formation of one enantiomer containing chiral molecular nanosilicas. The chiral orientation and chiroptical properties of POSS show pronounced dependence on the substituents of α-amino acids, affording an alternative way to control the folding behavior and POSS chirality in addition to the absolute configuration of amino acids. Through the kinetic nanoprecipitation protocol, one-dimensional aggregation enables chirality transfer from the molecular scale to the micrometer scale, self-assembling into helices in accordance with the packing propensity of POSS in a crystal phase. This work, by illustrating the construction of chiral molecular nanosilicas, paves a new way to obtain discrete chiral molecular nanoparticles for potential chiroptical applications.

A molecular folding strategy is developed to construct ferrocenyl diamino acid conjugated polyhedral oligosiloxane molecules. Hydrogen bonding-driven folding facilitates the chirality transfer from the molecular scale to the micrometer scale.     

Understanding the inelastic electron-tunneling spectra of alkanedithiols on gold

We present results for a simulated inelastic electron-tunneling spectra (IETS) from calculations using the "gDFTB" code. The geometric and electronic structure is obtained from calculations using a local-basis density-functional scheme, and a nonequilibrium Green's function formalism is employed to deal with the transport aspects of the problem. The calculated spectrum of octanedithiol on gold(111) shows good agreement with experimental results and suggests further details in the assignment of such spectra. We show that some low-energy peaks, unassigned in the experimental spectrum, occur in a region where a number of molecular modes are predicted to be active, suggesting that these modes are the cause of the peaks rather than a matrix signal, as previously postulated. The simulations also reveal the qualitative nature of the processes dominating IETS. It is highly sensitive only to the vibrational motions that occur in the regions of the molecule where there is electron density in the low-voltage conduction channel. This result is illustrated with an examination of the predicted variation of IETS with binding site and alkane chain length.     

First zeolite carbon replica with a well resolved X-ray diffraction pattern

The present study demonstrates that for the nanocasting process with zeolites, a careful choice of the zeolite structure type (EMT) allows the formation of faithful carbon replica exhibiting up to three well resolved XRD peaks.     

Efficient solution of Poisson's equation with free boundary conditions

Interpolating scaling functions give a faithful representation of a localized charge distribution by its values on a grid. For such charge distributions, using a fast Fourier method, we obtain highly accurate electrostatic potentials for free boundary conditions at the cost of O(N log N) operations, where N is the number of grid points. Thus, with our approach, free boundary conditions are treated as efficiently as the periodic conditions via plane wave methods.     

Synthesis of 4,5-dihydro-1<Emphasis Type="Italic">H</Emphasis>-pyrazoles with chiral substituents at position 3 or 5

New chiral 4,5-dihydro-1H-pyrazole hydroxy and amino derivatives containing functional groups at β-position of the side chain were obtained by the selective oxidation of the corresponding pyrazolidine derivatives with air oxygen at low temperature without affection of the centers of chirality.     

Detection and amplification of chirality by helical polymers

A unique feature of synthetic helical polymers for the detection and amplification of chirality is briefly described in this article. In sharp contrast to host-guest and supramolecular systems that use small synthetic receptor molecules, chirality can be significantly amplified in a helical polymer, such as poly(phenylacetylene)s with functional pendants, which enable the detection of a tiny imbalance in biologically important chiral molecules through a noncovalent bonding interaction with high cooperativity. The rational design of polymeric receptors can be possible by using chromophoric helical polymers combined with functional groups as the pendants, which target particular chiral guest molecules for developing a highly efficient chirality-sensing system. The chirality sensing of other small molecular and supramolecular systems is also briefly described for comparison.