Sign Of Chirality Research Articles

Molecular Docking of Chiral Drug Enantiomers With Different Bioactivities.

Chirality has an important role in the drug design because enantiomers may exhibit different bioactivity when interacting with macromolecules of a living organism. In our previous work, based on the analysis of a set of 100 chiral drugs, a relationship was established between the sign of chirality of enantiomers and their bioactivity. To understand the reasons for the observed patterns of chiral specificity of drug enantiomers, the interaction of 10 enantiomeric pairs of chiral drugs with the corresponding target proteins has been considered using molecular docking and further postprocessing by quantum chemistry methods. The data obtained confirm that the energetic aspect of the interaction between opposite enantiomers and target protein affects the enantiomer biological activity. In addition, the results show that molecular docking is able to distinguish between bioactive and inactive/less active enantiomers, although many docking programs are not accurate enough to distinguish a weak inhibitor from a strong one.

Stressmechanically Reconfigurable Chiroptical Meta‐devices in Visible Band

AbstractThe development of low‐cost and convenient procedure to produce large‐area reconfigurable chiroptical meta‐devices (CMDs) enantiomers with dynamically tunable chiroptical response in the visible band has generated significant interest, owing to its tremendous potential for applications such as optical rotary filtering, color switching, information storage, etc. Currently, many methods, such as phase change material, air pressure, bias, etc., are proposed to reconfigure the chiroptical response of the CMDs enantiomers, but still lack of ability to actively regulate the chiroptical response of the large‐area CMDs. Herein, the centimeter‐scale stressmechanically reconfigurable CMDs enantiomers with actively‐tunable chiroptical response in the visible band is proposed. The chirality sign switching and chirality intensity turning on–off of the CMDs enantiomers can be achieved by bending the flexible substrate to the desired curvature radius to turn the electromagnetic modes resonance of the CMDs enantiomers. The results provide an effective approach to supply the large‐area reconfigurable CMDs enantiomers with actively tunable chiroptical response and will open up new possibilities for chirality nanophotonic applications.

A Method for Calculating the Sign and Degree of Chirality of Supercoiled Protein Structures

Chirality plays an important role in studies of natural protein structures. Therefore, much attention is paid to solving the problems associated with the development of criteria and methods for assessing the chirality of biomolecules. In this paper, a new method for calculating the sign and degree of chirality of superhelices is proposed. The method makes it possible to characterize the chirality sign and to quantify coiled-coils and collagen superhelices. The degree of chirality is understood as a value indicating the intensity of twisting of individual helices around the axis of the superhelix. The calculation requires information about the relative spatial arrangement of the alpha carbon of the amino acid residues of the helices that make up the superhelix. The use of a small amount of raw data makes the method easy to apply, and the validity of the results of this study is confirmed through the analysis of real protein structures.

Exceptional points and lines and Dirac points and lines in magnetoactive cholesteric liquid crystals

We investigated the properties of cholesteric liquid crystals (CLCs) being in external static magnetic field directed along the helix axis. We have shown that in the case of the wavelength dependence of magneto-optic activity parameter, and in the presence of absorption new features appear in the optics of CLCs. We have shown that in this case new photonic band gaps (PBGs) appear. This new PBG is sensitive to the polarization of the incident light. But if the chirality sign of the polarization of the incident diffracting light for the basic PBG (which exist also at the absence of external magnetic field) is determined only by the chirality sign of the CLC helix, then for the second one it is determined by the external magnetic field direction (i.e., on whether the directions of the external magnetic field and the incident light are parallel, or they are antiparallel). We have shown that in this case besides Dirac points there appear also Dirac lines as well as exceptional points and exceptional lines. And moreover, near some of these points and lines the narrow bands or wide bands of magnetically induced transparency, and magnetically induced absorption appear, and near the others a wide coherent perfect absorption band appears that is insensitive to incident light polarization. And finally at some wavelength the same reflection, transmission and absorption takes place for any polarization of incident light, although it is not Dirac point nor exceptional point. This system can apply as tunable narrow-band or broad-band filters and mirrors, a highly tunable broad/narrow-band coherent perfect absorber, transmitter, ideal optical diode, and other devices.

Towards control of the chirality sign at ultrathin metal films: Bi at 2Ni/Co

Proximity effects can be used to introduce spin–orbit interactions in magnetic metallic layers in contact to a heavy metal (HM). This well known phenomenon has been exploited to induce chiral spin textures at Co ultrathin films, where the left- or right- handedness can be tuned by the HM layer position, based on the broken inversion symmetry of the film and the existence of an additive interface effect. Here we show that structural and chemical features introducing further symmetry reductions can be added to this scenario ultimately enabling control over the definition of a unique winding sense. We focus on 2Ni/Co heterostructures and Bi, a scarcely explored HM metal of large size, to combine a chemically inhomogeneous ferromagnetic stack along the normal to the surface with in-plane asymmetries. Our results are contrasted to 2Co layers combined with Ir.

НАРУШЕНИЕ СИММЕТРИИ – ФИЗИЧЕСКАЯ ОСНОВА СОВЕРШЕНИЯ «ПОЛЕЗНОЙ РАБОТЫ» БИОЛОГИЧЕСКИМИ МОЛЕКУЛЯРНЫМИ МАШИНАМИ

The physical basis for the functioning of living systems are molecular machines. The performance of "useful work" is the essence of their biological functions. Molecular machines are chiral hierarchically organized devices (constructions). They cyclically transform the form of energy by changing or switching symmetries in its chiral structural elements, which just realize the selected “quasi-mechanical” degrees of freedom in them. The phenomenon of chirality allows the formation of discrete chirally sign-alternating hierarchies of structures in macromolecular machines in the process of folding: starting from the level of asymmetric carbon in deoxyribose and amino acids. Previously, we have identified and analyzed the tendency of alternation of the sign of chirality of the intramolecular structural levels D-L-D-L for DNA and L-D-L-D for proteins. Helicity and superhelicity of intramolecular and supramolecular structures are also manifestations of chirality. Also, within the framework of the developed ideas, the chiral splitting of the properties of the elements of the structures ensures the unidirectional movement of machines along the energy cycle due to the nonlinear valve properties of the spiral structures. Spiral structures can serve as asymmetric, non-linear, mechanical, including switching, structural elements of molecular machines (like a ratchet-pawl device) in terms of rotational degrees of freedom.

Chiral superstructures of inorganic nanorods by macroscopic mechanical grinding

The development of mechanochemistry substantially expands the traditional synthetic realm at the molecular level. Here, we extend the concept of mechanochemistry from atomic/molecular solids to the nanoparticle solids, and show how the macroscopic grinding is being capable of generating chirality in self-assembled nanorod (NR) assemblies. Specifically, the weak van der Waals interaction is dominated in self-assembled NR assemblies when their surface is coated with aliphatic chains, which can be overwhelmed by a press-and-rotate mechanic force macroscopically. The chiral sign of the NR assemblies can be well-controlled by the rotating directions, where the clockwise and counter-clockwise rotation leads to the positive and negative Cotton effect in circular dichroism and circularly polarized luminescence spectra, respectively. Importantly, we show that the present approach can be applied to NRs of diverse inorganic materials, including CdSe, CdSe/CdS, and TiO2. Equally important, the as-prepared chiral NR assemblies could be served as porous yet robust chiral substrates, which enable to host other molecular materials and induce the chirality transfer from substrate to the molecular system.

Transition from spiral to ferromagnetic structure in Fe[formula omitted]Co[formula omitted]Si compounds: Small-angle neutron scattering study

The cubic noncentrosymmetric structure of the B20 compounds produces the spin helix with the wave vector ks=D/J balanced by the competition of two interactions: the large ferromagnetic exchange interaction J and small antisymmetric Dzyaloshinskii–Moriya (DM) interaction D. The mixed Fe1−xCoxSi compounds demonstrate a switch of the sign of magnetic chirality in dependence of concentration x. The sign of magnetic chirality is dictated by the structural chirality and chemical elements (Fe, Co) as well. The switch of chirality is accompanied by transformation of the helix structure to the ferromagnet and is observed at xc=0.65. Moreover, this transformation (helimagnet–ferromagnet) occurs as a function of temperature. We observe the decrease of the helical wave vector ks with lowering temperature from Tc=17 K and its abrupt zeroing at Tf=7 K. The magnetic field applied not along the easy but along the hard anisotropic axis is able to restore the helical structure in the temperature range below Tf. The mechanism of the transformation is theoretically described by a competition between the cubic anisotropy and the DM interaction. We show that anisotropy-induced ferromagnet has nonreciprocal magnon spectrum due to DM interaction even in the absence of external magnetic field.

Enhanced chiral sensing in achiral nanostructures with linearly polarized light

Chiral plasmonic nanostructures can generate large superchiral near fields owing to their intrinsic chirality, leveraging applications for molecule chirality sensing. However, the large structural chirality of chiral nanostructures poses the risk of overshadowing molecular chiral signals, hampering the practical application of chiral nanostructures. Herein, we propose an achiral nanorod that shows no structural chirality and presents strong superchiral near-fields with linearly polarized incidence. The mechanism of the strong superchiral near-field originates from the coupling between the evanescent fields of the localized surface plasmon resonance and incident light. The enhanced near-field optical chirality at the corners of the nanorods reached 25 at a wavelength of 790 nm. Meanwhile, the sign of optical chirality can be tuned by the polarization of the incident light, which provides a convenient way to control the handedness of the light. Furthermore, the enantiomers of D- and L-phenylalanine molecules were experimentally characterized using an achiral platform, which demonstrated a promising nanophotonic platform for chiral biomedical sensing.

Breaking of Odd Chirality in Magnetoelectrodeposition

Electrodeposition under magnetic fields (magnetoelectrodeposition; MED) can induce surface chirality on copper films. The chiral signs of MED films should depend on the magnetic field polarity; namely, the reversal of the magnetic field causes the opposite chiral sign. This represents odd chirality for the magnetic field polarity. However, odd chirality was broken in several MED conditions. This paper makes a survey of breaking of odd chirality in the MED conditions such as low magnetic fields, specific adsorption of chloride ions, micro-electrode, and cell rotation. These results indicate that the ordered fluctuation of magnetohydrodynamic micro-vortices induces the breaking of odd chirality and that the random fluctuation results in the disappearance of surface chirality.

Effect of Chiral Damping on the dynamics of chiral domain walls and skyrmions

Friction plays an essential role in most physical processes that we experience in our everyday life. Examples range from our ability to walk or swim, to setting boundaries of speed and fuel efficiency of moving vehicles. In magnetic systems, the displacement of chiral domain walls (DW) and skyrmions (SK) by Spin Orbit Torques (SOT), is also prone to friction. Chiral damping (αc), the dissipative counterpart of the Dzyaloshinskii Moriya Interaction (DMI), plays a central role in these dynamics. Despite experimental observation, and numerous theoretical studies confirming its existence, the influence of chiral damping on DW and SK dynamics has remained elusive due to the difficulty of discriminating from DMI. Here we unveil the effect that αc has on the flow motion of DWs and SKs driven by current and magnetic field. We use a static in-plane field to lift the chiral degeneracy. As the in-plane field is increased, the chiral asymmetry changes sign. When considered separately, neither DMI nor αc can explain the sign reversal of the asymmetry, which we prove to be the result of their competing effects. Finally, numerical modelling unveils the non-linear nature of chiral dissipation and its critical role for the stabilization of moving SKs.

Molecular Dynamics Simulation Study of the Self-Assembly of Phenylalanine Peptide Nanotubes.

In this paper, we propose and use a new approach for a relatively simple technique for conducting MD simulation (MDS) of various molecular nanostructures, determining the trajectory of the MD run and forming the final structure using external force actions. A molecular dynamics manipulator (MD manipulator) is a controlled MDS type. As an example, the applicability of the developed algorithm for assembling peptide nanotubes (PNT) from linear phenylalanine (F or Phe) chains of different chirality is presented. The most adequate regimes for the formation of nanotubes of right chirality D from the initial L-F and nanotubes of left chirality L of their initial dipeptides D-F modes were determined. We use the method of a mixed (vector–scalar) product of the vectors of the sequence of dipole moments of phenylalanine molecules located along the nanotube helix to calculate the magnitude and sign of chirality of self-assembled helical phenylalanine nanotubes, which shows the validity of the proposed approach. As result, all data obtained correspond to the regularity of the chirality sign change of the molecular structures with a hierarchical complication of their organization.

Skyrmion crystal and spiral phases in centrosymmetric bilayer magnets with staggered Dzyaloshinskii-Moriya interaction

We theoretically study a stabilization mechanism of the skyrmion crystal in centrosymmetric magnets with a bilayer structure. We show that the interplay between a layer-dependent staggered Dzyaloshinskii-Moriya interaction that arises from the absence of local inversion symmetry and the interlayer exchange interaction gives rise to a plethora of multiple-$Q$ states including the skyrmion crystal with a quantized topological number. By performing the simulated annealing for the bilayer triangular-lattice model under an external magnetic field, we demonstrate that the skyrmion forms the triangular-shaped crystals with different helicities in each layer owing to the staggered Dzyaloshinskii-Moriya interaction. Although the relative positions of the skyrmion core in each layer are different depending on the sign of the interlayer exchange interactions, the skyrmion crystal phases robustly appear under both ferromagnetic and antiferromagnetic interlayer interactions. We also find another two triple-$Q$ states with a uniform scalar chirality but without a quantized topological number in the low- and high-field regions. Especially, the low-field triple-$Q$ state exhibits the opposite sign of the scalar chirality to the skyrmion crystal, which is not found in the single-layer system. Our results indicate that the lack of local inversion symmetry in the lattice structure is another key ingredient to induce topological spin textures in centrosymmetric magnets.

ECD exciton chirality method today: a modern tool for determining absolute configurations.

The application of the exciton chirality method (ECM) to interpret electronic circular dichroism (ECD) spectra is a well‐established and still popular approach to assign the absolute configuration (AC) of natural products, chiral organic compounds, and organometallic species. The method applies to compounds containing at least two chromophores with electric dipole allowed transitions (e.g., π–π* transitions). The exciton chirality rule correlates the sign of an exciton couplet (two ECD bands with opposite sign and similar intensity) with the overall molecular stereochemistry, including the AC. A correct application of the ECM requires three main prerequisites: (a) the knowledge of the molecular conformation, (b) the knowledge of the directions of the electric transition moments (TDMs), and (c) the assumption that the exciton coupling mechanism must be the major source of the observed ECD signals. All these prerequisites can be easily verified by means of quantum‐mechanical (QM) calculations. In the present review, we shortly introduce the general principles that underpin the use of the ECM for configurational assignments and survey its applications, both classic ones and some reported in the recent literature. Based on these examples, we will stress the advantages of the ECM but also the key requisites for its correct application. Additionally, we will discuss the dependence of the couplet sign on geometrical parameters (angles α,β,γ between TDMs), which can be helpful for discerning the sign of exciton chirality in ambiguous situations. Finally, we will present a molecular orbital (MO) description of the exciton coupling phenomenon.

Modeling of Self-Assembled Peptide Nanotubes and Determination of Their Chirality Sign Based on Dipole Moment Calculations.

The chirality quantification is of great importance in structural biology, where the differences in proteins twisting can provide essentially different physiological effects. However, this aspect of the chirality is still poorly studied for helix-like supramolecular structures. In this work, a method for chirality quantification based on the calculation of scalar triple products of dipole moments is suggested. As a model structure, self-assembled nanotubes of diphenylalanine (FF) made of L- and D-enantiomers were considered. The dipole moments of FF molecules were calculated using semi-empirical quantum-chemical method PM3 and the Amber force field method. The obtained results do not depend on the used simulation and calculation method, and show that the D-FF nanotubes are twisted tighter than L-FF. Moreover, the type of chirality of the helix-like nanotube is opposite to that of the initial individual molecule that is in line with the chirality alternation rule general for different levels of hierarchical organization of molecular systems. The proposed method can be applied to study other helix-like supramolecular structures.

Chiral sensing with achiral anisotropic metasurfaces

Recently, we proposed a metasurface design for chiral sensing that (i) results in enhanced chiroptical signals by more than two orders of magnitude for ultrathin, subwavelength, chiral samples over a uniform and accessible area, (ii) allows for complete measurements of the total chirality (magnitude and sign of both its real and imaginary part), and (iii) offers the possibility for a crucial signal reversal (excitation with reversed polarization) that enables chirality measurements in an absolute manner, i.e., without the need for sample removal. Our design is based on the anisotropic response of the metasurface, rather than the superchirality of the generated near-fields, as in most contemporary nanophotonic-based chiral sensing approaches. Here, we derive analytically, and verify numerically, simple formulas that provide insight to the sensing mechanism and explain how anisotropic metasurfaces, in general, offer additional degrees of freedom with respect to their isotropic counterparts. We provide a detailed discussion of the key functionalities and benefits of our proposed design and we demonstrate practical measurement schemes for the unambiguous determination of an unknown chirality. Last, we provide the design principles towards broadband operation - from near-infrared to near-ultraviolet frequencies - opening the way for highly sensitive nanoscale chiroptical spectroscopy.

Absolute Asymmetric Catalysis, from Concept to Experiment: A Narrative

AbstractThe generally accepted hypothesis to explain the origin of biological homochirality (that is to say, the fact that proteinogenic amino acids are left-handed, and carbohydrates right-handed, in all living beings) is to assume, in the course of prebiotic chemical evolution, the appearance of an initial enantiomeric excess in a set of chiral molecular entities by spontaneous mirror-symmetry breaking (SMSB), together with suitable amplification and replication mechanisms that overcome the thermodynamic drive to racemization. However, the achievement of SMSB in chemical reactions taking place in solution requires highly specific reaction networks showing nonlinear dynamics based on enantioselective autocatalysis, and examples of its experimental realization are very rare. On the other hand, emergence of net supramolecular chirality by SMSB in the self-assembly of achiral molecules has been seen to occur in several instances, and the chirality sign of the resulting supramolecular system can be controlled by the action of macroscopic chiral forces. These considerations led us to propose a new mechanism for the generation of net chirality in molecular systems, in which the SMSB takes place in the formation of chiral supramolecular dissipative structures from achiral monomers, leading to asymmetric imbalances in their composition that are subsequently transferred to a standard enantioselective catalytic reaction, dodging in this way the highly limiting requirement of finding suitable reactions in solution that show enantio­selective autocatalysis. We propose the name ‘absolute asymmetric catalysis’ for this approach, in which an achiral monomer is converted into a nonracemic chiral aggregate that is generated with SMSB and that is catalytically active.Our aim in this Account is to present a step-by-step narrative of the conceptual and experimental development of this hitherto unregarded, but prebiotically plausible, mechanism for the emergence of net chirality in molecular reactions.1 Introduction: The Origin of Biological Homochirality and Spontaneous Mirror-Symmetry Breaking2 Experimental Chemical Models for Spontaneous Mirror-Symmetry Breaking: The Soai Reaction and Beyond3 Spontaneous Mirror-Symmetry Breaking in Supramolecular Chemistry: Plenty of Room at the Top4 Absolute Asymmetric Catalysis: An Alternative Mechanism for the Emergence of Net Chirality in Molecular Systems 5 Experimental Realization of Top-Down Chirality Transfer to the Molecular Level6 Conclusions and Outlook

Assembly of a Phenylalanine Nanotube by the use of Molecular Dynamics Manipulator

Studies of the processes of self-organization and self-assembly of various complexly organized (including spiral) structures based on amino acids intensively carried out in recent years. Various methods of molecular modeling, including molecular dynamics (MD) methods, are developed. In this paper, we propose a new approach for a relatively simple technique for conducting MD simulation (MDS) of various molecular nanostructures, determining the trajectory of the MD run and forming the final structure: a molecular dynamic manipulator (MD manipulator). It is an imitation of the operation of an existing or imaginary device or structure by applying force to the existing initial structure in order to obtain a new final structure, having the same chemical composition, but with a different geometry (topology). The PUMA-CUDA software package was applied as the main MD modeling program, which uses the physics of the PUMA software package, developed by the laboratory headed by N.K. Balabaev. Using this MDS tool, you can investigate the formation of helical structures from a linear sequence of any amino acids variation. As an example, the applicability of the developed algorithm for assembling nanotubes from linear phenylalanine (Phe) chains of different chirality (left L-Phe and right D-Phe) is considered by including additional force effects in the molecular dynamics simulation program for these structures. During the MD run, the applied actions, which are the same for the left and right helices of the formed nanotubes, lead the system to an α-helix structure. The work was carried out in an interactive mode using a number of additional programs, incl. trajectory analyzer program MD (TAMD). As a result, the modes that are most adequate for the formation of nanotubes of the right chirality D from the initial L-Phe monomer and nanotubes of the left chirality L from the D-Phe amino acid monomer were determined. The results obtained were compared with data from other works on modeling similar nanotubes of different chirality and experimental data. These are fully in line with the law of change in sign of chirality of molecular structures with complication of their hierarchical level of organization. The molecular animation of the assembly of a left-chiral nanotube from D-monomers is freely available at: http://lmd.impb.ru/Supplementary/PHE.avi.

Spontaneous chiral self-assembly of CdSe@CdS nanorods

Spontaneous chiral self-assembly of CdSe@CdS nanorods

Protein Helical Structures: Defining Handedness and Localization Features

The quantitative evaluation of the chirality of macromolecule structures remains one of the exciting issues in biophysics. In this paper, we propose methods for quantitative analysis of the chirality of protein helical and superhelical structures. The analysis of the chirality sign of the protein helical structures (α-helices and 310-helices) is based on determining the mixed product of every three consecutive vectors between neighboring reference points—α-carbons atoms. The method for evaluating the chirality sign of coiled-coil structures is based on determining the direction and value of the angle between the coiled-coil axis and the α-helices axes. The chirality sign of the coiled coil is calculated by averaging the value of the cosine of the corresponding angle for all helices forming the superhelix. Chirality maps of helical and superhelical protein structures are presented. Furthermore, we propose an analysis of the distributions of helical and superhelical structures in polypeptide chains of several protein classes. The features common to all studied classes and typical for each protein class are revealed. The data obtained, in all likelihood, can reflect considerations about molecular machines as chiral formations.