Molecular model for chirality phenomena

Amino acid chiral amplification using Monte Carlo dynamic

This study investigates the stability of chiral-molecule solution phases, with a specific focus on amino acids. The model framework is based on a two-dimensional square lattice model, where individual sites may be occupied by oriented chiral molecules or structureless solvent particles. Utilizing the Glauber dynamics and statistical mechanical formalism, as previously introduced and examined by Lombardo et al., we explore the influence of temperature, amino acid concentration, enantiomeric excess, and homochiral interaction strength on nucleation mechanisms, equilibrium phase behavior, and crystal composition. Our findings offer thermodynamic insights into the chiral amplification process of amino acids, contributing to a deeper understanding of the underlying processes.

Critical behavior in a chiral molecular model

Understanding the condensed-phase behavior of chiral molecules is important in biology as well as in a range of technological applications, such as the manufacture of pharmaceuticals. Here, we use molecular dynamics simulations to study a chiral four-site molecular model that exhibits a second-order symmetry-breaking phase transition from a supercritical racemic liquid into subcritical D-rich and L-rich liquids. We determine the infinite-size critical temperature using the fourth-order Binder cumulant, and we show that the finite-size scaling behavior of the order parameter is compatible with the 3D Ising universality class. We also study the spontaneous D-rich to L-rich transition at a slightly subcritical temperature of T = 0.985Tc, and our findings indicate that the free energy barrier for this transformation increases with system size as N2/3, where N is the number of molecules, consistent with a surface-dominated phenomenon. The critical behavior observed herein suggests a mechanism for chirality selection in which a liquid of chiral molecules spontaneously forms a phase enriched in one of the two enantiomers as the temperature is lowered below the critical point. Furthermore, the increasing free energy barrier with system size indicates that fluctuations between the L-rich and D-rich phases are suppressed as the size of the system increases, trapping it in one of the two enantiomerically enriched phases. Such a process could provide the basis for an alternative explanation for the origin of biological homochirality. We also conjecture the possibility of observing nucleation at subcritical temperatures under the action of a suitable chiral external field.

Pre-Smectic Ordering and the Unwinding Helix in Monte Carlo Simulations of Cholesteric Liquid-Crystals

In this paper, molecular chirality is studied for liquid-crystal fluids represented by hard rods with the addition of an attractive chiral dispersion term. Chiral forces between molecular pairs are assumed to be long-ranged and are described in terms of the pseudotensor of Goossens [W. J. A. Goossens, Mol. Cryst. Liq. Cryst. 1971, 12, 237-244]. Following Varga and Jackson [S. Varga and G. Jackson, Chem. Phys. Lett. 2003, 377, 6-12], this is combined with a hard-spherocylinder core. We investigate the relationship between molecular chirality and the helical pitch of the system, which occurs in the absence of full three-dimensional periodic boundary conditions. The dependence of the wavenumber of this pitch on the thermodynamic variables, temperature, and density is measured. We also explore the use of a novel surface boundary interaction model. As a result of this approach, we are able to lower the temperature of the system without the occurrence of nematic droplets, which would interfere with the formation of a uniaxial pitch. Regarding the theoretical predictions of Wensink and Jackson [H. H. Wensink and G. Jackson, J. Chem. Phys. 2009, 130, 234911], on the one hand, we have qualitative agreement with the observed non-monotonic density dependence of the wavenumber. Initially increasing with density, the wavenumber reaches a maximum, before falling as the density moves toward the point of phase transition from cholesteric to smectic. However, further analysis for shorter rods, in the presence of novel boundary conditions, reveals some disagreement with the theory, at least in this case; the unwinding of the cholesteric helix in the cholesteric phase occurs simultaneously with subtle increases in smectic ordering. These pre-smectic fluctuations have not been accounted for so far in theories on cholesterics but turn out to play a key role in controlling the pitch of cholesteric phases of rod-shaped mesogens with a small to moderate aspect ratio.

Crystal Prediction via Genetic Algorithms in a Model Chiral System

Chiral crystals and their constituent molecules play a prominent role in theories about the origin of biological homochirality and in drug discovery, design, and stability. Although the prediction and identification of stable chiral crystal structures is crucial for numerous technologies, including separation processes and polymorph selection and control, predictive ability is often complicated by a combination of many-body interactions and molecular complexity and handedness. In this work, we address these challenges by applying genetic algorithms to predict the ground-state crystal lattices formed by a chiral tetramer molecular model, which we have previously shown to exhibit complex fluid-phase behavior. Using this approach, we explore the relative stability and structures of the model's conglomerate and racemic crystals, and present a structural phase diagram for the stable Bravais crystal types in the zero-temperature limit.

Phase transitions affected by natural and forceful molecular interconversion

If a binary liquid mixture, composed of two alternative species with equal amounts, is quenched from a high temperature to a low temperature, below the critical point of demixing, then the mixture will phase separate through a process known as spinodal decomposition. However, if the two alternative species are allowed to interconvert, either naturally (e.g., the equilibrium interconversion of enantiomers) or forcefully (e.g., via an external source of energy or matter), then the process of phase separation may drastically change. In this case, depending on the nature of interconversion, two phenomena could be observed: either phase amplification, the growth of one phase at the expense of another stable phase, or microphase separation, the formation of nongrowing (steady-state) microphase domains. In this work, we phenomenologically generalize the Cahn–Hilliard theory of spinodal decomposition to include the molecular interconversion of species and describe the physical properties of systems undergoing either phase amplification or microphase separation. We apply the developed phenomenology to accurately describe the simulation results of three atomistic models that demonstrate phase amplification and/or microphase separation. We also discuss the application of our approach to phase transitions in polyamorphic liquids. Finally, we describe the effects of fluctuations of the order parameter in the critical region on phase amplification and microphase separation.

Interconversion-controlled liquid-liquid phase separation in a molecular chiral model

Liquid-liquid phase separation of fluids exhibiting interconversion between alternative states has been proposed as an underlying mechanism for fluid polyamorphism and may be of relevance to the protein function and intracellular organization. However, molecular-level insight into the interplay between competing forces that can drive or restrict phase separation in interconverting fluids remains elusive. Here, we utilize an off-lattice model of enantiomers with tunable chiral interconversion and interaction properties to elucidate the physics underlying the stabilization and tunability of phase separation in fluids with interconverting states. We show that introducing an imbalance in the intermolecular forces between two enantiomers results in nonequilibrium, arrested phase separation into microdomains. We also find that in the equilibrium case, when all interaction forces are conservative, the growth of the phase domain is restricted only by the system size. In this case, we observe phase amplification, in which one of the two alternative phases grows at the expense of the other. These findings provide novel insights on how the interplay between dynamics and thermodynamics defines the equilibrium and steady-state morphologies of phase transitions in fluids with interconverting molecular or supramolecular states.

Effect of configuration-dependent multi-body forces on interconversion kinetics of a chiral tetramer model

We describe a reformulation of the four-site molecular model for chiral phenomena introduced by Latinwo et al. ["Molecular model for chirality phenomena," J. Chem. Phys. 145, 154503 (2016)]. The reformulation includes an additional eight-body force that arises from an explicit configuration-dependent term in the potential energy function, resulting in a coarse-grained energy-conserving force field for molecular dynamics simulations of chirality phenomena. In this model, the coarse-grained interaction energy between two tetramers depends on their respective chiralities and is controlled by a parameter λ, where λ < 0 favors local configurations involving tetramers of opposite chirality and λ > 0 gives energetic preference to configurations involving tetramers of the same chirality. We compute the autocorrelation function for a quantitative chirality metric and demonstrate that the multi-body force modifies the interconversion kinetics such that λ ≠ 0 increases the effective barrier for enantiomer inversion. Our simulations reveal that for λ > 0 and temperatures below a sharply defined threshold value, this effect is dramatic, giving rise to spontaneous chiral symmetry breaking and locking molecules into their chiral identity.

Phase amplification in spinodal decomposition of immiscible fluids with interconversion of species

A fluid composed of two molecular species may undergo phase segregation via spinodal decomposition. However, if the two molecular species can interconvert, e.g., change their chirality, then a phenomenon of phase amplification, which has not been studied so far to our best knowledge, emerges. As a result, eventually, one phase will completely eliminate the other one. We model this phenomenon on an Ising system which relaxes to equilibrium through a hybrid of Kawasaki-diffusion and Glauber-interconversion dynamics. By introducing a probability of Glauber-interconversion dynamics, we show that the particle conservation law is broken, thus resulting in phase amplification. We characterize the speed of phase amplification through scaling laws based on the probability of Glauber dynamics, system size, and distance to the critical temperature of demixing.

Mirror Symmetry Breaking in Liquids and Their Impact on the Development of Homochirality in Abiogenesis: Emerging Proto-RNA as Source of Biochirality?

Recent progress in mirror symmetry breaking and chirality amplification in isotropic liquids and liquid crystalline cubic phases of achiral molecule is reviewed and discussed with respect to its implications for the hypothesis of emergence of biological chirality. It is shown that mirror symmetry breaking takes place in fluid systems where homochiral interactions are preferred over heterochiral and a dynamic network structure leads to chirality synchronization if the enantiomerization barrier is sufficiently low, i.e., that racemization drives the development of uniform chirality. Local mirror symmetry breaking leads to conglomerate formation. Total mirror symmetry breaking requires either a proper phase transitions kinetics or minor chiral fields, leading to stochastic and deterministic homochirality, respectively, associated with an extreme chirality amplification power close to the bifurcation point. These mirror symmetry broken liquids are thermodynamically stable states and considered as possible systems in which uniform biochirality could have emerged. A model is hypothesized, which assumes the emergence of uniform chirality by chirality synchronization in dynamic “helical network fluids” followed by polymerization, fixing the chirality and leading to proto-RNA formation in a single process.

Thermodynamics of supercooled and stretched water: Unifying two-structure description and liquid-vapor spinodal

We have applied a two-structure approach to the description of the thermodynamic properties of supercooled and stretched water, metastable toward vapor, ice, or both, by incorporating the stability limit of liquid with respect to vapor at negative pressures. In addition to the properties of water considered in previous studies, we include new data recently obtained in deeply supercooled and stretched regions. Our model reproduces the experimentally observed anomalies in metastable water up to 400 MPa and down to -140 MPa, and can provide a physically based extrapolation in regions where no measurements are available yet. Moreover, we are able to elucidate the thermodynamic nature of the alternative "states" of liquid water, namely, high-temperature denser water (state A) and "mother-of-ice" lighter water (state B). Based on the internal consistency of the described anomalies and new data on the isothermal compressibility, we exclude the critical-point-free scenario in which the first-order liquid-liquid transition line would continue into the stretched liquid state (doubly metastable) crossing the vapor-liquid spinodal. A "singularity-free" scenario remains an option for explaining supercooled water's anomalies within the framework of two-state thermodynamics; however, the extreme case of the singularity-free scenario, ideal mixing of A and B, seems improbable. We have also clarified the concept of fast interconversion of alternative states in supercooled water as a phenomenological representation of distribution of short-ranged local structures.

The Power Without the Glory: Multiple Roles of Hydrogen Peroxide in Mediating the Origin of Life

The hydrogen peroxide (HP) crucible hypothesis proposed here holds that life began in a localized environment on Earth that was perfused with a flow of hydrogen peroxide from a sustained external source, which powered and mediated molecular evolution and the protocellular RNA world. In this article, we consolidate and review recent evidence, both circumstantial and tested in simulation in our work and in the laboratory in others' work, for its multiple roles in the evolution of the first living systems: (1) it provides a periodic power source as the thiosulfate-hydrogen peroxide (THP) redox oscillator, (2) it may act as an agent of molecular change and evolution and mediator of homochirality, and (3) the THP oscillator, subject to Brownian input perturbations, produces a weighted distribution of output thermal fluctuations that favor polymerization and chemical diversification over chemical degradation and simplification. The hypothesis can help to clarify the hero and villain roles of hydrogen peroxide in cell function, and on the singularity of life: of necessity, life evolved early an armory of catalases, the continuing, and all-pervasive presence of which prevents hydrogen peroxide from accumulating anywhere in sufficient quantities to host a second origin. The HP crucible hypothesis is radical, but based on well-known chemistry and physics, it is eminently testable in the laboratory, and many of our simulations provide recipes for such experiments.

Critical Point Confluence Phenomenon

Experimental observation of coexisting isotropic chiral liquids for a single molecular substance has motivated creation of a simple lattice model to investigate phase transitions in such systems. Specifically, this model permits the simultaneous existence of two distinct types of critical points, the familiar liquid-vapor case, and a case involving spontaneous chiral symmetry breaking within the fluid system. The molecular interactions involved may extend beyond nearest neighbor lattice cells. The mean field approximation has been invoked to attain explicit results, which include a description of the singular situation for which the two critical points undergo confluence in the temperature-density plane. In particular, this confluence enhances the chiral symmetry breaking phenomenon, leading to a modified critical exponent.

Cholesteric ordering predicted using a coarse-grained polymeric model with helical interactions

The understanding of cholesteric liquid crystals at a molecular level is challenging. Limited insights are available to bridge between molecular structures and macroscopic chiral organization. In the present study, we introduce a novel coarse-grained (CG) molecular model, which is represented by flexible chain particles with helical interactions (FCh), to study the liquid crystalline phase behavior of cholesteric molecules such as double strand DNA and α-helix polypeptides using molecular dynamics (MD) simulations. The isotropic-cholesteric phase transitions of FCh molecules were simulated for varying chain flexibilities. A wall confinement was used to break the periodicity along the cholesteric helix director in order to predict the equilibrium cholesteric pitch. The left-handed cholesteric phase was shown for FCh molecules with right-handed chiral interactions, and a spatially inhomogeneous distribution of the nematic order parameter profile was observed in cholesteric phases. It was found that the chain flexibility plays an important role in determining the macroscopic cholesteric pitch and the structure of the cholesteric liquid crystal phase. The simulations provide insight into the relationship between microscopic molecular characteristics and the macroscopic phase behavior.