Parity violation energy of biomolecules--I: polypeptides

Parity Violation Energy Difference Calculation of Atropisomers

Enantiomers have a different energy due to the parity violation effects. Up to now, these effects are difficult to calculate and their final effect on the choice of one enantiomer in the homochirality issue is still a matter of debate. Nevertheless, many scientists support the role of this tiny energy difference in the triggering of homochirality. In this work, we studied the energy difference in atropisomers, a class of stereoisomers in which the chirality is given by the block of rotation around one bond. Atropisomers might have a low energy barrier for the interconversion and this is interesting for the equilibration of the two enantiomers and the choice of the most stable enantiomer. Moreover, structures might be extended like in the case of polymers or crystals having helical framework and thus giving an additive effect on the parity violation energy of the whole structure. The parity violation energy difference here is discussed with the correlation on the general structure of the final molecule giving a qualitative model to predict the sign of local contributions of atoms.

Synchronization in Non-Mirror-Symmetrical Chirogenesis: Non-Helical π–Conjugated Polymers with Helical Polysilane Copolymers in Co-Colloids

A curious question is whether two types of chiroptical amplifications, called sergeants-and-soldiers (Ser-Sol) and majority-rule (Maj) effects, between non-charged helical copolymers and non-charged, non-helical homopolymers occur when copolymer encounter homopolymer in co-colloids. To address these topics, the present study chose (i) two helical polysilane copolymers (HCPSs) carrying (S)- or (R)-2-methylbutyl with isobutyl groups as chiral/achiral co-pendants (type I) and (S)- and (R)-2-methylbutyl groups as chiral/chiral co-pendants (type II) and (ii) two blue luminescent π-conjugated polymers, poly[(dioctylfluorene)-alt-(trans-vinylene)] (PFV8) and poly(dioctylfluorene) (PF8). Analyses of circular dichroism (CD) and circularly polarized luminescence (CPL) spectral datasets of the co-colloids indicated noticeable, chiroptical inversion in the Ser-Sol effect of PFV8/PF8 with type I HCPS. PF8 with type IIHCPS showed the anomalous Maj rule with chiroptical inversion though PFV8 with type IIHCPS was the normal Maj effect. The noticeable non-mirror-symmetric CD-and-CPL characteristics and marked differences in hydrodynamic sizes of these colloids were assumed to originate from non-mirror-symmetrical main-chain stiffness of HCPSs in dilute toluene solution. The present chirality/helicity transfer experiments alongside of previous/recent publications reported by other workers and us allowed to raise the fundamental question; is mirror symmetry on macroscopic levels in the ground and photoexcited states rigorously conserved?

Parity Violation Energy of Biomolecules - V: Protein Metal Centers

The parity-violation difference between mirror images of chiral metal centers found in naturally occurring proteins and enzymes is computed at the Dirac-Hartree-Fock level, for both equilibrium and transition state configurations. The systems, selected on the likelihood of yielding high parity violation energies based on atomic mass and coordination geometry, are extracted from: type I Blue Copper Protein active site, Zn and Cd Carbon Anhydrase, Ni Acetyl-Coenzyme-A Synthase, and Mo based CO-Dehydrogenase. Our values provide an approximate upper limit to possible parity-violation effects in biological systems based on static effects.

Stochastic and empirical models of the absolute asymmetric synthesis by the Soai-autocatalysis

Absolute asymmetric synthesis (AAS) is the preparation of pure (or excess of one) enantiomer of a chiral compound from achiral precursor(s) by a chemical reaction, without enantiopure chiral additive and/or without applied asymmetric physical field. Only one well-characterized example of AAS is known today: the Soai-autocatalysis. In an attempt at clarification of the mechanism of this particular reaction we have undertaken empirical and stochastic analysis of several parallel AAS experiments. Our results show that the initial steps of the reaction might be controlled by simple normal distribution ("coin tossing") formalism. Advanced stages of the reaction, however, appear to be of a more complicated nature. Symmetric beta distribution formalism could not be brought into correspondence with the experimental observations. A bimodal beta distribution algorithm provided suitable agreement with the experimental data. The parameters of this bimodal beta function were determined by a Pólya-urn experiment (simulated by computer). Interestingly, parameters of the resulting bimodal beta function give a golden section ratio. These results show, that in this highly interesting autocatalysis two or even perhaps three catalytic cycles are cooperating. An attempt at constructing a "designed" Soai-type reaction system has also been made.

Theory, modelling and simulation in origins of life studies

Origins of life studies represent an exciting and highly multidisciplinary research field. In this review we focus on the contributions made by theory, modelling and simulation to addressing fundamental issues in the domain and the advances these approaches have helped to make in the field. Theoretical approaches will continue to make a major impact at the "systems chemistry" level based on the analysis of the remarkable properties of nonlinear catalytic chemical reaction networks, which arise due to the auto-catalytic and cross-catalytic nature of so many of the putative processes associated with self-replication and self-reproduction. In this way, we describe inter alia nonlinear kinetic models of RNA replication within a primordial Darwinian soup, the origins of homochirality and homochiral polymerization. We then discuss state-of-the-art computationally-based molecular modelling techniques that are currently being deployed to investigate various scenarios relevant to the origins of life.

Small cofactors may assist protein emergence from RNA world: clues from RNA-protein complexes

It is now widely accepted that at an early stage in the evolution of life an RNA world arose, in which RNAs both served as the genetic material and catalyzed diverse biochemical reactions. Then, proteins have gradually replaced RNAs because of their superior catalytic properties in catalysis over time. Therefore, it is important to investigate how primitive functional proteins emerged from RNA world, which can shed light on the evolutionary pathway of life from RNA world to the modern world. In this work, we proposed that the emergence of most primitive functional proteins are assisted by the early primitive nucleotide cofactors, while only a minority are induced directly by RNAs based on the analysis of RNA-protein complexes. Furthermore, the present findings have significant implication for exploring the composition of primitive RNA, i.e., adenine base as principal building blocks.

Parity-violation energy of biomolecules-IV: protein secondary structure

The parity-violation energy difference between enantiomeric forms of the same amino acid sequence, from the amyloid β-peptide involved in Alzheimer's disease, in both α-helix and β-sheet configurations, is investigated with ab-initio techniques. To this end, we develop an extension of the N2 computational scheme that selectively includes neighboring amino acids to preserve the relevant H-bonds. In agreement with previous speculations, it is found that the helical α structure is associated with larger parity-violation energy differences than the corresponding β form. Implications for the evolution of biological homochirality are discussed as well as the relative importance of various effects in determining the parity-violation energy.

Progress toward the first observation of parity violation in chiral molecules by high-resolution laser spectroscopy

Parity violation (PV) effects in chiral molecules have so far never been experimentally observed. To take up this challenge, a consortium of physicists, chemists, theoreticians, and spectroscopists has been established and aims at measuring PV energy differences between two enantiomers by using high-resolution laser spectroscopy. In this article, we present our common strategy to reach this goal, the progress accomplished in the diverse areas, and point out directions for future PV observations. The work of André Collet on bromochlorofluoromethane (1) enantiomers, their synthesis, and their chiral recognition by cryptophanes made feasible the first generation of experiments presented in this article.

Chiral oxorhenium(V) complexes as candidates for the experimental observation of molecular parity violation: a structural, synthetic and theoretical study

We report the synthesis and resolution of a series of new chiral "3 + 1" oxorhenium(V) complexes, designed for high-resolution laser spectroscopy experiments probing molecular parity-violation (PV) effects in the Re=O stretching mode frequency. These complexes display a particularly simple chemical structure, with the rhenium atom as the stereogenic center, and show large PV energy differences according to our calculations. They were obtained in the racemic and enantioenriched forms, in the latter case by using either semi-preparative chiral HPLC resolution or enantioselective synthesis. The vibrational transition frequency differences between the enantiomeric pairs due to PV have been calculated with two- and four-component relativistic Hamiltonians using Hartree-Fock (HF) and density functional theory (DFT). For three complexes, including one synthesized in enantioenriched form, our HF calculations predict frequency differences above the present resolution limit of 1 Hz. These results confirm the order of magnitude for the calculated HF PV vibrational frequency differences reported earlier for this class of compounds [P. Schwerdtfeger and R. Bast, J. Am. Chem. Soc., 2004, 126, 1652]. However, at the DFT level the PV vibrational frequency differences are in some cases reduced by an order of magnitude, but are still within the sensitivity of 0.01 Hz, which is the anticipated sensitivity in a new proposed experiment. We therefore believe that the present study represents an important step towards the experimental observation of PV in molecular systems, and emphasizes the extreme sensitivity of the PV vibrational frequency difference to the chemical environment around the rhenium center.

Homochirality and the need for energy

The mechanisms for explaining how a stable asymmetric chemical system can be formed from a symmetric chemical system, in the absence of any asymmetric influence other than statistical fluctuations, have been developed during the last decades, focusing on the non-linear kinetic aspects. Besides the absolute necessity of self-amplification processes, the importance of energetic aspects is often underestimated. Going down to the most fundamental aspects, the distinction between a single object-that can be intrinsically asymmetric-and a collection of objects-whose racemic state is the more stable one-must be emphasized. A system of strongly interacting objects can be described as one single object retaining its individuality and a single asymmetry; weakly or non-interacting objects keep their own individuality, and are prone to racemize towards the equilibrium state. In the presence of energy fluxes, systems can be maintained in an asymmetric non-equilibrium steady-state. Such dynamical systems can retain their asymmetry for times longer than their racemization time.

Electroweak parity-violating energy shifts of amino acids: the "conformation problem"

The preceding paper described our coupled-perturbed Hartree-Fock (CPHF) and density functional theory (DFT) methods of computing the parity-violating energy shift (PVES). This paper addresses the "conformation problem"-the difficulty determining which hand of amino acids in solution is favoured by the weak force due to the difficulty determining the solution conformation. We attempt to resolve this by using the methods of the preceding paper to compute the PVES of solution and gas-phase amino acid structures determined by other groups from high level optimizations that include solvation. We conclude that the conformational hypersensitivity of the PVES still precludes a definite conclusion as to the sign of the PVES of L-alanine in solution, but that there is no problem in the gas phase: the PVES of gas-phase L-alanine is decisively negative. We show that the PVES is very sensitive to certain torsion angles, but is not hypersensitive to bondlengths or bond angles. In determining structures for PVES computations, there is therefore no need for expensive full optimizations: one can just optimize the crucial torsion angles. We present new computations of gas-phase amino acids PVESs, using partial optimizations with small basis sets, and the results agree well with those from higher level techniques. In the following paper we apply these less costly techniques to larger amino acids. The "conformation problem" has led some to dismiss the PVES as the source of life's handedness, but we believe this is premature: we show here that amino acids are a special case because their favoured conformations are almost achiral.

First experimental evidence for the preferential stabilization of the natural D- over the nonnatural L-configuration in nucleic acids

The homochirality of biomolecules is a prerequisite for the origin and evolution of terrestrial life. The unique selection of D-monosaccharides, in particular, D-ribose in RNA and D-deoxyribose in DNA, leads to the construction of proteins by L-amino acids. This points to the exclusive role of stereoselectivity in the most important physiological processes. So far, there is no experimental confirmation for the theoretical calculations of the energy differences between enantiomers used for the explanation of the stereoselection of biomolecules. Therefore, the question of why nature prefers one configuration over the other still lacks a definitive answer. Here, we present the first experimental evidence that the D-enantiomer of RNA has a different electronic structure compared to the corresponding L-enantiomer. When varying the incident photon energy of the ultraviolet Raman probe across 5 eV, D- and L-isomers of the RNA duplex with the sequence [r(CUGGGCGG).r(CCGCCUGG)] show differences in the intensity of the vibrational modes with energies of 124.0 meV to 210.8 meV. The intensity difference of these vibrational modes can be traced back to energy differences in the electronic levels of D- and L-RNA leading to the preferential stabilization of the naturally occurring D-configuration of RNA over the L-configuration.

Violation of Distribution Symmetry in Statistical Evaluation of Absolute Enantioselective Synthesis

Enantiomeric excesses obtained in absolute enantioselective synthesis by chiral autocatalysis (Soai-reaction) were statistically analyzed. Two sets of parallel experiments, which were performed under chemically different conditions, are available. One group contains 37, while the other contains 84 preparative results. The former group shows some interesting tendencies but does not give conclusive statistical results. The sample of 84 parallel experiments, providing 39 R- and 45 S-excesses have shown that these data represent two distinct, non-symmetric sets with different non-Gaussian distributions. Clear S preference was found.

Emergence of homochirality in far-from-equilibrium systems: mechanisms and role in prebiotic chemistry

Since the model proposed by Frank (Frank FC, Biochem Biophys Acta 1953;11:459-463), several alternative models have been developed to explain how an asymmetric non-racemic steady state can be reached by a chirally symmetric chemical reactive system. This paper explains how a stable non-racemic regime can be obtained as a symmetry breaking occurring in a far-from-equilibrium reactive system initiated with an initial imbalance. Departing from the variations around the original Frank's model that are commonly described in the literature, i.e. open-flow systems of direct autocatalytic reactions, we discuss recent developments emphasizing both an active recycling of components and an autocatalytic network of simple reactions. We will present our APED model as the most natural realization of such thermodynamic openness and non-equilibrium, of recycling and of network autocatalysis, each of these in prebiotic conditions. The different experimental and theoretical models in the literature will be classified according to mechanism. The place and role of such self-structured networks responsible for the presence of homochirality in the primitive Earth will be detailed.