The Life Story of Hydrogen Peroxide III: Chirality and Physical Effects at the Dawn of Life

Search for Chirality in Hydrogenated Magnesium Nanosilicates: A DFT and TD-DFT Investigation

The formation of silicate grains in the interstellar medium (ISM), especially those containing chiral surfaces such as clinopyroxenes, is poorly understood. Moreover, silicate interactions with various forms of hydrogen-proton (H+), neutral H (HI), and molecular hydrogen (H2) are of high importance as hydrogen comprises >90% of the ISM gas budget, and these species play important roles in the formation of new molecules in space. Furthermore, silicate surfaces catalyze the formation of H2 in the interstellar medium formed on dust grain surfaces by H-H association. The technical difficulty of in situ laboratory investigations of nanosilicate nucleation using astrophysically relevant environmental conditions makes computational chemistry a useful tool for studying potential nanosilicate structures. Furthermore, chiral surfaces interacting with chiral organic molecules could serve as templates that lead to the enantiomeric excess of l-amino acids and d-polyols detected in carbonaceous meteorites. However, in order for this effect to take place, an excess of one chiral form of a mineral is required to break the symmetry. This symmetry-breaking event could have been due to the asymmetric absorption of circularly polarized light by the nanosilicate as it traverses star-forming regions. We investigate this possibility using a metastable chiral form of an enstatite dimer as an input for density functional theory (DFT) and time-dependent (TD)-DFT calculations to obtain various properties and circular dichroism spectra. All in all, twenty-six magnesium nanosilicate structures were studied using varying degrees of hydrogenation: none, with HI, with H+, and with H2. The HSE06/aug-cc-pVQZ level of theory was used for the DFT calculations. TD-DFT calculations utilized the CAM-B3LYP/cc-pVQZ and ωB97X-D3/cc-pVQZ functional and basic set pairings. Results show that (1) all twenty-six structures have absorption bands that fall within the 0.6-28.3 μm range available with the newly launched James Webb Space Telescope and (2) there is a small enantioselective effect by UV-CPL on the eight chiral enstatite dimers (predicted g-values of up to 0.007). While the observed effect is small, it opens up the possibility that it is the inorganic material that becomes enantiomerically biased by UV-CPL, driving chiral enhancements in meteoric organic molecules.

About the Formation of NH2OH+ from Gas Phase Reactions under Astrochemical Conditions

We present here an analysis of several possible reactive pathways toward the formation of hydroxylamine under astrochemical conditions. The analysis is based on ab initio quantum chemistry calculations. Twenty-one bimolecular ion–molecule reactions have been studied and their thermodynamics presented. Only one of these reactions is a viable direct route to hydroxylamine. We conclude that the contribution of gas-phase chemistry to hydroxylamine formation is probably negligible when compared to its formation via surface grain chemistry. However, we have found several plausible gas-phase reactions whose outcome is the hydroxylamine cation.

Peptide-modulated pH rhythms

Many drugs adjust and/or control the spatiotemporal dynamics of periodic processes such as heartbeat, neuronal signaling and metabolism, often by interacting with proteins or oligopeptides. Here we use a quasi-biocompatible, non-equilibrium pH oscillatory system as a biomimetic biological clock to study the effect of pH-responsive peptides on rhythm dynamics. The added peptides generate a feedback that can lengthen or shorten the oscillatory period during which the peptides alternate between random coil and coiled-coil conformations. This modulation of a chemical clock supports the notion that short peptide reagents may have utility as drugs to regulate human body clocks.

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.

Tight electrostatic regulation of the OH production rate from the photolysis of hydrogen peroxide adsorbed on surfaces

Recently, experimental and theoretical works have reported evidence indicating that photochemical processes may significantly be accelerated at heterogeneous interfaces, although a complete understanding of the phenomenon is still lacking. We have carried out a theoretical study of interface and surface effects on the photochemistry of hydrogen peroxide (H2O2) using high-level ab initio methods and a variety of models. Hydrogen peroxide is an important oxidant that decomposes in the presence of light, forming two OH radicals. This elementary photochemical process has broad interest and is used in many practical applications. Our calculations show that it can drastically be affected by heterogeneous interfaces. Thus, compared to gas phase, the photochemistry of H2O2 appears to be slowed on the surface of apolar or low-polar surfaces and, in contrast, hugely accelerated on ionic surfaces or the surface of aqueous electrolytes. We give particular attention to the case of the neat air-water interface. The calculated photolysis rate is similar to the gas phase, which stems from the compensation of two opposite effects, the blue shift of the n→σ* absorption band and the increase of the absorption intensity. Nevertheless, due to the high affinity of H2O2 for the air-water interface, the predicted OH production rate is up to five to six orders of magnitude larger. Overall, our results show that the photochemistry of H2O2 in heterogeneous environments is greatly modulated by the nature of the surface, and this finding opens interesting new perspectives for technological and biomedical applications, and possibly in various atmospheres.

Molecules to Microbes

How did life begin on Earth? And is there life elsewhere in the Cosmos? Challenging questions, indeed. The series of conferences established by NoR CEL in 2013 addresses these very questions. This paper comprises a summary report of oral presentations that were delivered by NoR CEL’s network members during the 2018 Athens conference and, as such, disseminates the latest research which they have put forward. More in depth material can be found by consulting the contributors referenced papers. Overall, the outcome of this conspectus on the conference demonstrates a case for the existence of “probable chemistry” during the prebiotic epoch.

Molecules to Microbes

How did life begin on Earth? And is there life elsewhere in the Cosmos? Challenging questions, indeed. The series of conferences established by NoR CEL in 2013, addresses these very same questions. The basis for this paper is the summary report of oral presentations that were delivered by NoR CEL’s network members during the 2018 Athens conference and, as such, disseminates the latest research which they have put forward. More in depth material can be found by consulting the contributors referenced papers. Overall, the outcome of this conspectus on the conference demonstrates a case for the existence of “probable chemistry” during the prebiotic epoch.

Molecules to Microbes

How did life begin on Earth? And is there life elsewhere in the Cosmos? Challenging questions, indeed. The series of conferences established by NoR CEL in 2013, addresses these very same questions. The basis for this paper is the summary report of oral presentations that were delivered by NoR CEL’s network members during the 2018 Athens conference and, as such, disseminates the latest research which they have put forward. More in depth material can be found by consulting the contributors referenced papers. Overall, the outcome of this conspectus on the conference demonstrates a case for the existence of “probable chemistry” during the prebiotic epoch.

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.

Theoretical Investigation on H2O2-Ng (He, Ne, Ar, Kr, Xe, and Rn) Complexes Suitable for Stereodynamics: Interactions and Thermal Chiral Rate Consequences

Although molecular collisions of noble gases (Ng) can be theoretically used to distinguish between the enantiomers of hydrogen peroxide - H₂O₂ (HP), little is known about the effects of HP-Ng interactions on the chiral rate. In this work, the chiral rate as a function of temperature (CRT) between enantiomeric conformations of HP and Ng (Ng=He, Ne, Ar, Kr, Xe, and Rn) are presented at MP2(full)/aug-cc-pVTZ level of theory through a fully basis set superposition error (BSSE) corrected potential energy surface. The results show that: (a) the CRT is highly affected even at a small decrease in the height of trans-barrier; (b) its smallest values occur with Ne for all temperatures between 100 and 4,000 K; (c) that the decrease of CRT shows an inverse correlation with respect to the average valence electron energy of the Ng and (d) Ne and He may be the noble gases more suitable for study the oriented collision dynamics of HP. In addition to binding energies, the electron density ρ and its Laplacian ∇²ρ topological analyses were also performed within the atoms in molecules (AIM) theory in order to determine the nature of the HP-Ng interactions. The results of this work provide a more complete foundation on experiments to study HP's chirality using Ng in crossed molecular beams without a light source.

Internal- and rho-axis systems of molecules with one large amplitude internal motion: The geometry of rho

The internal-axis system (IAS) of molecules with a large amplitude internal motion (LAM) is determined by integrating the kinematic equation of the IAS by Lie-group and Lie-algebraic methods. Numerical examples on hydrogen peroxide, nitrous acid, and acetaldehyde demonstrate the methods. By exploiting the special product structure of the solution matrix, simple methods are devised for calculating the transformation to the rho-axis system (RAS) along with the value of the parameter ρ characterizing a RAS rotational-LAM kinetic energy operator. The parameter ρ so calculated agrees exactly with that one obtained by the Floquet method as shown in the example of acetaldehyde. Geometrical interpretation of ρ is given. The advantageous property of the RAS over the IAS in retaining simple periodic boundary conditions is numerically demonstrated.

A Tale of Two Concepts: Harmonizing the Free Radical and Antagonistic Pleiotropy Theories of Aging

SIGNIFICANCE

The two foremost concepts of aging are the mechanistic free radical theory (FRT) of how we age and the evolutionary antagonistic pleiotropy theory (APT) of why we age. Both date from the late 1950s. The FRT holds that reactive oxygen species (ROS) are the principal contributors to the lifelong cumulative damage suffered by cells, whereas the APT is generally understood as positing that genes that are good for young organisms can take over a population even if they are bad for the old organisms. Recent Advances: Here, we provide a common ground for the two theories by showing how aging can result from the inherent chemical reactivity of many biomolecules, not just ROS, which imposes a fundamental constraint on biological evolution. Chemically reactive metabolites spontaneously modify slowly renewable macromolecules in a continuous way over time; the resulting buildup of damage wrought by the genes coding for enzymes that generate such small molecules eventually masquerades as late-acting pleiotropic effects. In aerobic organisms, ROS are major agents of this damage but they are far from alone.

CRITICAL ISSUES

Being related to two sides of the same phenomenon, these theories should be compatible. However, the interface between them is obscured by the FRT mistaking a subset of damaging processes for the whole, and the APT mistaking a cumulative quantitative process for a qualitative switch.

FUTURE DIRECTIONS

The manifestations of ROS-mediated cumulative chemical damage at the population level may include the often-observed negative correlation between fitness and the rate of its decline with increasing age, further linking FRT and APT. Antioxid. Redox Signal. 29, 1003-1017.

Reactive Oxygen Species: Radical Factors in the Evolution of Animal Life: A molecular timescale from Earth's earliest history to the rise of complex life

Introduction of O₂ to Earth's early biosphere stimulated remarkable evolutionary adaptations, and a wide range of electron acceptors allowed diverse, energy-yielding metabolic pathways. Enzymatic reduction of O₂ yielded a several-fold increase in energy production, enabling evolution of multi-cellular animal life. However, utilization of O₂ also presented major challenges as O₂ and many of its derived reactive oxygen species (ROS) are highly toxic, possibly impeding multicellular evolution after the Great Oxidation Event. Remarkably, ROS, and especially hydrogen peroxide, seem to play a major part in early diversification and further development of cellular respiration and other oxygenic pathways, thus becoming an intricate part of evolution of complex life. Hence, although harnessing of chemical and thermo-dynamic properties of O₂ for aerobic metabolism is generally considered to be an evolutionary milestone, the ability to use ROS for cell signaling and regulation may have been the first true breakthrough in development of complex life.

Reaching multi-nanosecond timescales in combined QM/MM molecular dynamics simulations through parallel horsetail sampling

We report an enhanced sampling technique that allows to reach the multi-nanosecond timescale in quantum mechanics/molecular mechanics molecular dynamics simulations. The proposed technique, called horsetail sampling, is a specific type of multiple molecular dynamics approach exhibiting high parallel efficiency. It couples a main simulation with a large number of shorter trajectories launched on independent processors at periodic time intervals. The technique is applied to study hydrogen peroxide at the water liquid-vapor interface, a system of considerable atmospheric relevance. A total simulation time of a little more than 6 ns has been attained for a total CPU time of 5.1 years representing only about 20 days of wall-clock time. The discussion of the results highlights the strong influence of the solvation effects at the interface on the structure and the electronic properties of the solute. © 2017 Wiley Periodicals, Inc.

Thiosulfate-Hydrogen Peroxide Redox Oscillator as pH Driver for Ribozyme Activity in the RNA World

The RNA world of more than 3.7 billion years ago may have drawn on thermal and pH oscillations set up by the oxidation of thiosulfate by hydrogen peroxide (the THP oscillator) as a power source to drive replication. Since this primordial RNA also must have developed enzyme functionalities, in this work we examine the responses of two simple ribozymes to a THP periodic drive, using experimental rate and thermochemical data in a dynamical model for the coupled, self-consistent evolution of all reactants and intermediates. The resulting time traces show that ribozyme performance can be enhanced under pH cycling, and that thermal cycling may have been necessary to achieve large performance gains. We discuss three important ways in which the dynamic hydrogen peroxide medium may have acted as an agent for development of the RNA world towards a cellular world: proton gradients, resolution of the ribozyme versus replication paradox, and vesicle formation.

The life story of hydrogen peroxide II: a periodic pH and thermochemical drive for the RNA world

It is now accepted that primordial non-cellular RNA communities must have been subject to a periodic drive in order to replicate and prosper. We have proposed the oxidation of thiosulfate by hydrogen peroxide as this drive. This reaction system behaves as (i) a thermochemical and (ii) a pH oscillator, and in this work, we unify (i) and (ii) for the first time. We report thermally self-consistent, dynamical simulations in which the system transitions smoothly from nearly isothermal pH to fully developed thermo-pH oscillatory regimes. We use this oscillator to drive simulated replication of a 39-bp RNA species. Production of replicated duplex under thermo-pH drive was significantly enhanced compared with that under purely thermochemical drive, effectively allowing longer strands to replicate. Longer strands are fitter, with more potential to evolve enzyme activity and resist degradation. We affirm that concern over the alleged toxicity of hydrogen peroxide to life is largely misplaced in the current context, we survey its occurrence in the solar system to motivate its inclusion as a biosignature in the search for life on other worlds and highlight that pH oscillations in a spatially extended, bounded system manifest as the fundamental driving force of life: a proton gradient.