The Winding Road from Origin to Emergence (of Life).

Humanity's strive to understand why and how life appeared on planet Earth dates back to prehistoric times. At the beginning of the 19th century, empirical biology started to tackle this question yielding both Charles Darwin's Theory of Evolution and the paradigm that the crucial trigger putting life on its tracks was the appearance of organic molecules. In parallel to these developments in the biological sciences, physics and physical chemistry saw the fundamental laws of thermodynamics being unraveled. Towards the end of the 19th century and during the first half of the 20th century, the tensions between thermodynamics and the "organic-molecules-paradigm" became increasingly difficult to ignore, culminating in Erwin Schrödinger's 1944 formulation of a thermodynamics-compliant vision of life and, consequently, the prerequisites for its appearance. We will first review the major milestones over the last 200 years in the biological and the physical sciences, relevant to making sense of life and its origins and then discuss the more recent reappraisal of the relative importance of metal ions vs. organic molecules in performing the essential processes of a living cell. Based on this reassessment and the modern understanding of biological free energy conversion (aka bioenergetics), we consider that scenarios wherein life emerges from an abiotic chemiosmotic process are both thermodynamics-compliant and the most parsimonious proposed so far.

Dissolved metal ions and mineral-liposome hybrid systems: Underlying interactions, synthesis, and characterization.

Liposomes are versatile lipid-based vesicles with interesting physicochemical properties, making them excellent candidates for interdisciplinary applications in the medicinal, biological, and environmental sciences. The synthesis of mineral-liposome hybrid systems lends normally inert vesicles with the catalytic, magnetic, electrical, and optical properties of the integrated mineral species. Such applications require an understanding of the physicochemical interactions between organic molecules and inorganic crystal structures. This review provides an overview on these interactions and details on synthesis and characterization methods for these systems.

Methanol on the rocks: green rust transformation promotes the oxidation of methane.

Shared coordination geometries between metal ions within reactive minerals and enzymatic metal cofactors hints at mechanistic and possibly evolutionary homology between particular abiotic chemical mineralogies and biological metabolism. The octahedral coordination of reactive Fe2+/3+ minerals such as green rusts, endemic to anoxic sediments and the early Earth's oceans, mirrors the di-iron reaction centre of soluble methane monooxygenase (sMMO), responsible for methane oxidation in methanotrophy. We show that methane oxidation occurs in tandem with the oxidation of green rust to lepidocrocite and magnetite, mimicking radical-mediated methane oxidation found in sMMO to yield not only methanol but also halogenated hydrocarbons in the presence of seawater. This naturally occurring geochemical pathway for CH4 oxidation elucidates a previously unidentified carbon cycling mechanism in modern and ancient environments and reveals clues into mineral-mediated reactions in the synthesis of organic compounds necessary for the emergence of life.

Fuseless side-pump combiner for efficient fluoride-based double-clad fiber pumping.

We report a novel technique for side-pumping fluoride-based double-clad fibers, allowing a record coupling efficiency of 93% and a maximum power handling near 100 W at 981 nm. Our simple technique is based on wrapping a silica taper around a fluoride fiber and, therefore, does not require any complex fusion between these two dissimilar fibers. Under passive cooling, pump combiners made of undoped and erbium-doped fluoride fibers were successfully operated during several hours at respective incident powers of 91 and 44 W. Heat management issues and active cooling strategies are also discussed. This innovative combiner is a keystone towards the development of compact and robust high-power mid-infrared fiber lasers and amplifiers.

High-power supercontinuum generation in the mid-infrared pumped by a soliton self-frequency shifted source.

We report the demonstration of a fiber-based supercontinuum source delivering up to 825 mW of average output power between 2.5 and 5.0 µm generated in all-normal dispersion regime. The pumping source consists of an amplified ultrafast Er3+:ZrF4 fiber laser providing high peak power femtosecond pulses at 3.6 µm with an average output power exceeding the watt-level. These pulses are spectrally broadened through self-phase modulation using commercial chalcogenide-based step-index fibers. Al2O3 anti-reflection coatings were sputtered on chalcogenide fiber tips to increase the launching efficiency from 54% to 82%, making this record output power possible, and thus confirming that such coatings can support watt-level pumping with intense femtosecond pulses. To the best of our knowledge, this result represents the highest average output power ever achieved from a As2Se3-based mid-IR supercontinuum source with the potential of a high degree of coherence.

Direct Inscription of on-surface waveguides in polymers using a mid-ir fiber laser.

A detailed study of photo-inscribed optical waveguides in PMMA and polycarbonate using a mid-IR laser is presented. The wavelength of the laser is tuned near the absorption peaks of stretching C-H molecular bonds and the focused beam is scanned onto the surface of planar polymer samples. For the first time, we report the formation of optical waveguides in both polymers through resonant absorption of the laser beam. The optical properties of the waveguides were thoroughly assessed. An elliptic Gaussian mode is guided at the surface of both polymers. Insertion losses of 3.1 dB for a 30 mm long on-surface waveguide inscribed in PMMA were recorded. Such waveguides can interact with the external medium through evanescent coupling. As a proof of concept, the surface waveguides are used as highly sensitive refractometric sensors. An attenuation dynamical range of 35 dB was obtained for a liquid that matches the index of the PMMA substrate. Our results pave the way for large scale manufacturing of low cost biocompatible photonic devices.

Fougerite: the not so simple progenitor of the first cells.

We here review the extraordinary mineralogical properties of green rusts and their naturally occurring form, fougerite, and discuss the pertinence of these properties within the alkaline hydrothermal vent (AHV) hypothesis for life's emergence. We put forward an extended version of the AHV scenario which enhances the conformity between extant life and its earliest progenitor by extensively making use of fougerite's mechanistic and catalytic particularities.

Ultrafast Dy3+:fluoride fiber laser beyond 3 µm.

We report a passively mode-locked Dy3+:fluoride fiber laser emitting around 3.1 µm based on the nonlinear polarization evolution technique in a ring configuration, using in-band pumping at 2.8 µm. Transform-limited and self-starting mode-locked pulses as short as 828 fs with a center wavelength around 3.1 µm and repetition rates up to 60 MHz are obtained. In the single-pulse regime, a maximum average output power of 204 mW is measured, corresponding to a peak power of 4.2 kW and a pulse energy of 4.8 nJ. This first demonstration, to the best of our knowledge, of a femtosecond mode-locked fiber laser emitting directly beyond 3 µm paves the way for frequency comb synthesis in the molecular fingerprint region.

20 W splice-free erbium-doped all-fiber laser operating at 1610 nm.

We report on a splice-free erbium-doped all-fiber laser emitting over 20 W at a wavelength of 1610 nm, with a slope efficiency of 19.6 % and an overall efficiency of 18.3% with respect to the launched pump power at 976 nm. The simple cavity design takes advantage of fiber Bragg gratings written directly in the gain fiber through the polymer coating and clad-pumping from a single commercial pump diode to largely simplify the assembling process, making this cavity ideal for large-scale commercial deployment. Two single-mode and singly erbium-doped silica fibers were fabricated in-house: the first to assess the effects of a high erbium concentration (0.36 mol.% Er2O3), yielding a low efficiency of 2.5 % with respect to launched pump power, and the second to achieve the improved result mentioned above (0.03 mol.% Er2O3). Numerical simulations show the link between the performance of each cavity and ion pair-induced quenching.

On the Natural History of Flavin-Based Electron Bifurcation.

Electron bifurcation is here described as a special case of the continuum of electron transfer reactions accessible to two-electron redox compounds with redox cooperativity. We argue that electron bifurcation is foremost an electrochemical phenomenon based on (a) strongly inverted redox potentials of the individual redox transitions, (b) a high endergonicity of the first redox transition, and (c) an escapement-type mechanism rendering completion of the first electron transfer contingent on occurrence of the second one. This mechanism is proposed to govern both the traditional quinone-based and the newly discovered flavin-based versions of electron bifurcation. Conserved and variable aspects of the spatial arrangement of electron transfer partners in flavoenzymes are assayed by comparing the presently available 3D structures. A wide sample of flavoenzymes is analyzed with respect to conserved structural modules and three major structural groups are identified which serve as basic frames for the evolutionary construction of a plethora of flavin-containing redox enzymes. We argue that flavin-based and other types of electron bifurcation are of primordial importance to free energy conversion, the quintessential foundation of life, and discuss a plausible evolutionary ancestry of the mechanism.

Watt-level fiber-based femtosecond laser source tunable from 2.8 to 3.6 µm.

The development of compact and reliable ultrafast sources operating in the mid-infrared region could lead to major advances in both fundamental and applied sciences. In this Letter, we report on a simple and efficient laser system based entirely on erbium-doped fluoride glass fibers that generates high-energy Raman soliton pulses tunable from 2.8 to 3.6 µm at a high average output power. Stable 160 fs pulses at 3.4 µm with a maximum energy of 37 nJ, a corresponding average output power above 2 W, and an estimated peak power above 200 kW are demonstrated. This tunable source promises direct applications in laser processing of polymers and biological materials.

Negative cooperativity in the nitrogenase Fe protein electron delivery cycle.

Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen (N2) to two ammonia (NH3) molecules through the participation of its two protein components, the MoFe and Fe proteins. Electron transfer (ET) from the Fe protein to the catalytic MoFe protein involves a series of synchronized events requiring the transient association of one Fe protein with each αß half of the α2ß2 MoFe protein. This process is referred to as the Fe protein cycle and includes binding of two ATP to an Fe protein, association of an Fe protein with the MoFe protein, ET from the Fe protein to the MoFe protein, hydrolysis of the two ATP to two ADP and two Pi for each ET, Pi release, and dissociation of oxidized Fe protein-(ADP)2 from the MoFe protein. Because the MoFe protein tetramer has two separate αß active units, it participates in two distinct Fe protein cycles. Quantitative kinetic measurements of ET, ATP hydrolysis, and Pi release during the presteady-state phase of electron delivery demonstrate that the two halves of the ternary complex between the MoFe protein and two reduced Fe protein-(ATP)2 do not undergo the Fe protein cycle independently. Instead, the data are globally fit with a two-branch negative-cooperativity kinetic model in which ET in one-half of the complex partially suppresses this process in the other. A possible mechanism for communication between the two halves of the nitrogenase complex is suggested by normal-mode calculations showing correlated and anticorrelated motions between the two halves.

The H-bond network surrounding the pyranopterins modulates redox cooperativity in the molybdenum-bisPGD cofactor in arsenite oxidase.

While the molybdenum cofactor in the majority of bisPGD enzymes goes through two consecutive 1-electron redox transitions, previous protein-film voltammetric results indicated the possibility of cooperative (n=2) redox behavior in the bioenergetic enzyme arsenite oxidase (Aio). Combining equilibrium redox titrations, optical and EPR spectroscopies on concentrated samples obtained via heterologous expression, we unambiguously confirm this claim and quantify Aio's redox cooperativity. The stability constant, Ks, of the Mo(V) semi-reduced intermediate is found to be lower than 10(-3). Site-directed mutagenesis of residues in the vicinity of the Mo-cofactor demonstrates that the degree of redox cooperativity is sensitive to H-bonding interactions between the pyranopterin moieties and amino acid residues. Remarkably, in particular replacing the Gln-726 residue by Gly results in stabilization of (low-temperature) EPR-observable Mo(V) with KS=4. As evidenced by comparison of room temperature optical and low temperature EPR titrations, the degree of stabilization is temperature-dependent. This highlights the importance of room-temperature redox characterizations for correctly interpreting catalytic properties in this group of enzymes. Geochemical and phylogenetic data strongly indicate that molybdenum played an essential biocatalytic roles in early life. Molybdenum's redox versatility and in particular the ability to show cooperative (n=2) redox behavior provide a rationale for its paramount catalytic importance throughout the evolutionary history of life. Implications of the H-bonding network modulating Molybdenum's redox properties on details of a putative inorganic metabolism at life's origin are discussed.

All-fiber amplifier similariton laser based on a fiber Bragg grating filter.

This article presents, for the first time to our knowledge, an all-fiber amplifier similariton laser based on a fiber Bragg grating filter. The laser emits 2.9 nJ pulses at a wavelength of 1554 nm with a repetition rate of 31 MHz. The dechirped pulses have a duration of 89 fs. The characteristic features of the pulse profile and spectrum along with the dynamics of the laser are highlighted in representative simulations. These simulations also address the effect of the filter shape and detuning with respect to the gain spectral peak.

In-amplifier mid-infrared supercontinuum generation.

Mid-infrared supercontinuum (SC) generation from 2.6 to 4.1 µm is demonstrated in a single-mode erbium-doped fluoride glass fiber amplifier pumped at 976 nm and seeded by an optical parametric generation (OPG) source emitting 400 ps pulses at 2.75 µm. Up to 82% of the SC power is generated beyond 3 µm. This novel and simple in-amplifier SC generation approach is promising for the development of compact and efficient sources operating in the mid-infrared, especially in the 3-5 µm band.

Fe protein-independent substrate reduction by nitrogenase MoFe protein variants.

The reduction of substrates catalyzed by nitrogenase normally requires nucleotide-dependent Fe protein delivery of electrons to the MoFe protein, which contains the active site FeMo cofactor. Here, it is reported that independent substitution of three amino acids (ß-98(Tyr→His), α-64(Tyr→His), and ß-99(Phe→His)) located between the P cluster and FeMo cofactor within the MoFe protein endows it with the ability to reduce protons to H2, azide to ammonia, and hydrazine to ammonia without the need for Fe protein or ATP. Instead, electrons can be provided by the low-potential reductant polyaminocarboxylate-ligated Eu(II) (Em values of -1.1 to -0.84 V vs the normal hydrogen electrode). The crystal structure of the ß-98(Tyr→His) variant MoFe protein was determined, revealing only small changes near the amino acid substitution that affect the solvent structure and the immediate vicinity between the P cluster and the FeMo cofactor, with no global conformational changes observed. Computational normal-mode analysis of the nitrogenase complex reveals coupling in the motions of the Fe protein and the region of the MoFe protein with these three amino acids, which suggests a possible mechanism for how Fe protein might communicate subtle changes deep within the MoFe protein that profoundly affect intramolecular electron transfer and substrate reduction.

Formation of high-valent iron-oxo species in superoxide reductase: characterization by resonance Raman spectroscopy.

Superoxide reductase (SOR), a non-heme mononuclear iron protein that is involved in superoxide detoxification in microorganisms, can be used as an unprecedented model to study the mechanisms of O2 activation and of the formation of high-valent iron-oxo species in metalloenzymes. By using resonance Raman spectroscopy, it was shown that the mutation of two residues in the second coordination sphere of the SOR iron active site, K48 and I118, led to the formation of a high-valent iron-oxo species when the mutant proteins were reacted with H2O2. These data demonstrate that these residues in the second coordination sphere tightly control the evolution and the cleavage of the O-O bond of the ferric iron hydroperoxide intermediate that is formed in the SOR active site.

A confirmation of the quench-cryoannealing relaxation protocol for identifying reduction states of freeze-trapped nitrogenase intermediates.

We have advanced a mechanism for nitrogenase catalysis that rests on the identification of a low-spin EPR signal (S = 1/2) trapped during turnover of a MoFe protein as the E4 state, which has accumulated four reducing equivalents as two [Fe-H-Fe] bridging hydrides. Because electrons are delivered to the MoFe protein one at a time, with the rate-limiting step being the off-rate of oxidized Fe protein, it is difficult to directly control, or know, the degree of reduction, n, of a trapped intermediate, denoted En, n = 1-8. To overcome this previously intractable problem, we introduced a quench-cryoannealing relaxation protocol for determining n of an EPR-active trapped En turnover state. The trapped "hydride" state was allowed to relax to the resting E0 state in frozen medium, which prevents additional accumulation of reducing equivalents; binding of reduced Fe protein and release of oxidized protein from the MoFe protein both are abolished in a frozen solid. Relaxation of En was monitored by periodic EPR analysis at cryogenic temperature. The protocol rests on the hypothesis that an intermediate trapped in the frozen solid can relax toward the resting state only by the release of a stable reduction product from FeMo-co. In turnover under Ar, the only product that can be released is H2, which carries two reducing equivalents. This hypothesis implicitly predicts that states that have accumulated an odd number of electrons/protons (n = 1, 3) during turnover under Ar cannot relax to E0: E3 can relax to E1, but E1 cannot relax to E0 in the frozen state. The present experiments confirm this prediction and, thus, the quench-cryoannealing protocol and our assignment of E4, the foundation of the proposed mechanism for nitrogenase catalysis. This study further gives insights into the identity of the En intermediates with high-spin EPR signals, 1b and 1c, trapped under high electron flux.

Ultrashort pulses from an all-fiber ring laser incorporating a pair of chirped fiber Bragg gratings.

By incorporating two linearly chirped ultrabroadband fiber Bragg gratings of opposite dispersion in an all-fiber ring laser, we demonstrate a mode-locking regime in which a femtosecond pulse evolving in the normal dispersion gain segment is locally transformed into a highly chirped picosecond pulse that propagates in the remaining section of the cavity. By minimizing nonlinear effects and avoiding soliton pulse shaping in this anomalous-dispersion section, low repetition rate fiber lasers can be made to produce high-energy ultrashort pulses. Using this approach, 98 fs pulses with 0.96 nJ of energy are obtained from an erbium-doped fiber laser operated in the highly anomalous dispersion regime at a repetition rate of 9.4 MHz.

Electron transfer precedes ATP hydrolysis during nitrogenase catalysis.

The biological reduction of N2 to NH3 catalyzed by Mo-dependent nitrogenase requires at least eight rounds of a complex cycle of events associated with ATP-driven electron transfer (ET) from the Fe protein to the catalytic MoFe protein, with each ET coupled to the hydrolysis of two ATP molecules. Although steps within this cycle have been studied for decades, the nature of the coupling between ATP hydrolysis and ET, in particular the order of ET and ATP hydrolysis, has been elusive. Here, we have measured first-order rate constants for each key step in the reaction sequence, including direct measurement of the ATP hydrolysis rate constant: kATP = 70 s(-1), 25 °C. Comparison of the rate constants establishes that the reaction sequence involves four sequential steps: (i) conformationally gated ET (kET = 140 s(-1), 25 °C), (ii) ATP hydrolysis (kATP = 70 s(-1), 25 °C), (iii) Phosphate release (kPi = 16 s(-1), 25 °C), and (iv) Fe protein dissociation from the MoFe protein (kdiss = 6 s(-1), 25 °C). These findings allow completion of the thermodynamic cycle undergone by the Fe protein, showing that the energy of ATP binding and protein-protein association drive ET, with subsequent ATP hydrolysis and Pi release causing dissociation of the complex between the Fe(ox)(ADP)2 protein and the reduced MoFe protein.