Thiophosphate photochemistry enables prebiotic access to sugars and terpenoid precursors.

Over the past few years, evidence has accrued that demonstrates that terrestrial photochemical reactions could have provided numerous (proto)biomolecules with implications for the origin of life. This chemistry simply relies on UV light, inorganic sulfur species and hydrogen cyanide. Recently, we reported that, under the same conditions, reduced phosphorus species, such as those delivered by meteorites, can be oxidized to orthophosphate, generating thiophosphate in the process. Here we describe an investigation of the properties of thiophosphate as well as additional possible means for its formation on primitive Earth. We show that several reported prebiotic reactions, including the photoreduction of thioamides, carbonyl groups and cyanohydrins, can be markedly improved, and that tetroses and pentoses can be accessed from hydrogen cyanide through a Kiliani-Fischer-type process without progressing to higher sugars. We also demonstrate that thiophosphate allows photochemical reductive aminations, and that thiophosphate chemistry allows a plausible prebiotic synthesis of the C5 moieties used in extant terpene and terpenoid biosynthesis, namely dimethylallyl alcohol and isopentenyl alcohol.

Thermally Accessible Prebiotic Pathways for Forming Ribonucleic Acid and Protein Precursors from Aqueous Hydrogen Cyanide.

The search for prebiotic chemical pathways to biologically relevant molecules is a long-standing puzzle that has generated a menagerie of competing hypotheses with limited experimental prospects for falsification. However, the advent of computational network exploration methodologies has created the opportunity to compare the kinetic plausibility of various channels and even propose new pathways. Here, the space of organic molecules that can be formed within four polar or pericyclic reactions from water and hydrogen cyanide (HCN), two established prebiotic candidates for generating biological precursors, was comprehensively explored with a state-of-the-art exploration algorithm. A surprisingly diverse reactivity landscape was revealed within just a few steps of these simple molecules. Reaction pathways to several biologically relevant molecules were discovered involving lower activation energies and fewer reaction steps compared with recently proposed alternatives. Accounting for water-catalyzed reactions qualitatively affects the interpretation of the network kinetics. The case-study also highlights omissions of simpler and lower barrier reaction pathways to certain products by other algorithms that qualitatively affect the interpretation of HCN reactivity.

Can a Finite Chain of Hydrogen Cyanide Molecules Model a Crystal?

When calculating structural or spectroscopic properties of molecular crystals, the question arises whether it is sufficient to simulate only a single molecule or a small molecular cluster or whether the simulation of the entire crystal is indispensable. In this work we juxtapose calculations on the high-pressure structural properties of the (periodic) HCN crystal and chains of HCN molecules of finite length. We find that, in most cases, the behavior of the crystal can be reproduced by computational methods simulating only around 15 molecules. The pressure-induced lengthening of the C-H bond in HCN found in calculations on both the periodic and finite material are explained in terms of orbital interaction. Our results pave the way for a more thorough understanding of high-pressure structural properties of materials and give incentives for the design of materials that expand under pressure. In addition, they shed light on the complementarity between calculations on periodic materials and systems of finite size.

Weakly Bound Complex Formation between HCN and CH3Cl: A Matrix-Isolation and Computational Study.

The matrix-isolated infrared spectrum of a hydrogen cyanide-methyl chloride complex was investigated in a solid argon matrix. HCN and CH3Cl were co-condensed onto a substrate held at 10 K with an excess of argon gas, and the infrared spectrum was measured using Fourier-transform infrared spectroscopy. Quantum chemical geometry optimization, harmonic frequency, and natural bonding orbital calculations indicate stabilized hydrogen- and halogen-bonded structures. The two resulting weakly bound complexes are both composed of one CH3Cl molecule bound to a (HCN)3 subunit, where the three HCN molecules are bound head-to-tail in a ring formation. Our study suggests that─in the presence of CH3Cl─the formation of (HCN)3 is promoted through complexation. Since HCN aggregates are an important precursor to prebiotic monomers (amino acids and nucleobases) and other life-bearing polymers, this study has astrophysical implications toward the search for life in space.

Amygdalin: Toxicity, Anticancer Activity and Analytical Procedures for Its Determination in Plant Seeds.

Amygdalin (d-Mandelonitrile 6-O-ß-d-glucosido-ß-d-glucoside) is a natural cyanogenic glycoside occurring in the seeds of some edible plants, such as bitter almonds and peaches. It is a medically interesting but controversial compound as it has anticancer activity on one hand and can be toxic via enzymatic degradation and production of hydrogen cyanide on the other hand. Despite numerous contributions on cancer cell lines, the clinical evidence for the anticancer activity of amygdalin is not fully confirmed. Moreover, high dose exposures to amygdalin can produce cyanide toxicity. The aim of this review is to present the current state of knowledge on the sources, toxicity and anticancer properties of amygdalin, and analytical methods for its determination in plant seeds.

Chemical Diversity of Plant Cyanogenic Glycosides: An Overview of Reported Natural Products.

Cyanogenic glycosides are an important and widespread class of plant natural products, which are however structurally less diverse than many other classes of natural products. So far, 112 naturally occurring cyanogenic glycosides have been described in the phytochemical literature. Currently, these unique compounds have been reported from more than 2500 plant species. Natural cyanogenic glycosides show variations regarding both the aglycone and the sugar part of the molecules. The predominant sugar moiety is glucose but many substitution patterns of this glucose moiety exist in nature. Regarding the aglycone moiety, four different basic classes can be distinguished, aliphatic, cyclic, aromatic, and heterocyclic aglycones. Our overview covers all cyanogenic glycosides isolated from plants and includes 33 compounds with a non-cyclic aglycone, 20 cyclopentane derivatives, 55 natural products with an aromatic aglycone, and four dihydropyridone derivatives. In the following sections, we will provide an overview about the chemical diversity known so far and mention the first source from which the respective compounds had been isolated. This review will serve as a first reference for researchers trying to find new cyanogenic glycosides and highlights some gaps in the knowledge about the exact structures of already described compounds.

Double-Hybrid DFT Functionals for the Condensed Phase: Gaussian and Plane Waves Implementation and Evaluation.

Intermolecular interactions play an important role for the understanding of catalysis, biochemistry and pharmacy. Double-hybrid density functionals (DHDFs) combine the proper treatment of short-range interactions of common density functionals with the correct description of long-range interactions of wave-function correlation methods. Up to now, there are only a few benchmark studies available examining the performance of DHDFs in condensed phase. We studied the performance of a small but diverse selection of DHDFs implemented within Gaussian and plane waves formalism on cohesive energies of four representative dispersion interaction dominated crystal structures. We found that the PWRB95 and ωB97X-2 functionals provide an excellent description of long-ranged interactions in solids. In addition, we identified numerical issues due to the extreme grid dependence of the underlying density functional for PWRB95. The basis set superposition error (BSSE) and convergence with respect to the super cell size are discussed for two different large basis sets.

Cometary Delivery of Hydrogen Cyanide to the Early Earth.

Delivery of water and organics by asteroid and comet impacts may have influenced prebiotic chemistry on the early Earth. Some recent prebiotic chemistry experiments emphasize hydrogen cyanide (HCN) as a feedstock molecule for the formation of sugars, ribonucleotides, amino acids, and lipid precursors. Here, we assess how much HCN originally contained in a comet would survive impact, using parametric temperature and pressure profiles together with a time-dependent chemistry model. We find that HCN survival mainly depends on whether the impact is hot enough to thermally decompose H2O into reactive radicals, and HCN is therefore rather insensitive to the details of the chemistry. In the most favorable impacts (low impact angle, low velocity, small radius), this temperature threshold is not reached, and intact delivery of HCN is possible. We estimate the global delivery of HCN during a period of Early and Late Heavy Bombardment of the early Earth, as well as local HCN concentrations achieved by individual impacts. In the latter case, comet impacts can provide prebiotically interesting HCN levels for thousands to millions of years, depending on properties of the impactor and of the local environment.

Sensitivity boosts by the CPMAS CryoProbe for challenging biological assemblies.

Despite breakthroughs in MAS NMR hardware and experimental methodologies, sensitivity remains a major challenge for large and complex biological systems. Here, we report that 3-4 fold higher sensitivities can be obtained in heteronuclear-detected experiments, using a novel HCN CPMAS probe, where the sample coil and the electronics operate at cryogenic temperatures, while the sample is maintained at ambient temperatures (BioSolids CryoProbe™). Such intensity enhancements permit recording 2D and 3D experiments that are otherwise time-prohibitive, such as 2D 15N-15N proton-driven spin diffusion and 15N-13C double cross polarization to natural abundance carbon experiments. The benefits of CPMAS CryoProbe-based experiments are illustrated for assemblies of kinesin Kif5b with microtubules, HIV-1 capsid protein assemblies, and fibrils of human Y145Stop and fungal HET-s prion proteins - demanding systems for conventional MAS solid-state NMR and excellent reference systems in terms of spectral quality. We envision that this probe technology will be beneficial for a wide range of applications, especially for biological systems suffering from low intrinsic sensitivity and at physiological temperatures.

New paths of cyanogenesis from enzymatic-promoted cleavage of ß-cyanoglucosides are suggested by a mixed DFT/QTAIM approach.

Cyanogenesis is an enzyme-promoted cleavage of ß-cyanoglucosides; the release of hydrogen cyanide is believed to produce food poisoning by consumption of certain crops as Cassava (Manihot esculenta Crantz). The production of hydrogen cyanide by some disruption of the plant wall is related to the content of two ß-cyanoglucosides (linamarin and lotaustralin) which are stored within the tuber. Some features about the mechanistic bases of these transformations have been published; nevertheless, there are still questions about the exact mechanism, such as the feasibility of a difference in the kinetics of cyanogenesis between both cyanoglucosides. In this work, we have performed a theoretical analysis using DFT and QTAIM theoretical frameworks to propose a feasible mechanism of the observed first step of the enzyme-catalyzed rupture of these glucosides; our results led us to explain the observed difference between linamarin and lotaustralin. Meanwhile, DFT studies suggest that there are no differences between local reactivity indexes of both glucosides; QTAIM topological analysis suggests two important intramolecular interactions which we found to fix the glucoside in such a way that suggests the linamarin as a more reactive system towards a nucleophilic attack, thus explaining the readiness to liberate hydrogen cyanide.

Solution degradant of mirabegron extended release tablets resulting from a Strecker-like reaction between mirabegron, minute amounts of hydrogen cyanide in acetonitrile, and formaldehyde in PEG during sample preparation.

During the related substances testing of mirabegron extended release tablets, an unknown peak was observed in HPLC chromatograms in a level exceeding the identification threshold. By using a strategy that combines LC-PDA/UV-MSn with mechanism-based stress studies, the unknown peak was rapidly identified as cyanomethyl mirabegron, a solution degradant that is caused by a Strecker-like reaction between the API, formaldehyde (an impurity in PEG), and HCN (an impurity in HPLC grade acetonitrile). The mechanism of the solution degradation chemistry was verified by stressing mirabegron with formaldehyde and trimethylsilyl cyanide (TMSCN, a synthetic reagent that generates HCN upon contact with water), in which the secondary amine group of mirabegron first reacts with formaldehyde to form the iminium ion intermediate; the latter then undergoes a nucleophilic attack by cyanide to yield the cyanomethyl mirabegron. The structure of the impurity was further confirmed through the synthesis of the impurity and subsequent structure characterization by 1D and 2D NMR. Due to the ubiquitous presence of formaldehyde in pharmaceutical excipients (e.g., PEG and polysorbate) and trace amount of HCN in HPLC grade acetonitrile, this type of solution degradation would likely occur in sample preparations of pharmaceutical finished products containing APIs with primary and secondary amine moieties. In a GMP environment, such an event may trigger undesirable out-of-specification (OOS) investigations; the results of this paper should help resolve such OOS investigations or even prevent these events from happening in the first place.

Exploring adsorption mechanism of hydrogen cyanide and cyanogen chloride molecules on arsenene nanoribbon from first-principles.

The SIESTA package is employed in examining the electronic and adsorption features of the toxic asphyxiants hydrogen cyanide (HCN) and cyanogen chloride (NCCl) on armchair arsenene (As-arm) nanoribbon. Based on the generalized gradient approximation (GGA) with the Perdew-Burke-Ernzerhof (PBE) level of theory, we explored the adsorption of HCN and NCCl on As-arm nanoribbon. The significant parameters necessary to validate the electronic and stable nature of As-arm nanoribbon are computed with the help of formation energy and energy gap change. The density of states (DOS) spectrum and the energy band structure are figured-out for both isolated and asphyxiants adsorbed As-arm nanoribbon, which affirms the transfer of electrons taking place between As-arm nanoribbon and the asphyxiants. Also, surface assimilating properties like Bader charge transfer, average energy gap variation, and adsorption energy are calculated for the asphyxiants adsorbed As-arm nanoribbon. Moreover, the comparison is made between the electron density of isolated and asphyxiants adsorbed As-arm nanoribbon to enunciate the utilization of As-arm nanoribbon as a chemisensor for detecting the asphyxiants HCN and NCCl molecules.

Metabolism of cyanogenic glycosides: A review.

Potential toxicity of cyanogenic glycosides arises from enzymatic degradation to produce hydrogen cyanide. Information on the metabolism of cyanogenic glycosides is available from in vitro, animal and human studies. In the absence of ß-glucosidase enzymes from the source plant material, two processes appear to contribute to the production of cyanide from cyanogenic glycosides; the proportion of the glycoside dose that reaches the large intestine, where most of the bacterial hydrolysis occurs, and the rate of hydrolysis of cyanogenic glycosides to cyanohydrin and cyanide. Some cyanogenic glycosides, such as prunasin, are actively absorbed in the jejunum by utilising the epithelial sodium-dependent monosaccharide transporter (SGLT1). The rate of cyanide production from cyanogenic glycosides due to bacterial ß-glycosidase activity depends on; the sugar moiety in the molecule and the stability of the intermediate cyanohydrin following hydrolysis by bacterial ß-glucosidase. Cyanogenic glycosides with a gentiobiose sugar, amygdalin, linustatin, and neolinustatin, undergo a two stage hydrolysis, with gentiobiose initially being hydrolysed to glucose to form prunasin, linamarin and lotaustralin, respectively. While the overall impact of these metabolic factors is difficult to predict, the toxicity of cyanogenic glycosides will be less than the toxicity suggested by their theoretical hydrocyanic acid equivalents.

Prebiotic plausibility and networks of paradox-resolving independent models.

The plausibility of any model in science comes from the extent of its interconnections to other models that are grounded in different premises and reasoning. Focusing research on paradoxes in those models, logic whereby they appear to generate unacceptable conclusions from seemingly indisputable premises, helps find those interconnections.

Reactions of Auranofin and Its Pseudohalide Derivatives with Serum Albumin Investigated through ESI-Q-TOF MS.

The reactions of auranofin and three pseudohalide derivatives with bovine serum albumin were explored by ESI-Q-TOF mass spectrometry; a detailed molecular description of the resulting adducts is achieved revealing even subtle differences in reactivity within this series of gold(I) complexes. Our study shows that this kind of investigative approach, formerly applied to the interactions of metal-based drugs with small model proteins of MW 10-15 kDa, e.g., cytochrome c and lysozyme, may now be extended with success to far larger proteins such as serum albumin (MW 66 kDa).

Theoretical Investigation of the Formation Mechanism of NH3 and HCN during Pyrrole Pyrolysis: The Effect of H2O.

Coal is a major contributor to the global emission of nitrogen oxides (NOx). The NOx formation during coal utilization typically derives from the thermal decomposition of N-containing compounds (e.g., pyrrolic groups). NH3 and HCN are common precursors of NOx from the decomposition of N-containing compounds. The existence of H2O has significant influences on the pyrrole decomposition and NOx formation. In this study, the effects of H2O on pyrrole pyrolysis to form NOx precursors HCN and NH3 are investigated using the density functional theory (DFT) method. The calculation results indicate that the presence of H2O can lead to the formation of both NH3 and HCN during pyrrole pyrolysis, while only HCN is formed in the absence of H2O. The initial interaction between pyrrole and H2O determines the N products. NH3 will be formed when H2O attacks the C2 position of pyrrole with its hydroxyl group. On the contrary, HCN will be generated instead of NH3 when H2O attacks the C3 position of pyrrole with its hydroxyl group. In addition, the DFT calculations clearly indicate that the formation of NH3 will be promoted by H2O, whereas the formation of HCN is inhibited.

A Mitochondria-Specific Fluorescent Probe for Visualizing Endogenous Hydrogen Cyanide Fluctuations in Neurons.

An ability to visualize HCN in mitochondria in real time may permit additional insights into the critical toxicological and physiological roles this classic toxin plays in living organisms. Herein, we report a mitochondria-specific coumarin pyrrolidinium-derived fluorescence probe (MRP1) that permits the real-time ratiometric imaging of HCN in living cells. The response is specific, sensitive (detection limit is ca. 65.6 nM), rapid (within 1 s), and reversible. Probe MRP1 contains a benzyl chloride subunit designed to enhance retention within the mitochondria under conditions where the mitochondria membrane potential is eliminated. It has proved effective in visualizing different concentrations of exogenous HCN in the mitochondria of HepG2 cells, as well as the imaging of endogenous HCN in the mitochondria of PC12 cells and within neurons. Fluctuations in HCN levels arising from the intracellular generation of HCN could be readily detected.

Oxygen-Free Biochemistry: The Putative CHN Foundation for Exotic Life in a Hydrocarbon World?

Since Earth's biochemistry is carbon-based and water-borne, the main strategies for searching for life elsewhere are "follow the carbon" and "follow the water." Recently, however, there is a growing focus on the prospect that putative exotic life on other planets could rely on unearthly biochemistries. Here, we hypothesize a novel oxygen-free organic chemistry for supporting potential exotic biosystems, which is named CHN biochemistry. This oxygen-free CHN biochemistry starts from simple oxygen-free species (including hydrocarbons, hydrogen cyanide, and nitriles) and produces a range of functional macromolecules that may function in similar ways to terran macromolecules, such as sugars (cyanosugars), acids (cyanoacids), amino acids (amino cyanoacids), and nucleobases (cyanonucleobases). These CHN macromolecules could further interact with each other to generate higher "cyanoester" and "cyanoprotein" systems. In addition, theoretical calculations indicate that the energy changes of some reactions are consistent with their counterparts in Earth's biochemistry. The CHN biochemistry-based life would be applicable in habitats with a low bioavailability of oxygen, such as the alkane lakes of Titan and non-aquatic liquids on extrasolar bodies. Key Words: Oxygen-free biochemistry-Titan-Hydrocarbons-Hydrogen cyanide-Nitriles. Astrobiology 17, 1173-1181.

High Energy Radical Chemistry Formation of HCN-rich Atmospheres on early Earth.

Recent results in prebiotic chemistry implicate hydrogen cyanide (HCN) as the source of carbon and nitrogen for the synthesis of nucleotide, amino acid and lipid building blocks. HCN can be produced during impact events by reprocessing of carbonaceous and nitrogenous materials from both the impactor and the atmosphere; it can also be produced from these materials by electrical discharge. Here we investigate the effect of high energy events on a range of starting mixtures representative of various atmosphere-impactor volatile combinations. Using continuously scanning time-resolved spectrometry, we have detected ·CN radical and excited CO as the initially most abundant products. Cyano radicals and excited carbon monoxide molecules in particular are reactive, energy-rich species, but are resilient owing to favourable Franck-Condon factors. The subsequent reactions of these first formed excited species lead to the production of ground-state prebiotic building blocks, principally HCN.

Storage and release of hydrogen cyanide in a chelicerate (Oribatula tibialis).

Cyanogenesis denotes a chemical defensive strategy where hydrogen cyanide (HCN, hydrocyanic or prussic acid) is produced, stored, and released toward an attacking enemy. The high toxicity and volatility of HCN requires both chemical stabilization for storage and prevention of accidental self-poisoning. The few known cyanogenic animals are exclusively mandibulate arthropods (certain myriapods and insects) that store HCN as cyanogenic glycosides, lipids, or cyanohydrins. Here, we show that cyanogenesis has also evolved in the speciose Chelicerata. The oribatid mite Oribatula tibialis uses the cyanogenic aromatic ester mandelonitrile hexanoate (MNH) for HCN storage, which degrades via two different pathways, both of which release HCN. MNH is emitted from exocrine opisthonotal oil glands, which are potent organs for chemical defense in most oribatid mites.