Laboratory Studies of Astronomical Ices: Reaction Chemistry and Spectroscopy.

ConspectusScientists have had evidence for molecules in both comets and interstellar space since the 19th and early 20th centuries. Since then, extraterrestrial molecules ranging from simple diatomics to C70 to amino acids have been detected and identified through remote spectroscopy, spacecraft, and sample return missions. These achievements have been made through the efforts of astronomers and laboratory chemists collaborating to identify molecules in a myriad of exotic environments. It is now understood that even in the coldest depths of dense molecular clouds there is a wealth of chemistry to explore, much of it driven by exposure to radiation. As molecular clouds condense to protostellar disks and eventually form new planetary systems, chemical processes continue and evolve. An understanding of these processes is paramount for explaining the compositions of different bodies in our Solar System and may provide insight into the origins of life.In this Account, we describe the work of the Cosmic Ice Laboratory at NASA's Goddard Space Flight Center to characterize the composition of and understand the chemistry occurring in icy bodies in the Solar System and beyond. Our work has touched on a wide range of extraterrestrial environments, including icy interstellar grains, small bodies such as comets and asteroids, and planets and moons. We are especially interested in the chemical and physical changes that occur in ices as a result of thermal changes or exposure to radiation. To this end, we conduct experiments designed to simulate cold extraterrestrial environments and measure physical properties of single- and multicomponent ices. We expose ices to radiation (e.g., MeV protons or keV-MeV electrons) or high-energy (e.g., UV) photons to initiate physical and chemical changes. We conduct experiments using cryo-vacuum chambers equipped with analytical tools and radiation sources to make most of our measurements, including the collection of all spectroscopic data, in situ. When possible and appropriate, we also collect reaction products for further ex situ analysis. The work of the Cosmic Ice Lab provides critical data to astrochemists and others seeking to understand observations, make predictions, and plan future space missions.

The Radiation Stability of Thymine in Solid H2O.

Nucleobases are of significant importance to all known organisms, may be an important building block of life, and could be important biosignatures of current or past life. Given their potential significance to the field of astrobiology, it is important to understand the survival of these molecules when subjected to ionizing radiation as is present in a range of extraterrestrial environments. In this work, we present data on the kinetics of the radiolytic destruction of pure thymine and water + thymine ice mixtures at temperatures from 13 to 150 K. Rate constants were measured using in situ infrared spectroscopy, and radiolytic half-lives for thymine were computed for different planetary and interstellar environments. Our results demonstrate that the survival of thymine decreases as the dilution of thymine in water increases. Additionally, we find that thymine survival increases with ice temperature and that this decrease may be related to structure of the ice matrix.

The Production and Potential Detection of Hexamethylenetetramine-Methanol in Space.

Numerous laboratory studies of astrophysical ice analogues have shown that their exposure to ionizing radiation leads to the production of large numbers of new, more complex compounds, many of which are of astrobiological interest. We show here that the irradiation of astrophysical ice analogues containing H2O, CH3OH, CO, and NH3 yields quantities of hexamethylenetetramine-methanol (hereafter HMT-methanol; C7N4H14O) that are easily detectible in the resulting organic residues. This molecule differs from simple HMT, which is known to be abundant in similar ice photolysis residues, by the replacement of a peripheral H atom with a CH2OH group. As with HMT, HMT-methanol is likely to be an amino acid precursor. HMT has tetrahedral (Td) symmetry, whereas HMT-methanol has C1 symmetry. We report the computed expected infrared spectra for HMT and HMT-methanol obtained using ab initio quantum chemistry methods and show that there is a good match between the observed and computed spectra for regular HMT. Since HMT-methanol lacks the high symmetry of HMT, it produces rotational transitions that could be observed at longer wavelengths, although establishing the exact positions of these transitions may be challenging. It is likely that HMT-methanol represents an abundant member of a larger family of functionalized HMT molecules that may be present in cold astrophysical environments.

The Formation of Nucleobases from the Ultraviolet Photoirradiation of Purine in Simple Astrophysical Ice Analogues.

Nucleobases are the informational subunits of RNA and DNA and are essential to all known forms of life. The nucleobases can be divided into two groups of molecules: the pyrimidine-based compounds that include uracil, cytosine, and thymine, and the purine-based compounds that include adenine and guanine. Previous work in our laboratory has demonstrated that uracil, cytosine, thymine, and other nonbiological, less common nucleobases can form abiotically from the UV photoirradiation of pyrimidine in simple astrophysical ice analogues containing combinations of H2O, NH3, and CH4. In this work, we focused on the UV photoirradiation of purine mixed with combinations of H2O and NH3 ices to determine whether or not the full complement of biological nucleobases can be formed abiotically under astrophysical conditions. Room-temperature analyses of the resulting photoproducts resulted in the detection of adenine, guanine, and numerous other functionalized purine derivatives. Key Words: Pyrimidine-Nucleobases-Interstellar; Ices-Cometary; Ices-Molecular processes-Prebiotic chemistry. Astrobiology 17, 761-770.

Mechanisms for the formation of thymine under astrophysical conditions and implications for the origin of life.

Nucleobases are the carriers of the genetic information in ribonucleic acid and deoxyribonucleic acid (DNA) for all life on Earth. Their presence in meteorites clearly indicates that compounds of biological importance can form via non-biological processes in extraterrestrial environments. Recent experimental studies have shown that the pyrimidine-based nucleobases uracil and cytosine can be easily formed from the ultraviolet irradiation of pyrimidine in H2O-rich ice mixtures that simulate astrophysical processes. In contrast, thymine, which is found only in DNA, is more difficult to form under the same experimental conditions, as its formation usually requires a higher photon dose. Earlier quantum chemical studies confirmed that the reaction pathways were favorable provided that several H2O molecules surrounded the reactants. However, the present quantum chemical study shows that the formation of thymine is limited because of the inefficiency of the methylation of pyrimidine and its oxidized derivatives in an H2O ice, as supported by the laboratory studies. Our results constrain the formation of thymine in astrophysical environments and thus the inventory of organic molecules delivered to the early Earth and have implications for the role of thymine and DNA in the origin of life.

ICE CHEMISTRY ON OUTER SOLAR SYSTEM BODIES: ELECTRON RADIOLYSIS OF N2-, CH4-, AND CO-CONTAINING ICES.

Radiation processing of the surface ices of outer Solar System bodies may be an important process for the production of complex chemical species. The refractory materials resulting from radiation processing of known ices are thought to impart to them a red or brown color, as perceived in the visible spectral region. In this work, we analyzed the refractory materials produced from the 1.2-keV electron bombardment of low-temperature N2-, CH4-, and CO-containing ices (100:1:1), which simulates the radiation from the secondary electrons produced by cosmic ray bombardment of the surface ices of Pluto. Despite starting with extremely simple ices dominated by N2, electron irradiation processing results in the production of refractory material with complex oxygen- and nitrogen-bearing organic molecules. These refractory materials were studied at room temperature using multiple analytical techniques including Fourier-transform infrared spectroscopy, X-ray absorption near-edge structure (XANES) spectroscopy, and gas chromatography coupled with mass spectrometry (GC-MS). Infrared spectra of the refractory material suggest the presence of alcohols, carboxylic acids, ketones, aldehydes, amines, and nitriles. XANES spectra of the material indicate the presence of carboxyl groups, amides, urea, and nitriles, and are thus consistent with the IR data. Atomic abundance ratios for the bulk composition of these residues from XANES analysis show that the organic residues are extremely N-rich, having ratios of N/C ~ 0.9 and O/C ~ 0.2. Finally, GC-MS data reveal that the residues contain urea as well as numerous carboxylic acids, some of which are of interest for prebiotic and biological chemistries.

Photosynthesis and photo-stability of nucleic acids in prebiotic extraterrestrial environments.

Laboratory experiments have shown that the UV photo-irradiation of low-temperature ices of astrophysical interest leads to the formation of organic molecules, including molecules important for biology such as amino acids, quinones, and amphiphiles. When pyrimidine is introduced into these ices, the products of irradiation include the nucleobases uracil, cytosine, and thymine, the informational sub-units of DNA and RNA, as well as some of their isomers. The formation of these compounds, which has been studied both experimentally and theoretically, requires a succession of additions of OH, NH2, and CH3groups to pyrimidine. Results show that H2O ice plays key roles in the formation of the nucleobases, as an oxidant, as a matrix in which reactions can take place, and as a catalyst that assists proton abstraction from intermediate compounds. As H2O is also the most abundant icy component in most cold astrophysical environments, it probably plays the same roles in space in the formation of biologically relevant compounds. Results also show that although the formation of uracil and cytosine from pyrimidine in ices is fairly straightforward, the formation of thymine is not. This is mostly due to the fact that methylation is a limiting step for its formation, particularly in H2O-rich ices, where methylation must compete with oxidation. The relative inefficiency of the abiotic formation of thymine to that of uracil and cytosine, together with the fact that thymine has not been detected in meteorites, are not inconsistent with the RNA world hypothesis. Indeed, a lack of abiotically produced thymine delivered to the early Earth may have forced the choice for an RNA world, in which only uracil and cytosine are needed, but not thymine.

Thymine and other prebiotic molecules produced from the ultraviolet photo-irradiation of pyrimidine in simple astrophysical ice analogs.

The informational subunits of RNA or DNA consist of substituted N-heterocyclic compounds that fall into two groups: those based on purine (C5H4N4) (adenine and guanine) and those based on pyrimidine (C4H4N2) (uracil, cytosine, and thymine). Although not yet detected in the interstellar medium, N-heterocycles, including the nucleobase uracil, have been reported in carbonaceous chondrites. Recent laboratory experiments and ab initio calculations have shown that the irradiation of pyrimidine in ices containing H2O, NH3, or both leads to the abiotic production of substituted pyrimidines, including the nucleobases uracil and cytosine. In this work, we studied the methylation and oxidation of pyrimidine in CH3OH:pyrimidine, H2O:CH3OH:pyrimidine, CH4:pyrimidine, and H2O:CH4:pyrimidine ices irradiated with UV photons under astrophysically relevant conditions. The nucleobase thymine was detected in the residues from some of the mixtures. Our results suggest that the abundance of abiotic thymine produced by ice photolysis and delivered to the early Earth may have been significantly lower than that of uracil. Insofar as the delivery of extraterrestrial molecules was important for early biological chemistry on early Earth, these results suggest that there was more uracil than thymine available for emergent life, a scenario consistent with the RNA world hypothesis.

The Infrared Spectra of Polycyclic Aromatic Hydrocarbons with Excess Peripheral H Atoms (Hn-PAHs) and their Relation to the 3.4 and 6.9 µm PAH Emission Features.

Polycyclic aromatic hydrocarbons (PAHs) are likely responsible for the family of infrared emission features seen in a wide variety of astrophysical environments. A potentially important subclass of these materials are PAHs whose edges contain excess H atoms (Hn-PAHs). This type of compound may be present in space, but it has been difficult to assess this possibility because of a lack of suitable laboratory spectra to assist with analysis of astronomical data. We present 4000-500 cm-1 (2.5-20 µm) infrared spectra of 23 Hn-PAHs and related molecules isolated in argon matrices under conditions suitable for interpretation of astronomical data. Spectra of molecules with mixed aromatic and aliphatic domains show characteristics that distinguish them from fully aromatic PAH equivalents. Two major changes occur as PAHs become more hydrogenated: (1) aromatic C-H stretching bands near 3.3 µm weaken and are replaced with stronger aliphatic bands near 3.4 µm, and (2) aromatic C-H out-of-plane bending mode bands in the 11-15 µm region shift and weaken concurrent with growth of a strong aliphatic -CH2-deformation mode near 6.9 µm. Implications for interpreting astronomical spectra are discussed with emphasis on the 3.4 and 6.9 µm features. Laboratory data is compared with emission spectra from IRAS 21282+5050, an object with normal PAH emission features, and IRAS 22272+5435 and IRAS 0496+3429, two protoplanetary nebulae with abnormally large 3.4 µm features. We show that 'normal' PAH emission objects contain relatively few Hn-PAHs in their emitter populations, but less evolved protoplanetary nebulae may contain significant abundances of these molecules.

Tunable energy transfer rates via control of primary, secondary, and tertiary structure of a coiled coil peptide scaffold.

Herein we report energy transfer studies in a series of Ru(II) and Os(II) linked coiled-coil peptides in which the supramolecular scaffold controls the functional properties of the assembly. A general and convergent method for the site-specific incorporation of bipyridyl Ru(II) and Os(II) complexes using solid-phase peptide synthesis and the copper-catalyzed azide-alkyne cycloaddition is reported. Supramolecular assembly positions the chromophores for energy transfer. Using time-resolved emission spectroscopy we measured position-dependent energy transfer that can be varied through changes in the sequence of the peptide scaffold. High level molecular dynamics simulations were used in conjunction with the spectroscopic techniques to gain molecular-level insight into the observed trends in energy transfer. The most efficient pair of Ru(II) and Os(II) linked peptides as predicted by molecular modeling also exhibited the fastest rate of energy transfer (with k(EnT) = 2.3 × 10(7) s(-1) (42 ns)). Additionally, the emission quenching for the Ru(II) and Os(II) peptides can be fit to binding models that agree with the dissociation constants determined for the peptides via chemical denaturation.

Is DNA's rigidity dominated by electrostatic or nonelectrostatic interactions?

Double-stranded DNA is among the stiffest biopolymers, whose bending propensity crucially influences many vital biological processes. It is not fully understood which among the two most likely forces, electrostatic self-repulsion or the compressive base pair stacking, plays a dominant role in determining the DNA's unique rigidity. Different theoretical and experimental studies led so far to contradictory results on this issue. In this Communication, we address this important question by means of Molecular Dynamics (MD) simulations using both atomistic and coarse-grained force fields. Using two independent sets of calculations, we found that electrostatic and nonelectrostatic effects play a comparable role in maintaining DNA's stiffness. Our findings substantially differ from predictions of existing theories for DNA rigidity and may indicate that a new conceptual understanding needs to be developed.

Counterion atmosphere and hydration patterns near a nucleosome core particle.

The chromatin folding problem is an exciting and rich field for modern research. On the most basic level, chromatin fiber consists of a collection of protein-nucleic acid complexes, known as nucleosomes, joined together by segments of linker DNA. Understanding how the cell successfully compacts meters of highly charged DNA into a micrometer size nucleus while still enabling rapid access to the genetic code for transcriptional processes is a challenging goal. In this work we shed light on the way mobile ions condense around the nucleosome core particle, as revealed by an extensive all-atom molecular dynamics simulation. On a hundred nanosecond time scale, the nucleosome exhibited only small conformational fluctuations. We found that nucleosomal DNA is better neutralized by the combination of histone charges and mobile ions compared with free DNA. We provide a detailed physical explanation of this effect using ideas from electrostatics in continuous media. We also discovered that sodium condensation around the histone core is dominated by an experimentally characterized acidic patch, which is thought to play a significant role in chromatin compaction by binding with basic histone tails. Finally, we found that the nucleosome is extensively permeated by over a thousand water molecules, which in turn allows mobile ions to penetrate deeply into the complex. Overall, our work sheds light on the way ionic and hydration interactions within a nucleosome may affect internucleosomal interactions in higher order chromatin fibers.

The neurotoxin 2'-NH2-MPTP degenerates serotonin axons and evokes increases in hippocampal BDNF.

1-Methyl-4-(2'-aminophenyl)-1,2,3,6-tetrahydropyridine (2'-NH2-MPTP) causes long-term depletions in cortical and hippocampal serotonin (5-HT) and norepinephrine (NE) that are accompanied by acute elevations in glial fibrillary acidic protein (GFAP) and argyrophilia. To further investigate the hypothesis that these changes are reflective of serotonergic and noradrenergic axonal degeneration, 2'-NH2-MPTP was administered to mice and innervation densities were determined immunocytochemically. Regional responses of the neurotrophin, brain-derived neurotrophic factor (BDNF), to putative damage were also assessed. Three days after 2'-NH2-MPTP, 5-HT axons exhibited a beaded, tortuous appearance indicative of ongoing degeneration. At 21 days, numbers of serotonin axons were significantly decreased, with the greatest axonal losses occurring in cortex and hippocampus. Serotonin axons in the amygdala were contrastingly spared long-term damage, as were 5-HT and NE cell bodies in the brain stem. BDNF protein levels were selectively increased in the hippocampus 3 days post-dose and returned to normal 21 days later. These results, in conjunction with previous findings, demonstrate that 2'-NH2-MPTP causes degeneration of serotonergic axons innervating the cortex and hippocampus on par with depletions in neurotransmitter levels. Moreover, damage to the hippocampus, a brain region important for learning and memory, and the modulation of anxiety and stress responsiveness, results in a transitory increase in BDNF.