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All sourcesNASA NTRSDOE OSTI
NASA NTRS1999

Molecules from Space and the Origin of Life

There is a growing concensus among space scientists that frozen molecules from space helped to make the Earth the pleasant place that it is today, and helped Life start on Earth, and perhaps elsewhere. The chain of logic that led scientists to posit a connection between extraterrestrial molecules and the origin of life is as follows. 1) The rapidity with which life arose demands that conditions on Earth were conducive to the formation of life very early on. 2) There is reason to believe that comets and meteorites fell oil the Earth from its inception. 3) We now know that comets and meteorites are replete with complex organic compounds, some of which resemble those in living systems. 4) Perhaps the input of molecules from comets and meteorites provided crucial constituents to the primordial soup and Jump started life on Earth. 5) These molecules formed out in deep space long before the Earth ever existed, by processes that we can reproduce in the laboratory. 6) The fact that organic molecules are seen by astronomers throughout our galaxy and in others makes it seem likely that they were (and are) available to help start life in other planetary systems.

Bernstein Max P.↗
NASA NTRS1997

Energetics of the lattice: packing elements in crystals of four-stranded intercalated cytosine-rich DNA molecules

Condensation of single molecules from solution into crystals represents a transition between distinct energetic states. In solution, the atomic interactions within the molecule dominate. In the crystalline state, however, a set of additional interactions are formed between molecules in close contact in the lattice--these are the packing interactions. The crystal structures of d(CCCT), d(TAACCC), d(CCCAAT), and d(AACCCC) have in common a four-stranded intercalated cytosine segment, built by stacked layers of cytosine.cytosine+ (C.C+) base pairs coming from two parallel duplexes that intercalate into each other with opposite polarity. The intercalated cytosine segments in these structures are similar in their geometry, even though the sequences crystallized in different space groups. In the crystals, adenine and thymine residues of the sequences are used to build the three-dimensional crystal lattice by elaborately interacting with symmetry-related molecules. The packing elements observed provide novel insight about the copious ways in which nucleic acid molecules can interact with each other--for example, when folded in more complicated higher order structures, such as mRNA and chromatin.

Non-NASA Center↗
NASA NTRS2004

Meteors do not break exogenous organic molecules into high yields of diatomics

Meteoroids that dominate the Earth's extraterrestrial mass influx (50-300 microm size range) may have contributed a unique blend of exogenous organic molecules at the time of the origin of life. Such meteoroids are so large that most of their mass is ablated in the Earth's atmosphere. In the process, organic molecules are decomposed and chemically altered to molecules differently from those delivered to the Earth's surface by smaller (<50 microm) micrometeorites and larger (>10 cm) meteorites. The question addressed here is whether the organic matter in these meteoroids is fully decomposed into atoms or diatomic compounds during ablation. If not, then the ablation products made available for prebiotic organic chemistry, and perhaps early biology, might have retained some memory of their astrophysical nature. To test this hypothesis we searched for CN emission in meteor spectra in an airborne experiment during the 2001 Leonid meteor storm. We found that the meteor's light-emitting air plasma, which included products of meteor ablation, contained less than 1 CN molecule for every 30 meteoric iron atoms. This contrasts sharply with the nitrogen/iron ratio of 1:1.2 in the solid matter of comet 1P/Halley. Unless the nitrogen content or the abundance of complex organic matter in the Leonid parent body, comet 55P/Tempel-Tuttle, differs from that in comet 1P/Halley, it appears that very little of that organic nitrogen decomposes into CN molecules during meteor ablation in the rarefied flow conditions that characterize the atmospheric entry of meteoroids approximately 50 microm-10 cm in size. We propose that the organics of such meteoroids survive instead as larger compounds.

Meteoroids↗
NASA NTRS2008

Making More-Complex Molecules Using Superthermal Atom/Molecule Collisions

A method of making more-complex molecules from simpler ones has emerged as a by-product of an experimental study in outer-space atom/surface collision physics. The subject of the study was the formation of CO2 molecules as a result of impingement of O atoms at controlled kinetic energies upon cold surfaces onto which CO molecules had been adsorbed. In this study, the O/CO system served as a laboratory model, not only for the formation of CO2 but also for the formation of other compounds through impingement of rapidly moving atoms upon molecules adsorbed on such cold interstellar surfaces as those of dust grains or comets. By contributing to the formation of increasingly complex molecules, including organic ones, this study and related other studies may eventually contribute to understanding of the origins of life.

Shortt, Brian↗
NASA NTRS2008

Molecules for Fluorescence Detection of Specific Chemicals

A family of fluorescent dye molecules has been developed for use in on-off fluorescence detection of specific chemicals. By themselves, these molecules do not fluoresce. However, when exposed to certain chemical analytes in liquid or vapor forms, they do fluoresce (see figure). These compounds are amenable to fixation on or in a variety of substrates for use in fluorescence-based detection devices: they can be chemically modified to anchor them to porous or non-porous solid supports or can be incorporated into polymer films. Potential applications for these compounds include detection of chemical warfare agents, sensing of acidity or alkalinity, and fluorescent tagging of proteins in pharmaceutical research and development. These molecules could also be exploited for use as two-photon materials for photodynamic therapy in the treatment of certain cancers and other diseases. A molecule in this family consists of a fluorescent core (such as an anthracene or pyrene) attached to two end groups that, when the dye is excited by absorption of light, transfer an electron to the core, thereby quenching the fluorescence. The end groups can be engineered so that they react chemically with certain analytes. Upon reaction, electrons on the end groups are no longer available for transfer to the core and, consequently, the fluorescence from the core is no longer quenched. The chemoselectivity of these molecules can be changed by changing the end groups. For example, aniline end groups afford a capability for sensing acids or acid halides (including those contained in chemical warfare agents). Pyridine or bipyridyl end groups would enable sensing of metal ions. Other chemicals that can be selectively detected through suitable choice of end groups include glucose and proteins. Moreover, the fluorescent cores can be changed to alter light-absorption and -emission characteristics: anthracene cores fluoresce at wavelengths around 500 nm, whereas perylene cores absorb and emit at wavelengths of about 600 nm.

Fedor, Steve↗
NASA NTRS2010

Synergism of Saturn, Enceladus and Titan and Formation of HCNO Exobiological Molecules

Saturn as a system has two very exotic moons Titan and Enceladus. Titan with energy input from Saturn's magnetosphere, solar UV irradiation, and cosmic rays can make HCN based molecules as discussed in earlier paper by [1]. Space radiation effects at both moons, and as coupled by the Saturn magnetosphere could cause an unexpected series of events leading to the evolution of biological models at Titan composed of HCNO with oxygen as the new ingredient. The "Old Faithful" model by [2] suggests that Enceladus, highly irradiated by Saturn magnetospheric electrons, has episodic ejections of water vapor driven by radiolytic oxidation gas products into Saturn's magnetosphere. At Titan Cassini discovered 1) that keV oxygen ions, evidently from Enceladus, are bombarding Titan's upper atmosphere [3] and 2) the discovery of heavy positive and negative ions within Titan's upper atmosphere [4]. Initial models of heavy ion formation in Titan's upper atmosphere invoked polymerization of aromatics such as Benzenes and their radicals to make PAHs [5], while a more recent model by [6] has raised the possibility of carbon chains forming from the polymerization of acetylene and its radicals to eventually make fullerenes. Laboratory measurements indicate that fullerenes, which are hollow carbon shells, can trap the keV oxygen and with the clustering of fullerenes and possible mixture with PAHs, some with nitrogen molecules, can make the larger aerosols with oxygen within them. Then with further ionizing irradiation from cosmic rays deep in the atmosphere "tholin" molecules are produced with all the molecular components present from which organic molecules can form. Among the molecular components are amino acids, the fundamental building blocks of life as we know it. This process maybe a common chemical pathway, both at the system level and at the molecular level, to form prebiotic and perhaps even biotic molecules. Such processes can be occurring throughout our universe, such as molecular clouds in the ISM.

Sittler, Edward C., Jr.↗
NASA NTRS2010

A Self-Perpetuating Catalyst for the Production of Complex Organic Molecules in Protostellar Nebulae

The formation of abundant carbonaceous material in meteorites is a long standing problem and an important factor in the debate on the potential for the origin of life in other stellar systems. Many mechanisms may contribute to the total organic content in protostellar nebulae, ranging from organics formed via ion-molecule and atom-molecule reactions in the cold dark clouds from which such nebulae collapse, to similar ion-molecule and atom-molecule reactions in the dark regions of the nebula far from the proto star, to gas phase reactions in sub-nebulae around growing giant planets and in the nebulae themselves. The Fischer-Tropsch-type (FTT) catalytic reduction of CO by hydrogen was once the preferred model for production of organic materials in the primitive solar nebula. The Haber-Bosch catalytic reduction of N2 by hydrogen was thought to produce the reduced nitrogen found in meteorites. However, the clean iron metal surfaces that catalyze these reactions are easily poisoned via reaction with any number of molecules, including the very same complex organics that they produce and both reactions work more efficiently in the hot regions of the nebula. We have demonstrated that many grain surfaces can catalyze both FTT and HB-type reactions, including amorphous iron and magnesium silicates, pure silica smokes as well as several minerals. Although none work as well as pure iron grains, and all produce a wide range of organic products rather than just pure methane, these materials are not truly catalysts.

Nuth, Joseph A.↗
NASA NTRS2011

Synergism of Saturn, Enceladus and Titan and Formation of HCNO Prebiotic Molecules

Saturn as a system has two very exotic moons Titan and Enceladus. Titan, taking in energy from Saturn's magnetosphere, solar UV irradiation, and cosmic rays, can make HCN based molecules as discussed in earlier paper by Raulin and Owen. Space radiation effects at both moons, and as coupled by the Saturn magnetosphere, could cause an unexpected series of events potentially leading to prebiotic chemical evolution at Titan with HCNO from magnetospheric oxygen as the new ingredient. The "Old Faithful" model suggests that Enceladus, highly irradiated by Saturn magnetospheric electrons and thus having a source of chemical energy from radiolytic gas production, has episodic ejections of water vapor, carbon dioxide, and various hydrocarbons into Saturn's magnetosphere. The hydrocarbons do not survive transport through the plasma environment, but oxygen ions from Enceladus water molecules become the dominant ion species in the outer magnetosphere. At Titan, Cassini discovered that 1) keV oxygen ions, evidently from Enceladus, are bombarding Titan's upper atmosphere and 2) heavy positive and negative ions exist in significant abundances within Titan's upper atmosphere. Initial models of heavy ion formation in Titan's upper atmosphere invoked polymerization of aromatics such as benzenes and their radicals to make polycyclic aromatic hydrocarbons (PAH) , while a more recent model by Sittler et al., has raised the possibility of carbon chains forming from the polymerization of acetylene and its radicals to make fullerenes. Laboratory measurements indicate that fullerenes, which are hollow carbon shells, can trap keV oxygen ions. Clustering of the fullerenes with aerosol mixtures from PAHs and the dominant nitrogen molecules could form larger aerosols enriched in trapped oxygen. Aerosol precipitation could then convey these chemically complex structures deeper into the atmosphere and to the moon surface. Ionizing solar UV, magnetospheric electron, and galactic cosmic ray irradiation would provide further energy for processing into more complex organic forms. Further ionizing irradiation from cosmic rays deep in the atmosphere "tho lin" molecules are produced with all the molecular components present from which prebiotic organic molecules can form. This synergy of Saturn system, exogenic irradiation, and molecular processes provides a potential pathway for accumulation of prebiotic chemistry on the surface of Titan. Since fullerenes are also thought to exist in interstellar space, similar processes may also occur there to seed molecular clouds with prebiotic chemical species. We will also discuss possible future laboratory experiments that could be done to investigate fullerene formation at Titan and the trapping of oxygen in fullerenes.

Sittler, Edward C.↗
NASA NTRS2017

Organic Molecules On the Surfaces of Iapetus and Phoebe

Absorption bands of both aliphatic and aromatic organic molecules are found in the reflectance spectra of Saturn satellites Iapetus, Phoebe, and Hyperion obtained with the Cassini Visible-Infrared Mapping Spectrometer (VIMS). The VIMS data do not fully resolve the individual bands of C-H functional groups specific to particular molecules, but instead show absorption envelopes representing blended clusters of the bands of aromatic (approximately 3.28 microns) and aliphatic (approximately 3.4 microns) hydrocarbons known in spectra of interstellar dust. In Cruikshank et al. (2014), we matched components of the unresolved hydrocarbon band envelopes with clusters of bands of a range of functional groups in specific types of organic compounds (e.g., normal and N-substituted polycyclic aromatic hydrocarbons, olefins, cycloalkanes, and molecules with lone-pair interactions of N and O with CH3+). In the work reported here, we revisit the spectra of Iapetus and Phoebe using VIMS data processed with improved radiometric and wavelength calibration (denoted RC19). The band envelopes of both aromatic and aliphatic hydrocarbons are now more clearly defined, corroborating the provisional assignment of specific classes of molecules in Cruikshank et al. 2014, but permitting a more reliable quantitative assessment of the relative contributions of those classes, and a revision to the earlier estimate of the ratio of the abundances of aromatic to aliphatic molecules.

Phoeb↗
NASA NTRS2020

Polycyclic Aromatic Hydrocarbons and Dust Particle Surface Interactions: Catalytic Hydrogenation of Polycyclic Aromatic Hydrocarbon Molecules under Vacuum Conditions

This work reports experiments on the catalytic interaction occurring between polycyclic aromatic hydrocarbon (PAH) molecules and TiO2 dust grain surfaces under vacuum conditions. The investigation sheds light on the potential catalytic pathways that TiO2 dust surfaces provide in the hydrogenation of PAH molecules and the chemistry that can be driven by PAH-dust interactions under vacuum conditions. Naphthalene, anthracene, and coronene were chosen as the PAH molecules, while titanium dioxide was selected as the dust analog. PAH samples and dust analog mixtures were studied under vacuum for 24 h while monitored via diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS). The acquired spectra show that PAH molecules are hydrogenated when in contact with TiO2 dust particles without the need for external energy or hydrogen sources. Our results suggest that linear PAHs undergo a similar hydrogenation process where the dominant species are fully hydrogenated PAHs. For larger condensed PAHs, the hydrogenation process yields partially hydrogenated molecules. Fully hydrogenated species can be identified by a band around 2960 per cm, while partially hydrogenated species produce a band around 2825 per cm. In the case of the production of hydrogenated species, our results suggest that the smaller the PAH, the faster the hydrogenation rate.

polycyclic aromatic hydrocarbons↗
NASA NTRS2021

Neutral–neutral synthesis of organic molecules in cometary comae

Remote and in situ observations of cometary gases have revealed the presence of a wealth of complex organic molecules, including carbon chains, alcohols, imines, and the amino acid glycine. Such chemical complexity in cometary material implies that impacts by comets could have supplied reagents for prebiotic chemistry to young planetary surfaces. However, the assumption that some of the molecules observed in cometary comae at millimetre wavelengths originate from ices stored inside the nucleus has not yet been proven. In fact, the comae of moderately-active comets reach sufficient densities within a few thousand kilometres of the nucleus for an active (solar radiation-driven) photochemistry to ensue. Here, we present results from our latest chemical-hydrodynamic models incorporating an updated reaction network, and show that the commonly-observed HC3N (cyanoacetylene) and NH2CHO (formamide) molecules can be efficiently produced in cometary comae as a result of two-body, neutral–neutral, gas-phase reactions involving well-known coma species. In the presence of a near-nucleus distributed source of CN (similar to that observed by the Rosetta spacecraft at comet 67P), we find that sufficient HC3N and NH2CHO can be synthesized to match the abundances of these molecules observed previously in Oort cloud comets. The precise coma origins of these (and other) complex organic molecules can be verified through radio interferometric mapping observations, for example using the Atacama Large Millimeter/submillimeter Array.

Comets↗
NASA NTRS2026

Diverse organic molecules on Mars revealed by the first SAM TMAH experiment

The search for organic matter on Mars has rapidly evolved in the past decade with simple aromatic, S-heterocycles, and aliphatic organic molecules detected in Gale crater. We report the in situ detection of >20 organic molecules from clay-bearing sandstones in the ~3.5-billion-year-old Knockfarrill Hill member of Glen Torridon, Gale crater, by the Sample Analysis at Mars instrument suite onboard the Curiosity rover. These molecules were liberated by the onboard tetramethylammonium hydroxide wet chemistry experiment. Diverse thermochemolysis products, including benzothiophene, methyl benzoate, and single and dicyclic aromatic molecules were released and detected by evolved gas analysis and gas chromatography-mass spectrometry. Results indicate the experiment successfully released molecules preserved in ancient macromolecular or free organic matter within Martian bedrock despite ~3.5 billion years of diagenesis and radiation exposure.

Amy J Williams↗
DOE OSTI2025

Single-Molecule Conductance through Hybrid Radially and Linearly π-Conjugated Macromolecules Reveals an Unusual Intramolecular π-Interaction

We describe the design, synthesis, and single-molecule junction conductance of π-electron molecules bearing both radial and linear π-conjugation pathways, whereby cycloparaphenylene (CPP) radial cores are π-extended linearly with aryl alkyne substituents as models for previously reported CPP-arylene ethynylene conjugated polymers. Although radially and linearly conjugated molecules have been studied previously in isolation as junction-bridging molecular electronic units, this is the first study to examine molecules where both topologies are operative. Our results reveal that the presence of radial CPP components within the junction-spanning pathway leads to a reduction in the conductance of the backbone compared to model linear phenyl substituents. Through tight-binding and DFT-based calculations, we attribute this conductance change to intramolecular van der Waals (vdW) interactions between the CPP ring and the junction-spanning arylene-ethynylene molecular backbone. These interactions induce changes in the dihedral angles of the backbone, leading to a reduced overlap of π orbitals within the molecular junction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Photoluminescence Switching in Quantum Dots Connected with Carboxylic Acid and Thiocarboxylic Acid End-Group Diarylethene Molecules

We contrast the switching of photoluminescence (PL) of PbS quantum dots (QDs) cross-linked with photochromic diarylethene molecules with different end groups, 4,4′-(1-cyclopentene-1,2-diyl)bis[5-methyl-2-thiophenecarboxylic acid] ( 1C ) and 4,4′-(1-cyclopentene-1,2-diyl)bis[5-methyl-2-thiophenethiocarboxylic acid] ( 2T ). Our results show that the QDs cross-linked with the carboxylic acid end group molecules ( 1C ) exhibit a greater amount of switching in photoluminescence intensity compared to QDs cross-linked with the thiocarboxylic acid end group ( 2T ). We also demonstrate that regardless of the molecule used, greater switching amounts are observed for smaller quantum dots. Varying these parameters allows for the fabrication of photoswitches with tunable PL change. We relate these observations to the differences in the HOMO energy levels between the QDs and the photochromic molecules. Our findings demonstrate how the size of the QDs and the energy levels of the linker ligands influences the charge tunneling rate and thus the PL switching performance in tunneling-based photoswitches.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Recent Advances in Probing Electron Delocalization in Conjugated Molecules by Attached Infrared Reporter Groups for Energy Conversion and Storage

This review article reports an overview of the recent developments in the field of electron delocalization study in organic conjugated molecules by utilizing the vibration frequencies exhibited by the attached functional groups such as nitrile (–C≡N), alkyne (–C≡C–), or carbonyl (–C=O). A brief introduction to electron delocalization, methods for study, and their importance is given first, followed by the application of infrared spectroscopy in organic molecules. Details of molecules with various infrared reporter groups have been explained in respective subsections based on the functional groups. All the reported organic molecules have been structured and presented with the electron delocalization properties studied using an infrared reporter group. Finally, an outlook on this recently promising, exciting, and interesting field of probing electron delocalization using infrared reporter groups is provided.

25 ENERGY STORAGE↗
DOE OSTI2025

Single-Molecule Fluorescence Microscopy Reveals Energy Transfer Active versus Inactive Nanocrystal/Dye Conjugate Pairs

Defect-mediated energy transfer (EnT) is a radiative process that occurs between donor defect states in the forbidden bandgap of semiconductor nanocrystals (NCs) and dye molecules bound to their surfaces. The EnT efficiency depends on the number of dye molecules attached to each NC, the donor–acceptor distance, and the dipole orientation factor between the donor and acceptor, all of which vary across all individual NCs in a sample. While ensemble-level fluorescence spectroscopy measurements have provided average values for donor–acceptor distances, dye-to-NC ratios, and EnT rate constants, questions remain about the impact of donor/acceptor heterogeneity on observed EnT efficiencies. Notably, ensemble-level measurements cannot distinguish between bare NCs and EnT-active versus inactive NC/dye pairs in the same sample batch, limiting the ability to design systems with 100% EnT efficiency. To address this, we studied defect-mediated EnT between AlexaFluor 555 dye acceptors chemically bound to ZnO NC donors at the level of single molecules and single NCs. Interestingly, 20% of bound NC/dye pairs are EnT-inactive, likely contributing to residual defect photoluminescence (PL) observed in ensemble-level measurements and reducing overall EnT efficiency. Single particle-level ZnO defect PL and acceptor fluorescence trajectories exhibited distinct microfluctuations, which are absent in bare ZnO NCs. We hypothesized that our observations can be explained with a competitive dye fluorescence quenching pathway, possibly due to charge transfer between the excited state dye and the ZnO NC. Numerical simulations of single-molecule PL traces for this scenario produced microfluctuations consistent with the experimental results. These findings highlight the impact of sample heterogeneity on EnT processes and provide insights for designing light-harvesting systems with optimized EnT efficiency.

25 ENERGY STORAGE↗
DOE OSTI2025

Visualizing the Three-Dimensional Arrangement of Hydrogen Atoms in Organic Molecules by Coulomb Explosion Imaging

Structure-sensitive methods based on femtosecond light or electron pulses are now making it possible to measure how molecular structures change during light-induced processes. Despite significant progress, high-fidelity imaging of nuclear positions remains a challenge even for relatively small molecular systems and, notably, regarding the positions of hydrogen atoms. As demonstrated in recent work, X-ray-induced Coulomb explosion imaging (CEI) may overcome this obstacle, as its sensitivity does not depend on the mass of the imaged atoms. The photoinduced ring opening of the heterocyclic molecule 2(5 H )-thiophenone has attracted recent interest. Here, in this work, we show that CEI offers a powerful route to imaging the peripheral H atoms in this molecule and thus, more generally, to tracking detailed nuclear motions (e.g., isomerizations) in organic molecules on ultrafast time scales. Specifically, we record momentum-space Coulomb explosion images that report on the three-dimensional positioning of all nuclei within the molecule, for instance, distinguishing H atoms in C–H bonds that lie within or are directed out of the plane defined by the heavy atoms. The prospect of imaging peripheral H atoms to probe photochemical dynamics is explored by coupling ab initio molecular dynamics with classical Coulomb explosion simulations, thereby differentiating potential photoproduct isomers, including those whose structures primarily differ in the position of the hydrogens.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Ab Initio Polariton Spectra of ZnTPP Molecules Collectively Coupled Inside an Optical Cavity

Exciton-polaritons are quasi-particles formed by the quantum mechanical hybridization of electronic and photonic excitations. Despite extensive investigations, a fundamental understanding of molecular polariton spectra and the polariton delocalization from an ab initio theoretical perspective remains elusive. We simulate experimentally measured linear transmission spectroscopy of many Zinc(II) tetraphenylporphyrin (ZnTPP) molecules collectively coupled to a cavity from first principles. Our theoretical approach incorporates many low-lying electronic excitations in ZnTPP molecules, as well as collective light-matter couplings between ZnTPP and the quantized radiation modes, both of which are shown to be the key to accurately recovering the experimental spectra. We further analyzed to what extent the polariton and dark states are delocalized over many molecules, for the first time, using fully ab initio descriptions of the molecules. We finally investigate the line width as a function of detuning, providing new theoretical insights into the experimentally observed motional narrowing behavior. Our work presents first-ofits- kind theoretical studies on molecular polariton spectra, offering a new perspective on molecular polariton formation in realistic ab initio molecular systems whose rich, many-state nature provides spectral features enabled by the high density of electronic states beyond simple quantum optics models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗