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2006 Annual Science Report

University of Arizona Reporting  |  JUL 2005 – JUN 2006

Module 1: The Building Blocks of Life

Project Summary

This module is concerned with examining the contribution of interstellar chemistry to the biochemistry that led to living systems on Earth. One focus of this investigation is the simple sugar ribose and its precursors, starting with formaldehyde, but other possible pre-biotic species are being investigated as well

4 Institutions
3 Teams
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Field Sites

Project Progress

This module is concerned with examining the contribution of interstellar chemistry to the biochemistry that led to living systems on Earth. One focus of this investigation is the simple sugar ribose and its precursors, starting with formaldehyde, but other possible pre-biotic species are being investigated as well. This module is attempting to accurately establish the presence of simple sugars, their precursors, and other pre-biotic species in interstellar gas, investigate their possible connection to evolved stars, planetary nebulae, and diffuse gas, examine possible gas-phase mechanisms leading to such molecules, and study how such biotic precursors might have found their way to a planet surface. This module combines high resolution laboratory spectroscopy, radio astronomy of interstellar and circumstellar molecules, synthetic organic chemistry in the gas-phase, theoretical calculations of reaction pathways, comet studies, and investigations of carbon isotope ratios. In addition this year we have added members studying Earth and meteorite organic chemistry and biochemistry in order to have a more rounded program.

This module addresses

  • Goal 3 of the Astrobiology Roadmap, Understand how life originates from cosmic and planetary precursors, Objectives 3.1 (sources of prebiotic materials) and 3.2 (origins and evolution of functional biomolecules), and
  • Goal 4 of the Astrobiology Roadmap, Understand how past life on Earth interacted with its changing planetary and Solar System environment, Objective 4.3 (effects of extraterrestrial events upon the Biosphere).

Highlighted Accomplishments

  • Pulsed molecular-beam Fourier transform microwave spectrometer now fully operational, with upgraded electronics from 3.5 — 40 GHz.
  • Completed analysis of both A and E conformers of acetol.
  • Completed measurements of two lowest energy conformers of lactonitrile, with associated high-level ab initio calculations.
  • Continued confusion-limited 2 and 3 mm (70 — 170 GHz) spectral-line survey of the molecular cloud Sgr B2(N), which is about 60% completed. Survey had shown that dihydroxyacetone (DHA), hydroxyacetone, lactonitrile, lactic acid, formyl cyanide, and methylene cyclopropene are not present in this cloud down to the confusion limit. In contrast, glycolaldehyde and acetamide are present. Several other species are still under investigation.
  • Extensive survey of formamide (NH2CHO), a possible pre-biotic solvent, completed in molecular clouds.
  • Study of H2CO in Comets Hale-Bopp, T7/Linear, and Q4/Neat completed; analysis indicates that H2CO does not come from POMS (polyoxymethylene), but from CHON particles.
  • Detected the CCH radical for the first time in old, evolved planetary nebulae, which suggests that carbon-carbon bonds survive at least until the very end of stellar evolution.
  • Continued radio astronomical studies of carbon-rich and oxygen-rich circumstellar envelopes, with detections of C3O in the C-rich shell of IRC+10216, and HCO+, NaCl, and PN in VY CMa, an oxygen-rich supergiant.
  • Expanded collaborations within the University of Arizona between the astronomy and chemistry departments.
  • Performed over 1000 hours of observations using the Arizona Radio Observatory’s 12-meter telescope at Kitt Peak, Arizona and Sub-millimeter Telescope on Mt. Graham.

Laboratory Spectroscopic Studies of Gas-phase organic precursors of relevant pre-biotic molecules

The success in finding new molecules in space relies on precise laboratory measurements. Gas-phase spectra of even small asymmetric organic molecules become very complicated because they have three unique axis of rotation with usually large dipole moments along those axis, resulting in intense spectra, soft internal motions and vibrations-all of which act to increase the number of lines present in room temperature experiments. For this reason, we built a Fourier transform microwave (FTMW) spectrometer particularly well suited for recording spectra of organic molecules. This machine measures rotationally cooled spectra of molecules in a molecular beam, which cools to about 3 K. The cold gas ensures that we are recording the lowest energy states of the molecules, which will be most relevant to interstellar searches. The low frequency work is then extended up to as high as 800 GHz using one of our millimeter wave spectrometers. This low to high approach suppresses confusion, which leads to an accurate assignment. So far we have measured the spectra of two molecules, hydroxyacetone and lactonitrile. It is noteworthy that the spectra of these molecules consist of thousands of transitions of which as many as possible need to be accounted for before an accurate and unambiguous assignment can be made in the laboratory owing to high line densities. The Hamiltonians used to fit these spectra are soft enough to be able conform to several incorrectly assigned lines. Even one misplaced line could poison an analysis to the point where it has no predictable power even though at face value seems adequate. The clear danger is an astronomer armed with tabulated frequencies of incorrect laboratory determinations who will never be able to assign the space spectrum accurately. It is of utmost importance that the laboratory determinations be made thoroughly and completely-this unfortunately takes time and effort.

The room temperature rotational spectrum of hydroxyacetone is complicated because of its near prolate asymmetric structure, a low-barrier internal methyl rotor, and nearly-equal dipole moments along the a- and b-axes (μa = 2.22 D and μb = 2.17 D; Kattija-Ari & Harmony 1980; see Figure 1). These characteristics generate a confused spectrum consisting of many highly mixed, low-lying torsional states in two symmetry species (distinct A and E species), which are difficult to analyze owing to significant mixing of the internal methyl rotation to the end-over-end rotation of the molecule. Perturbations caused by this mixing are largest at low-frequencies;
hence, the microwave data (4 to 20 GHz) were essential in fitting rotational constants that accurately reproduced the rotational data through 2 mm wavelengths (175 GHz). A special Hamiltonian incorporating internal motions known as the rho-axis method was used to analyze our measurements.

Another laboratory project that we recently completed was the combined microwave and millimeter wave study of the rotational spectrum of lactonitrile. The spectrum was recorded from 4 to 18.5 GHz using the FTMW spectrometer, as well as from 100 to 120 GHz using one of the Ziurys’ group direct absorption millimeter wave spectrometers. Lactonitrile has the molecular formula of CH3CHOHCN, which is the cyanohydrin of the acetaldehyde—an abundant interstellar molecule. This molecule has a well resolved quadrupole hyperfine structure owing to the nitrogen nucleus. Figure 1.1 shows this structure in the 21,2 — 11,1 transition in its lowest energy conformation, which could be used to identify this species in cold interstellar material.

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In addition, we are nearly complete with our two scheduled upgrades of the FTMW spectrometer. First, a dual purpose shield was installed into the vacuum chamber. This shield is constructed out of a mu-metal, which shields the interaction region of the cavity from the effects of the Earth’s magnetic field. The reduction of the magnetic field allows for the measurement of radicals (i.e. molecules with unpaired electrons). Also, the shield is thermally isolated from the chamber walls, which allows for the cryopump to cool more efficiently. This extra cooling has already shown some promise as our pumping speed has already improved by about 50 to 75% after implementation. As expected, the shield is not 100% effective in reducing the magnetic field owing to the large opening leading towards the pump. We are in the process of building a magnetic shim to reduce the field further to just a few milligauss at the center of the cavity using an electromagnetic coil stet.

Second, the electronics for a frequency upgrade have recently been acquired and will be integrated into the system in August 2006. This upgrade was originally planned for this spring, but we postponed it to finish the lactonitrile experiment using the original 18 GHz band. The design incorporates two frequency bands, 3.5 to 18.5 GHz and 17.5 to 40 GHz. The bands are easily switched using computer logic and mechanical broadband microwave switches.

Radioastronomy Searches for Prebiotic Molecules

A true understanding of the chemical processes of the interstellar medium requires a complete and accurate molecular inventory. Many of the recent claims of gas phase interstellar molecules have been clouded with controversy, specifically glycine, dihydroxyacetone, ethylmethylether and glycolaldehyde, to mention a few. The controversy in these detections is owing to the large number of spectral features arising from primarily asymmetric organic molecules. The line density is so high in some star formation cores that astronomers are no longer system noise limited, but instead limited by signal confusion. In other words, there are more lines present than can comfortably fit in the spectral region. In this confusion limit, the chances for false identifications become high. One remedy to this confusion is extremely broadband spectral coverage, which effectively covers the entire spectrum of a particular molecule. Because physics requires that the spectrum of gas phase molecules be self consistent and exhibit a sensible temperature and abundance, this broadband approach allows us to assign the spectral features as a collection of molecules instead of molecules individually.

During the first 2 ½ years of the grant period, we have used this approach to study important, as well as practical, biologically relevant precursors that can be formed from the abundant interstellar molecules formaldehyde, hydrogen cyanide and water. These simple compounds will react to form a myriad of complex organic molecules from simple sugars to hydroxy acids to amino acids and potentially even nucleobases.

The richest known molecular source is near the galactic center in a region known as SgrB2(N). Past studies of this object have lacked the necessary sensitivity to identify the most recently detected molecule and the coverage has been sparse. We have started a major observing effort to cover from 70 to 170 GHz and 210 to 270 GHz using the Arizona Radio Observatory’s telescopes. Thus far, we have covered about 70% of these regions at or near the confusion limit and have recorded thousands of spectral features of which about half are unidentifiable. In these data we have confirmed the identifications of glycolaldehyde, ethylene glycol and tentatively cyclopropenone, but also disproved the detections of dihydroxyacetone and glycine (see Figure 1.2). We have also put forth tremendous effort to find new molecules in our survey data, but have only a couple of tentative detections so far, hydroxyacetonitrile and aminoacetonitrile. The
survey also shows that methylenecyclopropene, hydroxyacetone and lactic acid are not abundant interstellar molecules.

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We will continue and expand these efforts to new interstellar sources including W51M, Orion-KL and G34.3. All of these source posses complex spectra, but tend to have a lower confusion limit than SgrB2(N) owing to narrower spectral lines. We expect that deep confusion limited spectra of these source will reveal a yet unrealized chemical complexity equal to or surpassing that of SgrB2(N).

Additionally, we have successfully conducted and extensive survey of the molecule formamide towards a number of interstellar sources. In this survey, we found that formamide is a common constituent in warm molecular gas, presumably associated with star formation regions. So far it has been detected in Sgr B2, Orion-KL, G34.3, W51M, and W51e1e2. A large abundance of formamide could be important in life processes on planets at early times because of its polar aprotic solvent properties.

Chemical Studies of Late-type Carbon and Oxygen-rich Stellar Envelopes

Mass loss from stars usually occurs in the later stages of stellar evolution, particularly on the red giant and asymptotic giant branch stages. The material lost from these stars creates a circumstellar shell, which in certain cases have been found to exhibit complex gas-phase chemistry. The degree of chemical richness in the shell appears to depend on the elemental carbon to oxygen ratio, which is established by nucleosynthesis and the degree of convective mixing in a given star. Observations have suggested that carbon-rich circumstellar shells (C > O) exhibit a richer molecular content that their oxygen-rich analogs. In order to test this theory, we have conducted a very sensitive spectral-line molecular survey of the O-rich shell of the red supergiant VY Canis Majoris (VY CMa). VY CMa is one of the most luminous objects in the sky in the infrared, with a large and sporadic mass loss rate. These observations have resulted in the identification of several unusual chemical compounds in the envelope of VY CMa, including NaCl, PN, and HCO+, as well as more common molecules such as CS and SiS (see Figure 1.3). The line profiles exhibited by the molecules vary dramatically among the detected species, indicating that there are many distinct, layered chemical regions around the star, controlled in part by dust formation. These results suggest that oxygen-rich circumstellar shells are more complex chemical environments that previously thought. Further studies of O-rich shells, particularly of red supergiant stars such as VYCMa, may prove that this chemical richness is a more general phenomenon.

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The oxygen—bearing species C3O has been identified in the circumstellar envelope of the carbon-star IRC+10216 as well. The J=8 — 7, 9 — 8, 10 — 9, 14 — 13, and 15 — 14 transitions were detected at 2 and 3 mm using the Arizona Radio Observatory’s 12m telescope. Measurements of the J=9 — 8, 10 — 9, and 12 — 11 lines were simultaneously conducted at the IRAM 30m telescope. The line profiles of C3O are roughly U-shaped, indicating an extended shell distribution for this molecule in IRC+10216. The total column density derived for C3O is 1.2 × 1012 cm-2, at least an order of magnitude higher than predicted by current chemical models. However, a revised model that includes reactions of atomic oxygen with carbon-chain radicals, such as l-C3H and C4, can reproduce the observed abundance. This model also predicts that C3O arises from a shell source with an outer radius near r ~ 30”, consistent with the observations. These results suggest that gas phase neutral-neutral chemistry may be producing the oxygen-bearing molecules present in the outer envelope of IRC+10216. They also show that CO is not controlling the chemistry in C-rich envelopes.

Chemical Studies in Planetary Nebulae

Molecules are commonly found in circumstellar envelopes of evolved stars, but what becomes of them as the objects mature into planetary nebulae? What becomes of the molecules thereafter? Of particular interest are species with carbon-carbon bonds, which are quite abundant in C-rich circumstellar shells. In order to address these questions, a survey of the ethynyl radical, CCH, has been conducted towards evolved planetary nebulae (PNe) using the Arizona Radio Observatory’s 12m antenna and the Submillimeter Telescope (SMT). This species has been detected in NGC 6720 (Ring Nebula), NGC 6781, and NGC 7293 (Helix Nebula) via the two hyperfine components of the N = 1 → 0, J = 3/2 → 1/2 transition near 87.3 GHz (see Figure 3), as well as in M4-9 from the observations of two spin-rotation components of the N = 3 → 2 transition at 262.0 GHz. The LSR velocities and linewidths of CCH in the PNe are consistent with other molecules observed in these objects. The column densities obtained for CCH in the evolved planetary nebulae are in the range of 0.3-1.4 × 1013 cm-2, corresponding to fractional abundances of f(CCH/H2) ~ 10-7 – in reasonable agreement with certain chemical models. These abundances are roughly comparable to those found in the protoplanetary nebula CRL 2688 and CRL 618, but are less than those obtained for CCH in diffuse clouds. Other species found in evolved PNe such as HCN, CN, and HCO+ are also present in diffuse gas at decreased concentrations, suggesting that there may be a connection between the molecular content of these objects. C-rich circumstellar shells may be providing the carbon-carbon backbones that lead to the organic chemistry of dense clouds via planetary nebulae. The dispersion of these nebulae may be a major source of molecular enrichment to the ISM.

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Theoretical Calculations

Work conducted by L. Adamowicz, A. Jalbout, and students has centered on the study of structures and stabilities of some biologically-relevant species, in particular acetol and lactonitrile. This group has done ab initio calculations for these species, which has established the lower energy conformers. Their study has aided spectroscopic investigations in the laboratory. The group has started investigation of the mechanism of glycolaldehyde formation by performing calculations on the Nazarov-type reaction concerning addition of two aldehydes mediated by a hydronium cation. This is a possible reaction contributing to the process of the gas-phase formation of simple sugars.

Cometary Studies

Comets are considered to be composed of pristine interstellar material from the molecular cloud from which our solar system was originally formed. As a comet orbits the solar system, it becomes significantly close to the sun’s radiation at which point it begins to sublimate, ejecting ancient material into the solar system in the form of small particles and gases. These vaporizing gases trace the conditions of the molecular cloud from which our sun was formed 4.6 Gyr ago. Radioastronomy provides a mechanism by which cometary gases can be analyzed.

Observations of H2CO have been conducted towards comets C/1995 O1 (Hale-Bopp), C/2001 Q4 (NEAT), and C/2002 T7 (LINEAR) using the Arizona Radio Observatory (ARO) 12m telescope at 1.2 and 2 mm. Aperature synthesis and maps of H2CO at λ=3 mm have also been made using the Berkeley-Illinois-Maryland-Association (BIMA) interferometer towards Hale-Bopp. These data indicate that the production rate of ~ 3 × 1028 s-1 for H2CO at 1 AU, using a simple Monte Carlo model, with a nuclear origin for the molecule. However, the distribution of H2CO in Hale-Bopp, in comparison with CO maps, indicates an extended source with small-scale structure, oriented towards the comet dust tail. This result suggests a source of H2CO other than the comet nucleus, probably grains composed of a mixture of silicates and organic material (CHON particles). The production rate assuming an extended grain source for H2CO grains increases to Q ~ 3 × 1029 s-1, more in line with the production rate derived from direct measurements of formaldehyde in former Halley flyby missions. The spectra of H2CO measured towards Comet C/2002 T7 (LINEAR) shows a second velocity component, most likely arising from comet fragmentation. Such fragmentation may release grains, or CHON particles, which in turn release molecular material as they are heated by the solar radiation field.

Deep Impact Observations

July 4, 2005 allowed both amateur and professional astronomers the opportunity of a lifetime — the inside of a comet would be revealed after a collision with a ~800 lb copper impactor. The event was organized by NASA and came to be known as “Deep Impact”. At an impressive speed of 23,000 mph, comet 9P/Tempel 1 hit the 1-m wide impactor releasing pristine solar system gas and dust into space. Observations at telescopes all over the world were conducted to learn more about the preserved material from the formation of the planets. The Arizona Radio Observatory’s 12m telescope (Kitt Peak, AZ) and Submillimeter telescope (Mt. Graham, AZ) took part in the ground-based team with M. Womack, L. Ziurys, and S. Milam conducting observations for ~ 2 weeks. A comparison was made before the event and after the event in the molecular content of the comet coma. Due to the large distance with little activity, pre-impact detections were marginal and included CS and HCN. Post-impact detections were limited due to the source setting shortly thereafter and include a marginal HCN and possibly CH3OH. Later reports suggested a dust region was hit releasing little gas. Deep Impact press coverage:

Minnesota, M. Womack:

SCSU Prof., Students Train Eyes On NASA Mission — July 16, 2005

(Minnesota Colleges Press Club — — June 23

Arizona, S. Milam:

Fox 11-TV News, Tucson, Arizona

Channel 4 Eyewitness News (KVOA) TV, Tucson, Arizona
KPHO-TV — Phoenix, Arizona
KPNX-TV 12 — Phoenix, Arizona
KOLD-TV News 13 TV – Tucson, Arizona

Earth Chemistry and Biochemistry

Dr. Dante Lauretta of LPL has joined the group, so that we can link meteorite studies and Earth biochemistry issues to the chemistry of space. In addition we have just added Dr. Matt Pasek as Bessey Postdoctoral Fellow studying the acquisition of phosphorus by pre-biotic organic molecules.

Public Outreach:

Lucy Ziurys was a guest on the SETI Institute Weekly Radio Science Program in May 2006. She was interviewed on the topic of comets and their possible connection to the origin of life. This program, entitled Are We Alone?, is broadcast to the general public on Discovery Channel Radio. Dr. Ziurys explained in simple terms the composition of comets, where they originate in the Solar System, and how they might bring organic compounds from interstellar space. Other participants included Kathy Sawyer, author of “The Rock from Mars,” Joel Achenbach, a writer for the Washington Post, and Peter Jenniskens, PI of the SETI Institute.


ARO: Arizona Radio Observatory, Tucson, Arizona
BILMA: Berkeley-Illinois-Maryland-Associations
DHA: Dihydroxyacetone
FTMW: Fourier Transform Microwave Spectrometer
IRAM: Instituto de Radio Astronomía Milimétrica, Granda, Spain
ISM: InterStellar Medium%0
LAPLACE: Life And Planets Astrobiology Center, Tucson, Arizona
NASA: National Aeronautics and Space Administration
PI: Principal Investigator
SMT: Submillimeter Telescope, Mt. Graham, Arizona
SETI: Search for Extra Terrestrial Intelligence
VY CMa: VY Canis Majoris