Cleaves, H. James
- Cleaves, H. James
- Associate Professor
Main Publication List and Awards
Peer-Reviewed Journal Articles
45. Scharf, C., Virgo, N., Cleaves, H.J., II, Aono, M., Aubert-Kato, N., Aydinoglu, A., Barahona, A., Barge, L.M., Benner, S.A., Biehl, M., Brasser, R., Butch, C.J., Chandru, K., Cronin, L., Danielache, S., Fischer, J., Hernlund, J., Hut, P., Ikegami, T., Kimura, J., Kobayashi, K., Mariscal, C., McGlynn, S., Menard, B., Packard, N., Pascal, R., Pereto, J., Rajamani, S., Sinapayen, L., Smith, E., Switzer, C., Takai, K., Tian, F., Ueno, Y., Voytek, M., Witkowski, O., and Yabuta, H. (2015) A strategy for origins of life research. Astrobiology 15, doi:10.1089/ast.2015.1113
44. Jun Wang, Peter V. Bonnesen, E. Rangel, E. Vallejo, Ariadna Sanchez-Castillo, H. James Cleaves, Arthur P. Baddorf, Bobby G. Sumpter, Minghu Pan, Petro Maksymovych & Miguel Fuentes-Cabrera (2015) Supramolecular polymerization of a prebiotic nucleoside provides insights into the creation of sequence-controlled polymers. Scientific Reports 5:18891 | DOI: 10.1038/srep18891
43. Cleaves, HJ, Neish, C, Callahan, M & Dworkin, JP Amino Acid Production from Titan Tholins and Its Comparison with Miller Urey Type Reaction Products. (In Preparation)
42. Meringer, M, Cleaves, HJ, Freeland, SJ (Accepted) Beyond Terrestrial Biology: Charting the Chemical Universe of α-Amino Acid Structures. Journal of Chemical Information and Modeling.
41. Cleaves, HJ (2013) Prebiotic Chemistry: Geochemical Context and Reaction Screening. Life 3: 331-345.
40. Parker, ET, Cleaves, HJ, Burton, AS, Glavin, DP, Dworkin, JP, Zhou, M, Bada, JL & Fernández, FM (Accepted) Recreating the Miller-Urey Experiment. Journal of Visualized Experiments.
39. Bennett, RV, Cleaves, HJ, Davis, JM, Orlando, TO, Fernández, FM (2013) Desorption Electrospray Ionization Imaging Mass Spectrometry as a tool for investigating prebiotic model reactions on mineral surfaces. Anal. Chem. 85:1276-9.
38. Cleaves, HJ, (2012) Prebiotic chemistry: What we know, what we don’t. Evolution: Education and Outreach. 5: 342-360.
37. Cleaves, HJ, Michalkova Scott, A, Hill, FC, Leszczynski, J, Sahai, N, Hazen, R (2012). Mineral-organic interfacial processes: Potential roles in the origins of life. Chem. Soc. Rev. 41: 5502-5525.
36. Parker, ET, Cleaves, HJ, Callahan, MP, Dworkin, JP, Glavin, DP, Lazcano, A & Bada, JL (2011). Enhanced synthesis of alkyl amino acids in Miller’s 1958 H2S experiment. Origins of Life and Evol. Biospheres. 41: 569-574.
35. Callahan, MP, Smith, KE, Cleaves, HJ, Ruzicka, J, Stern, JC, Glavin, DP, House, CH & Dworkin, JP (2011). Carbonaceous meteorites contain a wide range of extraterrestrial nucleobases. Proc. Nat. Acad. Sci. USA 108: 13995-13998.
34. Parker, ET, Cleaves, HJ, Dworkin, JP, Glavin, DP, Callahan, MP, Aubrey, AD, & Bada, JL (2011). Primordial synthesis of amines and amino acids in a 1958 Miller H2S-rich spark discharge experiment: Implications for organic synthesis in carbonaceous chondrites. Proc. Nat. Acad. Sci. USA 108: 5526-5531.
33. Cleaves, HJ, Jonsson, CM, Jonsson, CL, Sverjensky, DA & Hazen, RM (2011). Interactions of single-stranded DNA with mineral surfaces. Chemosphere 83:1560-1567.
32. Parker, ET, Cleaves, HJ, Dworkin, JP, Callahan, MP, Bada, JL and Lazano, A (2010). Prebiotic synthesis of methionine and other sulfur-bearing organic compounds from primitive atmospheres: a contemporary reassessment. Origins of Life Evol. Biosphere 41:201-12.
31. Marshall-Bowman, K, Sverjensky, DA, Hazen, RM & Cleaves, HJ (2010). Mineral catalysis of peptide bond cleavage. Geochim. Cosmochim. Acta 74:5852-5861.
30. Jonsson, CM, Jonsson, CL, Estrada, C, Sverjensky, DA, Cleaves, HJ & Hazen, RM (2010). Adsorption of L-aspartate to rutile (α-TiO2): experimental and theoretical surface complexation studies. Geochim. Cosmochim. Acta 74: 2356-2367.
29. Cleaves, HJ, Jonsson, CM, Jonsson, CL, Sverjensky, DA & Hazen, RM (2010). Interactions of nucleic acid components with rutile surfaces. Astrobiol. 10:311-323.
28. Cleaves, HJ (2010). The origins of the coded amino acids. J. Theor. Biol. 263:490-498.
27. Cleaves, HJ (2010). The prebiotic synthesis of RNA and pre-RNA. Origins of Life Evol. Biosphere 40:433.
26. Cleaves, HJ (2010). Hierarchical definitions in the origin of life. Origins of Life Evol. Biosphere 40:489.
25. Aubrey, AD, Cleaves, HJ & Bada, JL (2009). Organic synthesis in submarine hydrothermal vent systems I: amino acids. Origins of Life Evol. Biosphere 39:91-108.
24. Cleaves, HJ, Aubrey, AD & Bada, JL (2009). Organic synthesis in submarine hydrothermal vent systems II: peptides. Origins of Life Evol. Biosphere 9:109-26.
23. Jonsson, CM, Jonsson, CL, Sverjensky, DA, Cleaves, HJ & Hazen, RM (2009). Attachment of L-Glutamate to rutile (α-TiO2): A potentiometric, adsorption, and surface complexation study. Langmuir 25:12127-12135.
22. Cleaves, HJ, Chalmers, JH, Lazcano, A, Miller, SL & Bada, JL (2008). Prebiotic organic synthesis in neutral planetary atmospheres. Origins of Life Evol. Biosphere 38:105-15.
21. Cleaves, HJ (2008). The Precambrian geochemistry of formaldehyde. Precamb. Res. 164:111-118.
20. Sverjensky, DA, Jonsson, CM, Jonsson, CL, Cleaves, HJ & Hazen, RM (2008). Glutamate surface speciation on amorphous titanium dioxide and hydrous ferric oxide. Environ. Sci. Technol. 42: 6034–6039.
19. Johnson, AP, Cleaves, HJ, Dworkin, JP, Glavin, DP, Lazcano, A & Bada, JL (2008). A new look at the Miller “volcanic” spark discharge apparatus. Science 322: 404.
18. Aubrey, A, Cleaves, HJ, Chalmers, JH, Skelley, AM, Mathies, RA, Grunthaner, FJ, Ehrenfreund, P. & Bada, JL (2006). Sulfate minerals and the preservation of organic compounds on Mars. Geology 34: 357-360.
17. Cleaves, HJ, Nelson, KE & Miller, SL (2006). The prebiotic synthesis of pyrimidines in frozen solution. Die Naturwissenschaften 93: 228-231.
16. Ehrenfreund, P, Rasmussen, S, Cleaves, J & Chen, L (2006). Experimentally tracing the key steps in the origin of life: The aromatic world. Astrobiol. 6: 490-520.
15. Skelley, A, Cleaves, H, Jayarajah, CM, Bada, J & Matthies, R (2006). Applications of the Mars organic analyzer to nucleobase and amine biomarker detection. Astrobiol. 6: 824-837.
14. Glavin, DP, Cleaves, HJ, Buch, A, Schubert, M, Aubrey, A, Bada, JL & Mahaffy, PR (2006). Sublimation extraction coupled with gas chromatography-mass spectrometry: A new technique for future in situ analyses of purines and pyrimidines on Mars. Planetary Space Sci. 54: 1584-1591.
13. Borquez, E, Cleaves, HJ, Lazcano, A & Miller, SL (2005). An investigation of prebiotic purine synthesis from the hydrolysis of HCN polymers. Origins of Life Evol. Biosphere 35:79-90.
12. Aubrey, AD, Cleaves, HJ, Chalmers, JH, & Bada JL (2005). Sulfate minerals as targets for biomolecule detection on Mars. Geochim. Cosmochim. Acta 69: A533.
11. Cleaves, HJ & Chalmers, J.H. (2004). Extremophiles may be irrelevant to the origin of life. Astrobiol. 4:1-9.
10. Glavin, DP, Cleaves, HJ, Schubert, M, Aubrey, A & Bada, JL (2004). A new method for estimating bacterial cell Abundances in natural samples using sublimation. App. and Environ. Microbiol. 70:5923-5928.
9. Cleaves, HJ & Salerno, CP (2004). A simple synthesis of photolabile α-methyl nitrobenzyl compounds. Synth. Comm. 34:2379-2386.
8. Cleaves, HJ (2003). The prebiotic synthesis of acrolein. Monatsh. Chem. 134:585-593.
7. Miyakawa, S, Cleaves, HJ & Miller, SL (2002). The cold origin of life: A. Implications based on the hydrolytic stabilities of hydrogen cyanide and formamide. Origins of Life Evol. Biosphere 32:195-208.
6. Miyakawa, S, Cleaves, HJ & Miller, SL (2002). The cold origin of life: B. Implications based on pyrimidines and purines produced from frozen ammonium cyanide solutions. Origins of Life Evol. Biosphere 32:209-218.
5. Cleaves, HJ (2002). The reactions of nitrogen heterocycles with acrolein: scope and prebiotic significance. Astrobiol. 2:403-15.
4. Miyakawa, S, Yamanashi, H, Kobayashi, K, Cleaves, HJ & Miller, SL (2002). Prebiotic synthesis from CO atmospheres: Implications for the origins of life. Proc. Nat. Acad. Sci. USA 99:14628-14631.
3. Cleaves, HJ & Miller, SL (2001). The nicotinamide biosynthetic pathway is a by-product of the RNA World. J. Mol. Evol. 52:73-77.
2. Muckerheide, M, Horn, J, Glavin, DP, Bada, JL, Levy, M, Nelson, K., Cleaves, HJ and Miller, SL (1999). Payload G-768: A space probe into the chemistry of life. pp.169-174. 1999 NASA Shuttle Small Payloads.
1. Cleaves, HJ & Miller, SL (1998). Oceanic protection of prebiotic organic compounds from ultraviolet radiation. Proc. Nat. Acad. Sci. USA 95:7260-7263.
Peer-Reviewed Book Chapters
1. Cleaves, HJ & Bada, JL The prebiotic chemistry of alternative nucleic acids. In Genesis: Origin of Life on Earth and Planets (Joseph Seckbach and Richard Gordon, Eds.)”. Cellular Origins, Life in Extreme Habitats and Astrobiology Series Springer, Berlin. (2012)
2. Cleaves, HJ A Hypothesis for a Unified Mechanism of Formation and Enantioenrichment of Polyols and Aldaric, Aldonic, Amino, Hydroxy and Sugar Acids in Carbonaceous Chondrites. In Origins of Life: The Primeval Syntheses. A. Mulkidjian, R. Egel and D. Lankenau, Eds. Springer, Berlin. (2011)
3. Cleaves, HJ & Lazcano, A Origin of Biomolecules. In Chemical Evolution II: From Origins of Life to Modern Society. American Chemical Society Symposium Series. Editors, Zaikowski, L. & Friedrich, J.M. Oxford University Press, New York. (2009)
4. Cleaves, HJ, Chalmers, JH, Lazcano, A, Miller, SL & Bada, JL Prebiotic Organic Synthesis in Neutral Planetary Atmospheres. In Chemical Evolution Across Space and Time: From the Big Bang to Prebiotic Chemistry. American Chemical Society Symposium Series #981. Editors, Zaikowski, L. & Friedrich, J.M. Oxford University Press, New York (2008)
5. Cleaves, HJ & Miller, SL Organic chemistry on the primitive Earth and beyond. In Systems Biology: Volume I: Genomics. Oxford University Press, New York (2007)
6. Miyakawa, S & Cleaves, HJ Eutectic reactions and the origin of life. In Recent Developments of (Photo)chemistry in Ice. Editor Norimichi Takenaka. Research Signpost, India (2007)
7. Cleaves, HJ Prebiotic chemistry and the primordial replicator. In Protocells: Bridging Living and Nonliving Matter. Editors, S. Rasmussen, M. Bedau., L. Chen, D. Deamer, D. Krakauer, N. Packard & P. Stadler, The MIT Press, Cambridge, MA. (2007)
8. Ehrenfreund, P & Cleaves, HJ (2003). Origins of Life. In Toward Other Earths: Darwin/ TPF and the Search for Extrasolar Terrestrial Planets. pp.195-203.
1.) Chief Chemistry Editor. (2011) The Encyclopedia of Astrobiology Springer, Berlin.
2.) Editor. (2007) Medical College Admissions Test (MCAT) Preparation Manual. Research Education Association.
3.) Editor. (2007) Chemical Principles, 4th Edition. Atkins, P. & Jones, L., W.H. Freeman.
1.) Cleaves, HJ, Lazcano, A, Peretó, J, Ledezma, I, Negrón-Mendoza, A (in press) The Works of Alfonso Herrera in Translation: A Mexican Pioneer in Origins of Life Research. Springer, Berlin.
2.) Cleaves, HJ & Mesler, WM (in preparation) Quest for Creation: The Secret History of Man’s Hunt for the Origin of Life. Norton Press.
3.) Cleaves, HJ & Hut, P (in preparation) The Origin of Life.
1.) Meringer, M, Cleaves, HJ & Freeland, SJ (2012) Biomolecules in Astrobiology.
Annual Report MF-ATP 2012, German Aerospace Center (DLR), pp. 55-57.
2009-2011 Senior Research Fellowship National Research Council/NASA Astrobiology Institute
2001-2003 Post-doctoral Fellowship NASA Specialized Center for Research and Training (NSCORT) in Exobiology
1996-2001 Pre-doctoral Fellowship NASA Specialized Center for Research and Training (NSCORT) in Exobiology
Organic compounds are thought to be required for the origin of life. Although considerable progress has been made in understanding how simple organic compounds can be synthesized under simulated early solar system conditions, many questions remain: Which organic compounds are formed? How do these compounds interact with each other and the surrounding environment? How do they self-assemble into living systems? How can organic compounds serve as diagnostics for biological or abiological processes? How do organic compounds decompose in planetary environments?
The abiotic synthesis and self-organization of organic compounds leading to the origin of life, and the loss of organized chemical signals, which may be diagnostic of the presence of life, over time in the environment.
Addressing these questions requires the application of analytical, organic and geochemical techniques, and modern high-sensitivity, high-resolution and high-throughput analytical methods are poised to revolutionize our understanding of solar system organic geochemistry. This in turn will deepen our insights into the chemistry that led to the origin of life, and facilitate the development of life-detection technologies. Within the context of these exciting research frontiers, my research can be grouped into four complementary themes.
1) Deconvoluting the Prebiotic Small Molecule Inventory
Carbonaceous chondrite meteorites offer bona fide samples of early solar system organic chemistry. Some contain several million small organic molecule types, including nucleobases and amino acids, and may offer insight into the types of chemicals that were available on the primitive Earth. Laboratory analogue materials such as those produced from electric discharge experiments and HCN polymerizations, can produce complex product mixtures similar to those observed in carbonaceous chondrites, and offer a way to study the formational chemistry of meteorite samples.
These heterogeneous mixtures are inherently difficult to analyze, thus their small molecule inventory is poorly understood. I study these mixtures to search for novel and known organic compounds that may have been important for pre-biological self-organization and the origin of life, and how the conditions of synthesis affect their production.
High resolution mass spectrometry is one method which can be used to rapidly screen such complex mixtures. However, even after determining the exact mass of an unknown compound, which allows determination of a precise molecular formula, this can represent hundreds or millions of structural isomers. To overcome this ambiguity, I use structure generation and retro-synthetic analysis software to solve the structures of unknown compounds. Given a molecular formula, one can compute all of the possible structural isomers, then filter the results according to restrictive criteria, including the presence of known functional groups, agreement with fragmentation spectra, and compatibility with expected synthetic pathways. These restrictions greatly reduce the number of possible isomers which must be explored.
2) Organic/Mineral Surface Interactions: High-Throughput Screening
Once organic compounds are introduced into the environment, they inevitably interact with the surrounding geochemical milieu. The interactions of small molecules and polymers with mineral surfaces is crucial for understanding the fate of prebiotic organic compounds, as well as organic pollutants and the nucleic acids of genetically modified organisms, in the environment. Mineral surfaces may promote synthesis, preservation, or degradation of small organic compounds, however relatively little is known about the ability minerals to carry out any of these functions. As there are ~ 4400 known naturally occurring minerals, studying the interactions of organic compounds with a variety of relevant minerals, under a variety of solution conditions represents a daunting combinatorial analysis problem. I am exploring methods of quickly screening these reaction landscapes.
3) Biosignatures and Abiosignatures
Studying early life on Earth, and detecting its possible existence elsewhere, depends on being able to recognize life’s organic remains, and distinguish these from the products of abiological processes. Organisms are composed of a limited set of monomer types, including amino and nucleic acids, lipids and carbohydrates. In principle, it should be easy to recognize these traces of life in ancient sediments. However, the detection of biosignatures depends on having a comprehensive abiological baseline for reference, and becomes increasingly difficult with the passage of time, as bioorganic matter is degraded in the geological record via microbial and chemical decomposition. The development of simple and sensitive detection methods for these molecules, and their breakdown products, is another research goal.
4) Self-Organization of Organic Materials
It is believed that the origin of life required the self-organization of simple organic compounds into chemical systems capable of self-replication. RNA is one candidate for this type of system, but because RNA is unstable and its prebiotic synthesis has proven difficult, some postulate that life began with another more robust abiotically synthesized RNA-like molecule, or some other type of self-reproducing organic system. A number of nucleic acid analogues are known which are strong base-pairing systems, including threose, glycerol and peptide nucleic acids. One of my research efforts is the search for novel, abiotically synthesizable analogues that can be polymerized and copied non-enzymatically.