Henderson Cleaves

• PhD
• Tokyo Institute of Technology

α-Amino acids are fundamental to biochemistry as the monomeric building blocks with which cells construct proteins according to genetic instructions. However, the 20 amino acids of the standard genetic code represent a tiny fraction of the number of α-amino acid chemical structures that could plausibly play such a role, both from the perspective of...

The origin of life on Earth is widely believed to have required the reactions of organic compounds and their self- and/or environmental organization. What those compounds were remains open to debate, as do the environment in and process or processes by which they became organized. Prebiotic chemistry is the systematic organized study of these pheno...

Mineral-assisted thermal decomposition of formamide (HCONH2) is a heavily studied model prebiotic reaction that has offered valuable insights into the plausible pathways leading to the chemical building blocks of primordial informational polymers. To date, most efforts have focused on the analysis of formamide reaction products released in solution...

Life is believed to have originated on Earth B4.4–3.5 Ga ago, via processes in which organic compounds supplied by the environment self-organized, in some geochemical environmental niches, into systems capable of replication with hereditary mutation. This process is generally supposed to have occurred in an aqueous environment and, likely, in the p...

How life on Earth began remains an unexplained scientific problem. This problem is nuanced in its practical details and the way attempted explanations feedback with questions and developments in other areas of science, including astronomy, biology, and planetary science. Prebiotic chemistry attempts to address this issue theoretically, experimental...

Life is believed to have originated on Earth ∼4.4-3.5 Ga ago, via processes in which organic compounds supplied by the environment self-organized, in some geochemical environmental niches, into systems capable of replication with hereditary mutation. This process is generally supposed to have occurred in an aqueous environment and, likely, in the p...

To adapt and survive, life as we know it must have a genetic component to pass on information accumulated during natural selection. It has been suggested that life may have begun with a self-replicating RNA molecule. This appears chemically untenable as the prebiotic synthesis of RNA was unlikely on the primitive Earth. It is now known that biologi...

Stanley Miller's 1958 H(2)S-containing experiment, which included a simulated prebiotic atmosphere of methane (CH(4)), ammonia (NH(3)), carbon dioxide (CO(2)), and hydrogen sulfide (H(2)S) produced several alkyl amino acids, including the α-, β-, and γ-isomers of aminobutyric acid (ABA) in greater relative yields than had previously been reported f...

All terrestrial organisms depend on nucleic acids (RNA and DNA), which use pyrimidine and purine nucleobases to encode genetic information. Carbon-rich meteorites may have been important sources of organic compounds required for the emergence of life on the early Earth; however, the origin and formation of nucleobases in meteorites has been debated...

Carbonaceous chondrites are a type of meteorite with a high organic content, which formed early in the history of the solar system. In addition to large amounts of insoluble high molecular weight organic polymer, they contain a variety of small organic molecules such as polycyclic aromatic hydrocarbons, polyols and aldaric, aldonic, amino, hydroxy...

Archived samples from a previously unreported 1958 Stanley Miller electric discharge experiment containing hydrogen sulfide (H(2)S) were recently discovered and analyzed using high-performance liquid chromatography and time-of-flight mass spectrometry. We report here the detection and quantification of primary amine-containing compounds in the orig...

alpha-Methyl nitrobenzyl compounds have demonstrated superior photochemical release properties when compared to nitrobenzyl compounds lacking a-methyl substitution at the benzylic position. The synthesis of 4-(I-hydroxy-ethyl)-3-nitro-benzoic acid ethyl ester and 4-(I-aminoethyl)- 3 -nitro-benzoic acid ethyl ester was each carried out in four steps...

Original extracts from an unpublished 1958 experiment conducted by the late Stanley L. Miller were recently found and analyzed using modern state-of-the-art analytical methods. The extracts were produced by the action of an electric discharge on a mixture of methane (CH(4)), hydrogen sulfide (H(2)S), ammonia (NH(3)), and carbon dioxide (CO(2)). Rac...

The abiotic polymerization of amino acids may have been important for the origin of life, as peptides may have been components of the first self-replicating systems. Though amino acid concentrations in the primitive oceans may have been too dilute for significant oligomerization to occur, mineral surface adsorption may have provided a concentration...

Biology uses essentially 20 amino acids for its coded protein enzymes, representing a very small subset of the structurally possible set. Most models of the origin of life suggest organisms developed from environmentally available organic compounds. A variety of amino acids are easily produced under conditions which were believed to have existed on...

Interactions between aqueous amino acids and mineral surfaces influence many geochemical processes from biomineralization to the origin of life. However, the specific reactions involved and the attachment mechanisms are mostly unknown. We have studied the adsorption of l-aspartate on the surface of rutile (α-TiO2, pHPPZC = 5.4) in NaCl(aq) over a w...

The current study is focused on surface interactions between L-arginine, the most basic protein amino acid, and rutile in NaCl media over a wide range of solution pH conditions, amino acid concentrations, and solution ionic strengths.

This study enables a better understanding of molecular level interactions between biological molecules and biomaterials such as titanium implants and may also be of importance for understanding the role of mineral-surface interactions in the origin of life.

Nucleic acids, the storage molecules of genetic information, are composed of repeating polymers of ribonucleotides (in RNA) or deoxyribonucleotides (in DNA), which are themselves composed of a phosphate moiety, a sugar moiety, and a nitrogenous base. The interactions between these components and mineral surfaces are important because there is a tre...

We report a synthetic model for the organics in carbonaceous chondrites from NH3, HCHO, and HCN. We use LC-MS to study the reaction products and compare them with compounds in meteorites. This may help constrain conditions on carbonaceous chondrite parent bodies.

The Miller-Urey Experiment in space (MUE) investigates the formation of potential prebiotic organic compounds in the early solar system environment. The MUE experiment will be sent to and retrieved from the International Space Station (ISS), where it will be performed inside the Microgravity Science Glovebox (MSG). The goal of this space experiment...

The ease of formation of amino acids, purines, pyrimidines, sugars and a wide variety of other organic compounds under plausible prebiotic conditions suggests that these molecules may have been present in the primitive terrestrial environment. It is likely that collisions of cometary nuclei with the primitive Earth, combined with the contribution f...

Various mechanisms could have delivered amino acids to the prebiotic Earth (Miller and Orgel 1974). The polymerization of amino acids may have been important for the origin of life, as peptides may have been components for the first self-replicating systems (Kauffman 1971; Yao et al 1998). Though amino acid concentrations in the primitive oceans we...

Previous studies have described feasible pathways for the synthesis of simple organic building blocks such as formaldehyde and hydrogen cyanide, and their reaction to form more complex biomolecules such as nucleotide bases, amino acids and sugars (Miller and Orgel 1974, Miller and Cleaves 2006). However, the polymerization of monomers into a useful...

Interactions between aqueous amino acids and mineral surfaces influence the bioavailability of amino acids in the environment, the viability of Ti implants in humans, and the role of mineral surfaces in the origin of life on Earth. We studied the adsorption of l-glutamate on the surface of rutile (alpha-TiO(2), pH(PPZC) = 5.4) in NaCl solutions usi...

There is little consensus regarding the plausibility of organic synthesis in submarine hydrothermal systems (SHSs) and its possible relevance to the origin of life. The primary reason for the persistence of this debate is that most experimental high temperature and high-pressure organic synthesis studies have neglected important geochemical constra...

It has been proposed that oligopeptides may be formed in submarine hydrothermal systems (SHSs). Oligopeptides have been synthesized previously under simulated SHS conditions which are likely geochemically implausible. We have herein investigated the oligomerization of glycine under SHS-like conditions with respect to the limitations imposed by star...

Surface complexation models provide a way of integrating the results of attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopic studies with bulk adsorption measurements. Assuming that glutamate adsorbs similarly on HFO and amorphous titanium dioxide (ATD), we used ATR-FTIR results for glutamate on ATD [1] to construct a sur...

Amino acids are the building blocks of proteins and are important for some models of the origin of life. Polymerization of amino acids from dilute solution is unlikely without a scaffold or catalyst. The surfaces of early Earth minerals are the most likely candidates for this role. The surface adsorption behavior of 12 amino acids (L-alanine, L-ser...

Interactions that occur at the interface between molecules and mineral surfaces in the presence of water are integral to many chemical and physical processes, including the behavior of pollutants in the environment, metal implants in the human body, and perhaps the origin of life. During the emergence of life, mineral surfaces may have played a rol...

With the aim of getting a fundamental understanding of the coordination chemistry and speciation of amino acids on mineral surfaces we have undertaken a study of the kinetics of glutamate and aspartate adsorption on titanium dioxide. We have performed potentiometric titrations and batch adsorption experiments to investigate the dependence of adsorp...

Miller's 1950s experiments used, besides the apparatus known in textbooks, one that generated a hot water mist in the spark flask, simulating a water vapor-rich volcanic eruption. We found the original extracts of this experiment in Miller's material and reanalyzed them. The volcanic apparatus produced a wider variety of amino acids than the classi...

Hydrous ferric oxide (HFO) and titanium dioxide exhibit similar strong attachment of many adsorbates including biomolecules. Using surface complexation modeling, we have integrated published adsorption data for glutamate on HFO over a range of pH and surface coverage with published in situ ATR-FTIR studies of glutamate speciation on amorphous titan...

Formaldehyde (HCHO), the simplest aldehyde, is an intermediate oxidation state one carbon molecule that exists transiently but prominently in the abiological carbon cycle, and is ubiquitous in the cosmos. Its potential prebiotic importance is suggested by the fact that it readily undergoes a variety of addition and redox reactions to give products...

The action of an electric discharge on reduced gas mixtures such as H(2)O, CH(4) and NH(3) (or N(2)) results in the production of several biologically important organic compounds including amino acids. However, it is now generally held that the early Earth's atmosphere was likely not reducing, but was dominated by N(2) and CO(2). The synthesis of o...

Sugars may have been necessary for the origin of life, specifically in the initial abiological synthesis of RNA. One possible mechanism sugars could have formed on the primitive Earth is the formose reaction, the base-catalyzed polymerization of HCHO. This reaction provides a plethora of sugar products, none of them in particularly high yield relat...

There are two main theories for the origin of life on Earth: the “pioneer metabolic theory” (a hot, volcanic origin) and the “prebiotic soup theory” (a cold, oceanic origin). In their Report “α-hydroxy and α-amino acids under possible Hadean, volcanic origin-of-life conditions” (27 Oct

We have developed a sublimation technique coupled with chemical derivatization and gas chromatography mass spectrometry (GC-MS) to detect nucleobases and other volatile organic compounds derived from bacteria in Mars analog materials. To demonstrate this technique, a sample of serpentine inoculated with Escherichia coli (E. coli) cells was heated t...

The Mars Organic Analyzer (MOA), a portable microfabricated capillary electrophoresis instrument being developed for planetary exploration, is used to analyze a wide variety of fluorescamine-labeled amine-containing biomarker compounds, including amino acids, mono and diaminoalkanes, amino sugars, nucleobases, and nucleobase degradation products. T...

The origin of life remains one of the humankind’s last great unanswered questions, as well as one of the most experimentally challenging research areas. It also raises fundamental cultural issues that fuel at times divisive debate. Modern scientific thinking on the topic traces its history across millennia of controversy, although current models ar...

Most prebiotic syntheses depend on the reaction of concentrated precursor compounds to produce bio-organic molecules. It is now believed that the early Earth's atmosphere was not reducing enough to have permitted copious synthesis of precursor molecules. Freezing allows reaction to occur even from dilute solution. This reaction has been demonstrate...

Strong evidence for evaporitic sulfate minerals such as gypsum and jarosite has recently been found on Mars. Although organic molecules are often codeposited with terrestrial evaporitic minerals, there have been no systematic investigations of organic components in sulfate minerals. We report here the detection of organic material, including amino...

The origin of life remains one of the humankind's last great unan- swered questions, as well as one of the most experimentally challenging research areas. It also raises fundamental cultural issues that fuel at times divisive debate. Modern scientific thinking on the topic traces its history across millennia of controversy, although current models...

The polymerization of concentrated NH4CN solutions has been studied at various temperatures and ammonia concentrations. The products of the oligomerization of ammonium cyanide include adenine and guanine, as well as trace amounts of 2,6-diaminopurine. Our results indicate that the adenine yield is not strongly dependent on temperature. Guanine is p...

We have developed a new method based on the sublimation of adenine from Escherichia coli to estimate bacterial cell counts in natural samples. To demonstrate this technique, several types of natural samples, including beach sand, seawater, deep-sea sediment, and two soil samples from the Atacama Desert, were heated to a temperature of 500°C for sev...

One of the primary objectives of the 1976 Viking missions was to determine whether organic compounds, possibly of biological origin, were present in the Martian surface soils. The Viking gas chromatography mass spectrometry (GCMS) instruments found no evidence for any organic compounds of Martian origin above a few parts per billion in the upper 10...

We have developed a new method based on the sublimation of adenine from Escherichia coli to estimate bacterial cell counts in natural samples. To demonstrate this technique, several types of natural samples including beach sand, seawater, deep-sea sediment, and two soil samples from the Atacama Desert were heated to a temperature of 500 C for sever...

In recent years, Bacteria and Archaea have been discovered living in practically every conceivable terrestrial environment, including some previously thought to be too extreme for survival. Exploration of our solar system has revealed a number of extraterrestrial bodies that harbor environments analogous to many of the terrestrial environments in w...

We have developed a sublimation (teclinlque coupled with chemical derivatization and gas chromatography-mass spectrometry (GC-MS) to detect nueleobases and other volatile organic compounds derived from bacteria in Mars analog materials. To demonstrate this technique, a sample of serpentine inoculated with Escherichia coll (E. coli) ceEs was heated...

Deciphering the origin of life requires some knowledge of the early planetary environment. Unfortunately, we lack definitive evidence of the atmospheric composition, surface temperature, oceanic pH, and other environmental conditions that may have been important for the appearance of the first living systems on Earth. The rock remnants of the early...

 Acrolein is a central intermediate in the prebiotic synthesis of several amino acids, pentaerythritol, as well as various postulated alternative genetic materials. Acrolein is highly reactive so that its steady-state concentration could not have been very high. The ease of synthesis of acrolein from the aqueous aldol condensation of acetaldehyde a...

Most models of the primitive atmosphere around the time life originated suggest that the atmosphere was dominated by carbon dioxide, largely based on the notion that the atmosphere was derived via volcanic outgassing, and that those gases were similar to those found in modern volcanic effluent. These models tend to downplay the possibility of a str...

It has been suggested that hydrogen cyanide (HCN) would not have been present in sufficient concentration to polymerize in the primitive ocean to produce nucleic acid bases and amino acids. We have measured the hydrolysis rates of HCN and formamide over the range of 30-150 degrees C and pH 0-14, and estimated the steady state concentrations in the...

A wide variety of pyrimidines and purines were identified as products of a dilute frozen ammonium cyanide solution that had been held at -78 degrees C for 27 years. This demonstrates that both pyrimidines and purines could have been produced on the primitive earth in a short time by eutectic concentration of HCN, even though the concentration of HC...

It has been suggested that life began with a self-replicating RNA molecule. However, after much research into the prebiotic synthesis of RNA, the difficulties encountered have lead some to hypothesize that RNA was preceded by a simpler molecule, one more easily synthesized prebiotically. Many of the proposed alternative molecules are based on acrol...

Many of the biosynthetic pathways, especially those leading to the coenzymes, must have originated very early, perhaps before enzymes were available to catalyze their synthesis. While a number of enzymatic reactions in metabolism are known to proceed nonenzymatically, there are no examples of entire metabolic sequences that can be achieved in this...

It is frequently stated that UV light would cause massive destruction of prebiotic organic compounds because of the absence of an ozone layer. The elevated UV flux of the early sun compounds this problem. This applies to organic compounds of both terrestrial and extraterrestrial origin. Attempts to deal with this problem generally involve atmospher...