Kensei Kobayashi’s flow-reactor, the SCWFR, part 2

Posted on August 28, 2014June 29, 2014 by Kuhan Chandru

The SCWFR at Kensei Kobayashi's lab at Yokohama National University — The SCWFR at Kensei Kobayashi’s lab at Yokohama National University

Kensei Kobayashi’s group with the help of Takeo Kanaeko (a brilliant man) came up with another design where they named it Super Critical Water Flow Reactor (SCWFR) utilizing an infrared (IR) gold image furnace (Figure above). This enables the fluid in this system to heat up to 400 °C (or any desired temperature) within seconds (without pre-heating). This one specification is important as most autoclave and other flow reactors utilized an electrical heater which takes time to heat up to the desired temperature. This is undesirable as this “pre-heating” is also making the initial chemicals to react (or altered) to lower and rising temperature, which is not very realistic to a real vent. In other case, this is one of the slightly more realistic simulators i have worked to date.

Kobayashi’s ex-student, Nazrul Islam performed the survivability experiment using several amino acids (aspartic acid, threonine, serine, sarcosine, glutamic acid, α-aminobutyric acid, β- alanine, γ-aminobutyric acid, 5-aminovaleric acid and 6- aminohexanoic acid), 10 mM each) by heating them up at four different temperatures (250, 300, 350 and 400°C ) at 25 MPa for 2 min (that’s pretty fast). They showed that amino acids tend to show better recovery when it is hydrolyzed, suggesting some kind of aggregation and/or condensation is happening within the system. Additionally they also showed oligomerization of glycine (100mM) with the same temperature. At 400°C, no oligomerization was found. However, at 200-350°C, diketopiperazine, diglycine, triglycine and tetraglycine were formed. It was suggested that the glycine reactions in a supercritical fluid (300°C to 400°C) are quite different from those in the liquid phase (at 200–350°C). There were many other peaks of unknown compounds in all of the chromatograms of the unhydrolyzed products. Most of those peaks disappeared after acid hydrolysis. This particular findings however remains a mystery.

Another of Kensei’s sudent, Hironari Kurihara, used the SCWFR to test the stability of complex compounds produced from simulated primitive atmosphere (similar to Miller and Urey’s work). He then tested these compounds to assess the stability of some known amino acids. The complex-combined amino acids (from the primitive atmosphere simulation) preserved more amino acids (including amino acid precursors that give amino acids after acid hydrolysis) than free amino acids after heating in simulated SHS environments. In other words, these complex chemicals which could come from atmosphere (or space) could be better preserved if they are come into contact with the hot hydrothermal system which could have existed during the prebiotic-earth setting. This also hints that “clean or perfect” chemicals like amino acids used in many kinds of experiments are not necessarily showing the right picture when comes to chemical evolution on early earth. More on this in the future.

Many critics of hydrothermal vent simulators often argues that, simulators mentioned on this post and previous ones have a rather short flow-rate and short flow-length (showing low residence time, meaning how long the sample stays in the system). Critics usually cite studies that refer to residence time of fluids in axial hydrothermal environments range from years to decades, while those in lower temperature off-axis diffuse flow systems may be on the order of thousands of years. The problem with these studies about residential axial time of fluids is that, they’re are based on models and calculation only, no work has been done so far in regards to real time sampling or measuring the length of vent system (although, there are work in measuring the velocity of fluid emitting from a vent which looks promising for future measuring). Despite this limitation, i believe the future of simulators will be done using computer simulators, where experimental data from physical simulators (like the ones mentioned in this blog) could be used as parameters. The biggest advantage in this, is that, we do experiments on a larger scale which is could make the origin of life more complicated, interesting and not so straightforward, which I believe is a good problem to have in the future.

Cellrelics needs your help! If you click on any of the social networking connections below, or share this post with a friend in any way, it will start a chain reaction of fun and knowledge across the world. Many thanks for reading! and Alexa, i hope you’re watching this, need some love here

The flow-reactor, a better hydrothermal vent simulator, part 1

Posted on July 28, 2014June 29, 2014 by Kuhan Chandru

flow-reactor (HCFR) build by Ei-ichi Imai at Nagaoka Institute of Technology.

In the previous post, i wrote about a conventional kind of submarine hydrothermal simulator (SHS) called the autoclave. In today’s post i will talk about the flow kind of reactor which is more realistic compared to the autoclave. Jack Corliss, the man who discovered a real SHS, came up with the notion that a flow-type reactor is essential for new origin of life experiments, as he argued that the quenching effect of the cold seawater is important to hold the short-lived intermediates (hydrogen cyanide, sugars and etc) or as he calls it “quasi-species” in prebiotic synthesis of bio-molecules. This essentially means that a flow kind of simulators are required to better represent a real SHS to produce more reliable results than the autoclave.

Initial Schematics of Jack Corliss in his paper

Co-incidentally, Koichiro Matsuno, designed a principle idea of a flow reactor which could reflow the fluids repeatedly in heat and cold (i will name here-forth as hydrothermal circulation flow-reactor (HCFR) for convenience). Ei-Ichi Imai, Koichiro Matsuno and co-workers went on to build (image above, schematics diagram below) the reactor and experimented using many bio-molecules.

Their first paper which made it to Nature (big thing for scientist), reported that oligomerization of glycine could occur at 200-250°C, where a monomer glycine solution was circulating for 2 hours or so. Oligomers up to Hexaglycine was reported when metal (Cu2+) and controlled pH was introduced. Without them, only oligomers up to triglycine could be obtained. They also tried the same experiment using glycine and alanine. They observed oligomerzation products such as

Schematic diagram of the HCFR system from Nagaoka Institute of Technology

diketopiperaxine, gly-ala, ala-gly, gly-ala-ala, ala-ala, ala-ala-ala and ala-ala-ala- ala was created when the solution was heated with similar conditions. What i described abover is a big thing in origin of life studies. This land-mark discovery, was the first to show that oligomerization (a shorter version of polymerization) could occur using basic amino acid (gly), without the help of DNA and RNA molecules which are crucial in making proteins in life.

In their other works, oligomerization of nucleotide up to trimers (basic monomer of DNA) was also observed when 20mM of adenosine monophosphate was used with 1mM ZnCl2 were reflowed at 110°C.

Despite the findings made by HCFR, the system is rather hypothetical, since we know that real live vents don’t really circulate in that manner (shown below) however, this kind of reactor is useful when it comes to monitor chemical changes in the system. In my next post, i will review another kind of flow-reactor in Japan which i have also worked on in the past.

HCFR mimicking a circulatory system in a real life vent. — HCFR mimicking a hypothetical circulatory system in a real life vent.

Basic characteristic of submarine hydrothermal systems (SHS)

Posted on April 1, 2014April 15, 2014 by Kuhan Chandru

The figure above shows the schematics of a typical submarine hydothermal system (SHS). The magma at the hottest zone is about 1200°C. Seawater from the sea penetrates into the crust of the spreading axis (down flows) and towards the “reaction zone” which is about ~400°C. Seawater-rock interaction happens here, the water is then released through and is cooled down rapidly by cold seawater. A quenching effect takes place here. The abundance of minerals and/or metals are also part of the system. Some of the chemical composition of a typical black- smoker type of SHS is shown here. The diagram above represent what we typically call a black-smoker, A black smoker is a type of hydrothermal vent typically found in the abyssal and hadal zones.

Common pictures on SHS are generally black smokers. They appear as black chimney-like structures that emits a cloud of black material containing high levels of sulfur-bearing minerals, or sulfides. Black smokers are formed in fields, hundreds of meters wide when superheated water from below earth’s crust comes through the ocean floor. This water is rich in dissolved minerals from the crust, most notably sulfides. When it comes in contact with cold ocean water, many minerals precipitate, forming a black chimney-like structure around each vent. Effluents from black smokers are acidic (pH 2-3) and are rich with transition metals. All the fluids gives out nutrients to all the unusual organisms at the area. Google it!!!

On the other hand, a diffuse flow is an area where hydrothermal fluids flow out instead of a chimney. The fluids from here are much cooler and slower compared compared to a typical SHS. Minerals are usually left behind in this fluids. White smoke appears to come out of the sea floor, hence the term white-smokers were coined. Unlike the black smokers, the fluids coming out of here lacks minerals which comes from their black counterparts. These two type of smokers are typical in a SHS environment. It is speculated that SHS could have existed throughout earth’s ocean, this subsequently fueled the idea that life could have started here, together with the heat loving bacteria. So far, the experiments of SHS are done with simulators at laboratories mainly in Japan and the U.S only. Research using simulators usually utilizes basic chemicals exposed to heat and pressure similar to the vent system (so far the black smokers). Another area of interest is to see the survivability of common bio-molecules such as amino acids in SHS simulators. This is important as data from these kind of experiment usually presents the thermal and pressure limits of the chemicals used in life’s processes. We know now that amino acids (not all) can survive in SHS simulators, which gives a good account to SHS being a good spot to origins. On the other hand, genetic materials (DNA and RNA) are instantly destroyed when exposed to the simulators. This proves to be a difficult scientific problem to solve so far.

In the next post i will be posting briefly about the LOST CITY type of hydrothermal systems, an entirely unique system and will follow with the various kind of SHS simulators i have used before.

Like this:

Like this:

Like this: