Nerve Agents: Sarin

Imagine this: you are a middle-aged Japanese man riding a subway train in the Tokyo Metro, waiting patiently to get off. The year is 1995. Suddenly, you hear shouting. You see a group of masked men running about. That nonchalant smell of air you're so used to...it's not there anymore. Your muscles, they start to contract involuntarily. You pass out. Are you conscious now? Are you dreaming? Are you paralyzed? Are you dead?  Will you ever get to see what happens to Ash and Pikachu in the season finale of Pokemon?!

The event that I am talking about is the Subway Sarin Incident. On March 20, 1995, domestic terrorists released gaseous sarin on several subway trains in the Tokyo Metro. Sarin is a nerve agent, a chemical that affects the nervous system. As a result, this terrorist attack killed 12 people and injured over 5,000 people. The victims of the attack experienced periods of temporary blindness. Many of them simply laid on the ground, unable to breathe. This is due to the fact that sarin attacks the central nervous system, paralyzing the lungs and thus causing difficulties throughout the respiratory system.

A transit worker squats beside the body of a man after the sarin gas attack in the Tokyo subway. 

Before we get into the nitty-gritty of Sarin's structural importance and its properties, we should first talk about nerve agents in general. Nerve agents can also be called neurotoxins, so don't be alarmed if I ever interchange the two words. Also, we should review the important parts of the nervous system to understand where and how sarin works. Now, what exactly is a nerve agent? Well, we know that it affects the nervous system. More specifically, a nerve agent is a phosphate-containing organic chemical, also known as an organophosphate. Nerve agents work by blocking the enzymes of neurotransmitters, found in the synaptic clefts between two neurons. Woah what did he just say?! Forgive me, reader, and Dr. Crane too if you're reading this, for I am about to talk about, dare I say it, biology. I promise I 'll try to be as brief as possible. 

Now, in the nervous system there are nerve cells known as neurons. You can see a picture of a neuron down below. Neurons are essentially the building blocks of the nervous system. Neurons, in my opinion, are the coolest types of cells, as their structure is highly unique to that of other cells found in the body. Neurons are extremely important, as they are the only cells that can process and transmit information. They can send information in the form of electrical or chemical messages. The chemical messages are known as neurotransmitters, and these are what we're going to focus on when we later talk about sarin. Now, neurons are made up of three basic parts: cell bodies (soma), dendrites, and axons. There are billions of neurons throughout the human body, and remember, these neurons need to send information from one neuron to the next. They communicate when the axon of one neuron passes along information to the dendrites of another. Now, neurons in the body do not touch each other when they transmit information. There is a gap between each neuron called the synapse. Information must be transmitted across the synapse. In most cases, neurotransmitters are sent across synapses. When neurotransmitters leave one neuron, they must bind to the post-synaptic receptors located on the dendrites of the next neuron. After binding to their receptors, neurotransmitters are reabsorbed and reused by the neuron. Neurotransmitter-specific enzymes such as acetylcholinesterase (AChE) help aid this re-uptake process of neurotransmitters. I have just described to you in a nutshell the basis of neuronal messaging throughout the body's nervous system.

Illustration of a neurons and neuronal messaging.

Neurotransmitters traveling across a synapse.

Now that we understand the importance of neurons and synapses, we can get back to talking about nerve agents. Nerve agents such as sarin mess around with various things in the synapse. In general, nerve agents bind to the enzymes present in the synapse that are supposed to bind to the neurotransmitters and take them away. Once a nerve agent binds to its specifically designated enzyme in the synapse, it renders the enzyme useless by blocking its active site. Remember, the active site of an enzyme is where it physically binds to its substrate (in this case neurotransmitters). Since nerve agents render the enzymes useless, there will be too great of a neurotransmitter concentration a single synapse. With no enzyme to do any re-uptaking, the excess concentration of neurotransmitters will cause all sorts of serious problems. This is also why nerve agents can be called neurotoxins. They "poison" the enzymes in the synapse and cause an uncontrolled build-up of neurotransmitters. Think of the enzyme as the off switch. When neurotransmitters bind to their post-synaptic receptors, the mechanism as a whole is turned on and information is passed down the chain. But there must be a certain point where the mechanism as a whole must be turned off, and this is where the enzymes do their job. However, "poisoned" enzymes cannot fulfill their duties, and therefore the mechanism as a whole will experience unfortunate consequences. This is precisely how the nerve agent sarin works. 

                         

         Normal transmission of acetylchline.             Tranmission with Nerve Agent interference. 


Sarin deals with the neurotransmitter known as acetylcholine. Acetylcholine is associated with memory, muscle contractions, and learning. A lack of this neurotransmitter, along with others, can lead to many neurodegenerative diseases such as Alzheimer's Disease or Dementia with Lewy Bodies. When acetylcholine is released from an axon terminal, it moves across a synapse to bind to its receptor on the other side of the synapse (on the post-synaptic membrane). In other parts of the body, acetylcholine is located in neuromuscular junctions, which are similar to synapses. Here, acetylcholine controls muscular contraction. As mentioned before, the action of acetylcholine is stopped by the enzyme acetylcholinerase (AChE). Sarin binds to AChE molecules and blocks the action of AChE. Again this means that there is no way to control the action of acetylcholine. Consequences of uncontrolled acetylcholine build-up include twitching, paralysis, respiratory failure, reduced vision, sweating, vomiting, headaches, comas, slurred speech, and unsteady muscular contractions, just to name a few.

Neurotransmitter acetylcholine

Enzyme acetylcholinesterase (AChE)

                               

Now that we have a fairly solid understanding of how sarin works with enzymes and neurotransmitters, let's take it down one more level. Let's look at all of these phenomena on a molecular level. First, what exactly is sarin, in terms of atoms. Sarin's molecular formula is C₄H₁₀FO₂P. Sarin is a chiral molecule, meaning that it can mirror itself. Another example of chirality would be your two hands. They are mirror images of one another. When you hold up your right hand in the mirror, it looks like your left hand. In chemistry, chiral molecules are typically ones where there are 4 groups attached to a center carbon atom. In a sarin molecule, there are four things attached to a central tetrahedral phosphorus atom. Sarin was first synthesized in 1938 during WWII. It is prepared from methylphsphonyl difluoride and a mixture of isopropyl alcohol. In other words:

CH₃P(O)F₂ + (CH₃)₂CHOH → [(CH₃)₂CHO]CH₃P(O)F + HF

The boiling point of sarin is around 158°C (316°F) and its melting point is -56°C (-69°F). Sarin is also miscible in water. Now the reason why sarin binds to acetylcholinesterase (AChE) has to do with acetylcholinesterase's structure. In its natural state, the enzyme is a monomer and has a molar mass around 60,000 g/mol. The enzyme has alpha/beta-linked proteins, as it contains 537 amino acids. The optimum pH for AChE is 7.0. Now what binds sarin to AChE? Well if look bag to the above picture of acetylcholine, the neurotransmitter appears to be positively charged. Therefore, acetylcholine has a high electron affinity for AChE. Likewise, sarin is the same. In addition, if we look at the below picture of sarin, we see lots of oxygen atoms and a fluorine atom at the end of the center phosphate atom. Given that AChe has hundreds of oxygen and hydrogen atoms, there is no doubt that there is immense hydrogen bonding between sarin and AChE. If we think about it, there are all these things in the synapse: acetylcholine, AChE, and sarin. AChE has to choose between sarin and acetylcholine, and obviously it chooses sarin, or sarin chooses AChE. Therefore, we can conclude that the intermolecular forces between sarin and AChE are much stronger than the ones between AChE and acetylcholine. Also, sarin has the end fluorine atom, which is the most electronegative atom. Again, this would contribute to its high electron affinity.

3-D molecule of sarin

                                     2-D structure of sarin




Fortunately, there is a cure for sarin poisoning. A drug known as atropine has been used as an antidote. Atropine works by blocking one type of acetylcholine receptor, therefore rendering useless any excess acetylcholine that's floating around in the synapse. 

 Presence of atropine at the synapse.

Nerve agents such as sarin are extremely dangerous. They can kill people within minutes of exposure. Militaries from many countries have used sarin. Germany during WWII, Iraq during the Iraq-Iranian War, and so on. There is a paradox that states: "In order to preserve peace, we must prepare for war." In order to sustain order in this world, or in any world for that matter, be it the physical world, the chemical world, the molecular world, we must find balance and hold on to it. As humans, we've reached great heights. But do you think we've climbed too far this time? How much longer will it be until the next worst thing is developed? Similar to my previous post on Agent Orange, this post again highlights the theme that while science can bring so much good into this world, it can equally bring as much bad. Thank you for reading, and as always, have a nice day.

By: Max Lauring

Agent Orange

In the words of Austrian psychologist Sigmund Freud: "If it is admitted that art and science have the power to do good, then it must also be admitted that they have the power to do harm." Personally, I am not the most enthusiastic advocate of Freud's work. I disagree with many of his theories pertaining to sex, the unconscious mind, and hysteria. However, I believe there is hardly anything truer than his statement - science, especially chemistry, has the potential to bring both good and bad into this world - order and chaos, construction and destruction - and it is this potential that worries me at times. My friends, I am about to take you through a brief history of the chemical warfare that occurred during the Vietnam War (1960 - 1975). More specifically, I am going to talk about the herbicide and defoliant known as Agent Orange. What you are about to read highlights both the beauty and the atrocity - the iniquity of Agent Orange and its everlasting mark on history.

Enough with the ominous and pessimistic introduction, and onto the chemistry! Now, what exactly is Agent Orange? Agent Orange is the code name for a powerful herbicide and defoliant developed primarily for military usage. The military first used Agent Orange during the Vietnam War, mainly from 1961-1971. The herbicide is called "Agent Orange" because during the war, it was shipped in orange-striped barrels. As you can probably guess, Agent Orange was used to kill plants and crops on the ground, in addition to defoliating the leaves off of plants and forest trees. Basically, it killed a lot of plants and trees. It is estimated that nearly 20 million gallons of Agent Orange were sprayed over various parts of Vietnam. 

U.S. military planes spraying Agent Orange over miles of Vietnam's forests. 

Now, what is so bad about Agent Orange? What makes it so harmful? We must first talk about the chemical makeup of Agent Orange. Agent Orange is a 50:50 mixture of two chemicals known as 2,4-D (2,4-dichlorophenoxyacetic acid or C₈H₆Cl₂O₃) and 2,4,5-T (2,4,5-trichlorophenoxyacetic acid or C₈H₅Cl₃O₃). These two compounds can act like plant hormones. In case you forgot what a hormone was, a hormone is essentially like a chemical messenger that transports signals from one cell to another. Hormones can affect the structure of organisms, such as the rigidity of cell walls in plants. By acting like false plant hormones, 2,4-D and 2,4,5-T destroy plants by interfering with their normal metabolism. When exposed to these substances, plants can experience sudden, uncontrolled growth, kind of like a plant cancer. Plants can't receive enough nutrients when growing uncontrollably, and eventually shed their leaves and die.

2,4-D

2,4,5-T

Agent Orange not only harms plants, but humans as well. This is due to the fact that the synthesis of Agent Orange produces dioxins as a byproduct. Dioxins are a group of chlorinated organic chemicals with similar structures. Some dioxins are extremely toxic while others aren't. Why is this? Well, the potential harm a dioxin can induce depends on the number and the position of the Cl atoms attached. The dioxin that is the synthesis's byproduct is known as 2,3,7,8-tetrachlorodibenzo-p-dioxin, or TCDD. Unfortunately, TCDD has been described by some scientists as "perhaps the most toxic molecule evry synthesized  by man." Since dioxins are carcinogenic to humans, it is important to note how dioxins enter the human body. Dioxins such as TCDD are emitted into the atmosphere and land in water or on ground. In water, dioxins bind strongly to small particles and other organic compounds. These molecules are inhaled by microorganisms, and eventually the dioxins will find their way up the food chain until we eat an organism with dioxin in it. Dioxins that land on the ground strongly bond with the organic compounds in the soil, and therefore any present groundwater isn't contaminated. Humans are also exposed to dioxins by air, especially when they come into contact with dioxin-containing herbicides. Dioxins are almost insoluble in water and have a high affinity for lipids (fat), such as the fat stored in the human body. Lastly, dioxins are highly stable due to their near perfect symmetry. Another group wrote about the symmetry of dioxins and Agent Orange on its blog.

Now let's analyze the structure and synthesis reactions of Agent Orange and its compounds. This part will be more conceptual. For me, seeing pictures sometimes helps me more when it comes to understanding certain material. It's helpful to see which atoms move where. Also, there's that saying that a picture is worth a thousand words...so I guess I could just have two pictures instead of this blog post...anyway, as I mentioned before, Agent Orange is just a one-to-one mixture of 2,4,5-T and 2,4-D. Dioxin is the unintentional byproduct of 2,4,5-T synthesis. The picture below shows the step-by-step synthesis of 2,4,5-T. Note that a key step in the formation of 2,4,5-T is the synthesis of 2,4,5-trichlorophenol.

Synthesis of 2,4,5-trichlorophenol, which is
important in the formation of 2,4,5-T. 

On the left is the synthesis of 2,4,5-T, a defoliant and herbicide used to Agent Orange.

The picture on the left shows each step of the production of the byproduct dioxin or 2,3,7,8-T. Notice how the Cl atoms are attached to the molecule at the 2nd,3rd,7th, and 8th Carbon atoms in each ring. This is where it gets its name from.

The New York Times published an article titled "Remedying the Effect of Agent Orange" in August 2012. The article talked about the horrors of Agent Orange's effect. The effects of Agent Orange are still seen today. Mothers in Vietnam still have birth defects. Their children are mutated. Dioxin-induced cancer is still present. The NY Times article stated that if we really want to help the victims of the war, :we should begin by financing a more widespread cleanup and by providing serious support to the families struggling with the birth defects that are one of the legacies of our invasion of their country."

Vietnamese army captain who was
exposed to Agent Orange during the
Vietnam War. 

Before dioxin poisoning.           After dioxin poisoning. 

I am sorry if you finished reading this post with a feeling of sadness or disgust. Unfortunately, this is life, and the reality of it can sometimes be overwhelming. I hope you were able to learn about the chemistry of Agent Orange and its mark on history. Unfortunately, Mr. Freud was right: if science has the power to help others, it has the power to do harm others. Feel free to comment about anything, and as always, have a nice day.


By: Max Lauring