Category Archives: Organic Chemistry

Re-wiring Your Brain For Sugar Craving

Have you ever wondered why we have desires for sweet food but not bitter food? Dr. Li Wang and other scientists at Columbia University have discovered that mammalian brains for tasting can be re-patterned or erased by performing a series of experiments on mice. This study has significance for future studies in eating disorders and weight management.

The taste sensory system 

Mammalians have a developed sensory system for identifying tastes and associating tastes with mechanisms of reward and aversion. This sensory system has two main parts: the tongue and the brain. There are many sensory neurons in our tongues. These sensory neurons, the detectors of the five basic tastes (sweet, sour, salty, bitter and umami), signal our brains and turn on the amygdala of the brains responsible for identifying and interpreting tastes. Dr. Li Wang and her team have confirmed that neurons in the sweet-responsive cortex project to a different area compared to those in the bitter-responsive cortex. The strong segregation of neuron projection transmits desirable, or aversive taste signals, as shown in Figures 1 and 2. Therefore, we cannot stop eating sweets since our amygdala associate sweets with appetitive, desirable signals.

Figure 1. b and c show the active bitter taste cortex and active sweet taste cortex respectively. Source: “Nature Journal”

 

Figure 2. Licks per second (Licks rate) of mice upon photostimulation of the sweet and bitter cortexes. Adapted from “Nature Journal

Rewiring the brain on taste

Dr. Wang and her team rewound the brain of mice on taste by using a drug to silence the neurons in the sweet-responsive cortex and the bitter-responsive cortex, respectively. The team used licks per second to quantify and verify the appetitive and aversive responses of the mice upon photo-stimulating the sweet and bitter cortexes independently. The team found out that by silencing the neurons in the sweet cortex, the lick rate decreased, according to Figure3. This showed that the mice could not recognize sweet when the neurons were silenced by the drug. This confirmed that the taste specific neurons are essential to recognize tastes.

Figure 3 also showed another interesting phenomenon that the team made the animals think they were tasting sweet, even when the animal was drinking water. In Figure3, without the presence of the sweet neuron silencer, the lick rate of the mice with their sweet cortex stimulated was two times higher compared to the mice without the stimulation. The increase in the lick rate in Figure 3. showed that neurons in the amygdala control an animal’s sensory perception of taste.

Figure 3. Photostimulated sweet cortex in the presence or absence of sweet neuron inhibitor. Adapted from “Nature Journal”

The finding that animals’ brains can be manipulated and rewound to change the perceptions of taste has implications in future studies in weight management and eating disorders. By using small drugs to target these taste-specific neurons, we may say no for eating more and more sweets.

Reference

Li Wang. The coding of valence and identity in the mammalian taste system. Nature Journal, 2018; 558, 127-131. DOI: https://www.nature.com/articles/s41586-018-0165-4

Pricia

2020-03-02

 

Where Fluke meets Fortune: How Chance Lead to Discovering Novel Green Chemistry Reactions

Dr. Petri Turhanen from the University of Eastern Finland discovered that Dowex, a cation exchange resin, opens up an untapped area of green chemistry – the scientific initiative to find chemical reactions that produce the least waste. The best part? It wasn’t on purpose.

While working on an organic synthesis project in 2015, Turhanen noticed that the cation exchange resin he was using, Dowex, produced an unintended byproduct in the presence of sodium iodide (NaI), an iodide (I) source. Further analysis unveiled that the byproduct was the result of an iodide addition reaction. This is a reaction where a double bond between two carbon atoms is converted into a single bond with a new atom on each carbon, one hydrogen and one iodine.

The novel and green iodide addition reaction discovered by Dr. Petri Turhanen

The source of this unique reactivity comes from the polymer known as Dowex. Dowex is a solid resin made of polystyrene sulfonate. Its main use is as a cation exchange resin, a type of solid that is able to exchange cations, such as H+, for other cations, such as Na+ or K+.

Why is this reaction significant? Iodinated molecules serve multiple purposes. They are often intermediate molecules in organic synthesis, acting as a precursor to building up larger, more complex organic molecules such as pharmaceuticals. Furthermore, radioactive iodine isotopes attached to organic molecules are used as tags in medical imaging.

The industrial processes used to iodinate compounds require toxic starting materials, harmful solvents and high temperatures. These include hazardous, or even carcinogenic, compounds such as iodine, hydrogen peroxide, trimethylsulfonium iodate and iodine monochloride and heavy metals catalysts. To contract, Dowex has low toxicity and can be reused after the reaction is complete.

Comparison of iodide addition reactions

Since the first experiment in 2015, Turhanen has expanded the library of reactions possible in the presence of Dowex, such as esterifications and the conversion ethylene to a di-iodide species. Continued organic synthesis initiatives such as Turhanen’s will pave the way for a greener future of science.

 

-Mark Rubinchik

Polyurethane – a chemical in your mattress

We are living in “the polymeric world”. What does it mean by the polymeric world? Look around you! We cannot keep away from the materials made up of polymers. Probably, the most common polymer exposed to our body would be a polyurethane, if you sleep on some sort of a comfortable mattress.

The use of polyurethanes

How does a mattress relate to a polyurethane?  The polyurethane is a cushioning material to produce a flexible and rigid foam. More than 50 % of polyurethanes are consumed to make the foams (Figure 1). In addition to the function of recovering an original shape, the rigidity in the range between a flexible rubber and a hard thermosetting plastic makes polyurethanes the best material for mattresses.


Figure 1. Uses of polyurethanes for various materials. Mainly, polyurethanes are used to produce foam materials. This figure is modified from the open source

The carbamate group and the backbone of polyurethanes

How could polyurethanes have rigid and flexible properties? The chemical structure of a polyurethane would explain its properties. The polyurethane is a block polymer produced from two monomers, a polyol and a diisocyanate. The reaction between hydroxyl and cyanate groups gives a rise to repeating carbamate groups in a long chain (Figure 2; left). The polar carbamate group can have intermolecular hydrogen bonding, resulting in the decrease of free volumes within a polymer system (Figure 2; right, Figure 3). Therefore, polyurethanes can have the rigid property associated with the carbamate group.

Figure 2. A chemical reaction of a diol and a diisocyanate to form a polyurethane (left). Intermolecular H-bonding of polyurethane chains (right).

Figure 3. A flexible polymer system due to a large free volume (left). A rigid polymer system due to a small free volume (right). Polyurethanes would resemble the small free volume system due to intermolecular hydrogen bonding.

The backbones of polyol and diisocyanate are also an important factor to control the flexibility of polyurethanes. The flexibility of a long hydrocarbon chain, which both or either the monomers can have, would be introduced intrinsically to the polymers. This implies that polyurethanes can be variously derivatized, switching the backbone of diols and diisocyanates.

-Young Cho

A greener approach to organic synthesis with reduced organic waste

It may sound counterintuitive, but it is in fact a reality. Organic solvent waste is one of the main contributors to pollution generated by the pharmaceutical industry worldwide. These substances are widely used in the preparation of drugs and other vital compounds, and recycling them represents a great challenge for many other industries. Fortunately, a team of researchers from the University of California Santa Barbara, has figured out a way to dramatically reduce the use of organic solvents in widely used synthetic procedures using micellar nano-reactors.

Formation of a Micelle Nano-reactor in aqueous medium. Adapted from https://www.kruss-scientific.com.

It is now possible to perform synthetic procedures in an inorganic solvent, such as water. The key aspect of this technology is the use of functionalized Vitamin E derivatives as nano-catalytic centres that enable organic molecules to react in an inorganic medium. Vitamin E is a lipid-soluble compound, when functionalized, it is able to form micelles in an aqueous environment that dissolve organic compounds as well as other reactants. Reactions take place inside each of these micelles due to their lipophilic character, enabling the entire process to be carried out in water.

Structure of Micellar nano-reactor. Adapted from ACS.

So far, this technique has been used in a wide variety of reactions which include but is not limited to: Cross-couplings, olefin metatheses, trifluoromethylations and aminations, with high yields, little waste and reduced costs. In many industries, waste is measured in E factors. An E factor is defined as the quotient between the amount of produced waste in kg, divided by the amount of desired product obtained by the process.

E Factor comparison between pharmaceutical methods and researchers work for cross coupling reactions. Adapted from Green Chemistry

 

The nano-reactor technology has demonstrated a decrease in E factors for as much as 98%, meaning that this method could drastically change the effect of big corporations in our environment.

-Aron Engelhard

The “AlphaGo” in Chemistry: Organic Retrosynthesis Using Artificial Intelligence

Since the AlphaGo defeated the world Go champion in 2016, artificial intelligence (AI) has revolutionized many fields in our life. It has also become a new star in science and opened up new possibilities to solve the most complicated problems by computers.

Not long ago, a group of chemists and computer scientists built the “AlphaGo” in chemistry. Published in Nature, they designed an AI tool that can plan organic retrosynthesis faster than any similar programs. In a double-blind AB test, chemists on average considered the AI-generated routes to be equivalent to reported literature routes. This achievement may shorten the process for drug designs and accelerate pharmaceutical research in the future.

Retrosynthetic analysis is the canonical technique used to plan the synthesis of organic molecules. In the past, scientists have also tried to design retrosynthetic routes by computers. Although this method can improve the synthesis efficiency, the traditional algorisms are slow and have many errors.

However, the AI developed by Segler’s group speeds up this process significantly. Described by Segler, the synthesis of molecules is very similar to playing Go: Each molecule can be constructed by synthons which are the “playing pieces”. Computers then design routes for the synthons and combine them together.

Figure 1. Translation of the traditional chemists’ retrosynthetic route representation to the search tree representation. Source: Nature

In the research, the AI tool learned more than 12 million single-step chemical reactions by the deep neural network. This can help AI predict any chemical reactions in the synthetic sequence. AI can also apply the neutral network repeatedly to plan routes and construct synthons until ending up with accessible starting reagents.

So far, much research focuses on combing deep neural networks with Monte Carlo tree search (MCTS). Monte Carlo tree search is a method widely used in video games to evaluate the movement of an object. After the player moving one step in the game, the computer will simulate infinite possibilities that may occur and choose the best step. Similarly, computers can also use this network to find the optimal method in organic synthesis.

In a trial test, Waller’s group used this algorism to propose a six-step synthesis for a precursor used in Alzheimer’s treatment. It turns out the AI designed the same route as the literature in less than 5.4 seconds

Figure 2. Comparison between the MCTS and two traditional algorisms: Neural and Heuristic Best First Search (BFS). (A) Performance characteristics of the different search algorithms by finding synthesis routes. (B) Amount of time per molecule to find the optimal route. Adapted from: Nature

More surprisingly, the AI can perform as good as organic chemists in predicting synthetic routes for novel drugs. Segler and his team invited 45 world-leading organic chemists from Germany and China to examine two potential synthetic routes for nine molecules. One route was designed by AI and the other by humans. Results show that chemists cannot distinguish between the two methods. 

Figure 3. Double-blind AB testing of AI route (MCTS) against literature and traditional (BFS) routes. AI route is as preferable as literature routes and much better than traditional methods. (Original)

What we have seen here is that this kind of artificial intelligence can capture this expert knowledge,” says Pablo Carbonell, a famous computational chemist at the University of Manchester. He describes the effort as “a landmark paper”. Maybe in the near future, AI will make a revolutionary change in chemical research and industry.

Revised: Effective Means of Diagnosing Alzheimer’s Disease

Alzheimer’s disease is an incurable disorder that must be treated early and carefully. It is a fatal disease that needs more attention. Biomarker analysis can be a method to detect early signs of the disease, and carbon nanomaterials can be a tool for this method to be applied.

It is estimated that 5.5 million Americans, mainly affecting people over the age of 65, suffer from Alzheimer’s disease without a cure, and is rapidly increasing. This does not mean nothing can be done to help treat the disease.

Researchers at the University of Porto studied carbon nanomaterials and their biosensing applications to determine the biomarkers of Alzheimer’s disease. The study in 2019 urged the importance of biomarkers for indication of Alzheimer’s disease.

To enhance treatment for this disease, early diagnosis is necessary and requires a method of indication. The study focused on biomarkers of pre-clinical stages of Alzheimer’s. Stage 1 includes increased amyloid burden, stage 2 includes neuronal injury and evidence of neurodegenerative change, and stage 3 includes subtle cognitive decline. Although the biomarkers developed can provide good results, various criteria must be met.

Biomarkers of Alzheimer’s Disease (Source: Laurent Hemoye)

Another study mentions the ability to produce biosensors from nanomaterials mainly because of their electrochemical activity and biocompatibility. Carbon nanotubes display exceptional electronic properties, due to its high surface-to-volume ratio, and is most commonly used for biosensing. Graphene is also common, and can be functionalized by various functional groups to improve selectivity to biomolecules.

Structure of Nanotubes (Source: Carneiro et al.)

A demand for more research on developing credible biomarkers for Alzheimer’s disease is crucial for early diagnosis, as more studies show biosensing as a challenge. This could potentially enhance the understanding of the disease and invent a cure.

-Wilson Wong

Revised: Targeting Oxygen sensitive Hypoxia-inducible factors (HIF-1s) can help cure cancer

The 2019 medicine Nobel Prize winner Dr. Gregg L. Semenza found out that targeting the oxygen-regulated hypoxia-inducible factors (HIF-1s) in the cells can help cure cancers.

What are HIF-1s?

We all need oxygen to be alive. In our body, only red blood cells that contain hemoglobin can deliver oxygen for all the other cells. During a shortage of oxygen, erythropoietin (EPO) increases the production of red blood cells. Hence, more red blood cells are available to bind and deliver oxygen from the lung to the other parts of the body.

Besides, vascular endothelial growth factors (VEGFs) can stimulate the formation of blood vessels in response to the lack of oxygen. By forming more blood vessels, the body can ensure that oxygen can get to other cells in different parts of the body.

Red blood cells transport. Source: HealthLink Canada

 

HIFs are the oxygen sensing knob in our bodies. Hypoxia-inducible factors (HIF-1s) are composed of two different subunits-one being an oxygen-regulated HIF alpha subunit and the other being an oxygen insensitive HIF beta subunit.

The alpha subunit of the HIFs can sense the oxygen concentration changes. When the oxygen level is low, the two HIF subunits join to assemble the dimeric HIF-1s. The HIF-1s can then bind to genes that express EPOs and VEGFs. As a result, more EPOs and VEGFs are available to deliver limited oxygen to cells in different parts of the body. Meanwhile, when the oxygen level is high, fewer HIF subunits form the dimeric HIF-1s. Thus, fewer HIF-1s can bind to EPOs and VEGFs genes, which further leads to less EPOs and VEGFs proteins being expressed.

How can the researchers target HIF-1s to cure cancers?
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Nobel Prize Winner, Gregg Semenza on the discovery of HIF-1. Source: Johns Hopkins Medicine

Cancer is a group of diseases with abnormal cell growth. Many studies have shown that tumor metastasis strongly correlates to the elevated levels of HIF-1s. Unlike normal cells, cancer cells have adaptive responses to hypoxic stress, meaning that they can survive and divide under low oxygen levels.

Therefore, HIF-1s can be targeted to treat cancer. By inhibiting the dimeric HIF-1s, cancer cells will have fewer EPOs and VEGFs. Without the adaptive response to low oxygen level, cancer cells will die. The HIF-1s inhibitors can combine with other anti-cancer drugs to kill off cancer cells.

The discovery of this oxygen-sensitive knob HIF-1s is a milestone in cancer treatments. Cancers perhaps are not that scary.

Journal Reference:

Gregg L. Semenza. Pharmacological targeting of hypoxia-inducible factors. Annual Review of Pharmacology and Toxicology, 2019; 59: 379-403 DOI: https://doi.org/10.1146/annurev-pharmtox-010818-021637

Georgina N. Masoud and Wei Li. HIF-1α pathway: role, regulation and intervention for cancer therapy. Acta Pharmaceutica Sinica B, 2015; 5: 378-389 DOI: https://doi.org/10.1016/j.apsb.2015.05.007

 

-Pricia Ouyang

Feb 15th, 2020

Revised:4 Elements Newly Found – the 7th Row of Periodic Table is Completed!

Have you ever curious about the abundance of elements in this world?

Research groups in Japan, Russia, and the USA published their discovery of elements 113,115,117 and 118. On November the 28th of 2016, International Union of Pure and Applied Chemistry (IUPAC) has formally approved the name of these elements as Nihonium (Nh), Moscovium (Mc), Tennessine (Ts), and Oganesson (Og). These four elements completed the 7th row of the periodic table and acted as an important stepping stone toward “superstable-elements” which are going to be influential in the future studies. 

Element 113, Nihonium (Nh), which called “The first element found in Asia” was found by Riken Center of Accelerator-Based Science in Japan. Joint Institute of Nuclear Research discovered three other elements of Moscovium (Mc), Tennessine (Ts), and Oganesson (Og) credited to Russia and the United States. After five months of public review, IUPAC eventually added them to the 7th row of the periodic table.

These four elements were classified as “super-heavy” elements with more than 104 protons. They were synthesized by using particle accelerators to fuse one nucleus to the other. Further experiments proved the existence of these elements by reproducing the synthesis procedures. However, the life of these “man-made” elements seem to be too short for further discovery. “A particular difficulty in establishing these new elements is that they decay into unknown isotopes very fast.” Said Paul Karol, chair of the IUPAC’s joint working party. Nihonium has a half-life of 20 seconds, which was the longest among the newly found elements. Moscovium and Tennessine have an even shorter half-life, which is only 220 milliseconds and 78 milliseconds respectively. 

Example of Super-heavy element. source:Vanderbilt University

What is the purpose of discovering these elements since they disappear almost right after they are produced?

There are “islands of stabilities” which describe certain super-heavy elements that are very stable when they have a certain number of protons or electrons, even though they are huge. Scientists believe that the next island will be in the 8th row of the periodic table. “the alleged but highly probable ‘island of stability’ at or near element 120 or perhaps 126.” Said by Paul Karol. These “Island of Stabilities” can stay from minutes to years which will be meaningful to study their chemistry.  

Although the life of these newly found elements is way too short to have a practical use, they are the sign of getting closer to the “Island of Stability” of “super-stable” heavy elements. Those “super-stable” radioactive elements are worthy of studying and could have a lot of industrial applications. For example, they might be useful as a stockpile of nuclear energy to maintain national safety. The discovery of these elements gave hope to scientists and encourage them to further discover the ultimate limit of the periodic table. Hopefully, they will be able to discover some stable super-heavy elements that are influential and have significant practical uses soon. The study of new elements would eventually be the breakthrough point of modern chemistry!

–Vicky Gu

Revised:4 Elements Newly Found – the 7th Row of Periodic Table is Completed!

Revised:4 Elements Newly Found – the 7th Row of Periodic Table is Completed!