Category Archives: Organic Chemistry

You will never know, what happens in an organic chemistry lab.

“Organic synthesis”, seems like a mysterious area to many people without a chemistry degree. Generally, organic chemists synthesize molecules with academic values or commercial values, like drugs and catalysts. However, there are some chemists like to create some fun molecules, which are usually thought to be useless.

Dr. James Tour at Rice University is a famous chemist in building “useless” molecules, such as “NanoKid” and “NanoCar”. In April 2003, he published an article of synthesis “NanoKid”, as well as “NanoProfessionals” based on the NanoKid.

Synthesis and Modifications of the NanoKid

A NanoKid is formed by two parts: an upper body and a lower body. The upper and lower bodies were connected by a Pd/Cu-catalyst through a Sonogashira Reaction. Meanwhile, the “head” of a NanoKid can be changed by changing the ketal part of the NanoKid. Dr. James Tour used a variety of diols to make NanoProfessionals, such as NanoChef, NanoAthlete and NanoScholar. Furthermore, by hydrogenating the triple bond on the “waist” to a single bond, and coupling “hands” of NanoKids, the research team got NanoBalletDancers and NanoKid-Polymer respectively.

Electron cloud-based space-filling model of NanoProfessionals (Copyright: James M. Tour)

NanoCar

Other than NanoKids, the research group of Dr. Tour also built NanoCars by carbon-based molecules and won the first prize in the NanoCar Race in 2017.

Three models of possible conformations of NanoCars under the scanning tunneling microscopy (STM) (Copyright: Organic Letters)

Summary of the NanoCar Race results. (Copyright: Nature)

Recently, many organic chemists use carbon atoms as building blocks to build molecules with unusual names. Such as “Broken Windowpane” which has a molecular formula of C8H12 and looks like a broken window, “Housane” which looks like a house and “Churchane” which looks like a church.

Is it a waste of taxpayers’ money?

Chemists have already synthesized the NanoKid, NanoCar and Broken Windowpane. In the future, chemists might build more interesting Nano-things. These research outcomes are very delighted, but some people might ask: Is it a waste of money? What is the meaning of these chemicals?
To synthesize a Broken Windowpane, chemists need to overcome an extraordinary intramolecular tension, to give birth to a NanoKid, researchers had to design and control the reaction accurately. “Beyond the molecular-sized domain, there is no conceivable entity upon which to tailor architectures that could have programmed cohesive interactions between the individual building blocks. It is at this size region that synthetic chemists have been inherently captivated; however, their fascination is rarely shared by the layperson.” Dr. Tour said. The Broken Windowpane might be adapted for more fantastic molecules, and the NanoCar might be used to deliver targeted drugs to a certain part of the body one day in the future. These molecules show that chemists can make whatever they want, and how magic chemistry is.

Microplastic issues? PLA can solve the problems!

Did you know that less than 11% of plastics have been recycled in Canada since the 1950s? Many plastics, such as water bottles, bags, and takeaway coffee cups, are buried in landfills and are disposed of into the oceans.

Over a long period of exposure to air, sunlight, and moisture, they eventually “disappear” – becoming invisible to the naked eye. In this case, are plastics degradable? While we may use the word “degradation”, they do not actually disappear. The invisible ones have taken the form of microplastics, thereby still existing and still polluting our ecosystem.

Video clip 1. Microplastics as a food for baby fishes.

 

To mitigate this issue, chemists have made an effort to develop biodegradable polymers that can be applied to produce commercial plastics. In modern polymer chemistry, considerable attention has been paid to polylactic acid, so-called PLA. Polylactic acid is produced from lactide which is derived from renewable resources such as corn and potato starch.

Figure 1. Chemical structures of lactide (monomer) and polylactic acid (polymer)  . ROP stands for ring-opening polymerization (a type of polymerization). DOI:10.1021/acs.accounts.7b00447

 

Unlike petroleum-based polymers used in plastics such as polyethylene (PE), polyethylene terephthalate (PET), and polypropylene (PP), PLA has biodegradability and biocompatibility.The enriched oxygen atoms in PLA and its structural flexibility make it undergo hydrolytic and enzymatic degradations, regenerating monomers and oligomers. The degraded substances are further broken down to water and carbon dioxide, precluding the formation of microplastics. Therefore, PLA is a great candidate to substitute for plastics derived from petroleum sources.

Although there are some general issues to resolve from an economical perspective, the environmentally friendly outcomes and industrial applications have made PLA a more attractive material for plastics PLA certainly has the potential to save our future!

-Young Cho

Effective Means of Diagnosing Alzheimer’s Disease

Alzheimer’s disease is an incurable disorder and mainly affects people over the age of 65. It is a fatal disease that must be treated early and carefully. A new method to detect early signs of the disease is currently being investigated. Researchers at the University of Porto studied carbon nanomaterials and their biosensing applications to determine the biomarkers of Alzheimer’s disease.

A recent study in 2019 urged the importance of biomarkers for indication of Alzheimer’s disease. It is estimated that 5.5 million Americans 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. 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

 

Targeting Oxygen sensitive Hypoxia-inducible factors (HIF-1s) can help cure Anemia and Cancers

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

What are HIF-1s and how are they related to oxygen? 

We all need Oxygen to be alive. At a cellular level, oxygen is essential to cell viability as it provides an energy source (ATP) for important cellular activities. 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.

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 the HIF-1s to cure cancer and Anemia?

YouTube Preview Image

Cancer is a group of diseases with abnormal cell growth. HIF-1s can be targeted to treat cancer because by inhibiting the dimeric HIF-1s, the cancer cells will have fewer EPOs and VEGFs. Therefore, the cancer cells will have much harder time oxygen and without enough oxygen, these cancer cells can die.

 “By adding a small molecule that inhibits HIF-1s, added on to the other cancer drugs that patients are receiving, will allow those other drugs to be more effective in fighting cancer,’ said Dr. Semenza

“And as for Anemia, targeting the HIF-1s could show promising effect.”

 He added: “Anemia is associated with the lower-than-normal amount of red blood cells or hemoglobin. By taking a pill of a drug that increases HIF-1s activity and turns on EPO.”

The discovery of this oxygen-sensitive knob HIF-1s is a milestone in cancer and Anemia treatments. Cancers and Anemia 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

-Pricia Ouyang

Jan 27th, 2020

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

International Union of Pure and Applied Chemistry https://writing-rag.com/2010/four-new-words/

Have you ever curious about the abundance of elements in this world? Research groups in Japan, Russia and 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 periodic table and act 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. Three other elements of Moscovium (Mc), Tennessine (Ts), and Oganesson (Og) were discovered by Joint Institute of Nuclear Research credited to Russia and the United State. After five month 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 nuclei 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 has even shorter half-life which is only 220 milliseconds and 78 milliseconds respectively. 

Vanderbilt University https://www.inverse.com/article/16794-tennessee-get-its-own-super-heavy-laboratory-synthesized-element-tennessine

What is 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 certain number of protons or electrons, even though they are huge in size. 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 are 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 to study and could have a lot of industrial applications. For example, they might be useful as a stockpile of nuclear energy to maintain the national safety. The discovery of these elements gave hope to scientists and encourage them to further discover the ultimate limit of 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!

 

You will never know, what happens in an organic chemistry lab.

“Organic synthesis”, seems like a mysterious area to many people outside of a chemistry degree. In many amateurs’ eyes, in an organic chemistry lab, some “wizards” are using “magic power” to create incredible things. However, organic chemistry is very “touchable”, not only many things that we are using are synthesized by chemists, but also some chemists in labs are synthesizing funny things which can add fun to our life.

In April 2003, an article published by Dr. James Tour at Rice University described the procedure of synthesis a “NanoKid”, as well as “NanoProfessionals” based on the NanoKid.

Synthesis and Modifications of the NanoKid

A NanoKid is formed of two parts: an upper body and a lower body. The upper and lower bodies were synthesized in the first several steps, and the last step involved the coupling of the top and bottom portions. This was accomplished by using a Pd/Cu-catalyst through a Sonogashira Reaction.

Synthesis of a NanoKid (Copyright: The Journal of Organic Chemistry)

After Dr. Tour’s team synthesized the NanoKid successfully, he changed the “head” of the NanoKid to make NanoProfessionals, such as NanoChef, NanoAthlete and NanoScholar. Furthermore, by hydrogenating the triple bond on the “waist” to a single bond, and coupling the “hand” of NanoKids, the research team got NanoBalletDancers and NanoKid-Polymer respectively.

Electron cloud-based space-filling model of NanoProfessionals (Copyright: James M. Tour)

Other relevant synthesis projects

Other than NanoKids, the research group of Dr. Tour constructed NanoCars by carbon-based molecules and won the first prize in the NanoCar Race in 2017.

Three models of possible conformations of NanoCars under the scanning tunneling microscopy (STM) (Copyright: Organic Letters)

Summary of the NanoCar Race results. (Copyright: Nature)

Recently, many organic chemists use carbon atoms as building blocks to build molecules with unusual names. Such as “Broken Windowpane” which has a molecular formula of C8H12 and looks like a broken window, “Housane” which looks like a house and “Churchane” which looks like a church.

Is it a waste of taxpayers’ money?

Chemists have already synthesized the NanoKid, NanoCar and Broken Windowpane, and in the future, chemists might build more interesting Nano-things. These research outcomes are very delighted, but some people might ask: Is it a waste of money? What is the meaning of these chemicals?
To synthesize a Broken Windowpane, chemists need to overcome an extraordinary intramolecular tension, to give birth to a NanoKid, researchers had to design and control the reaction accurately. “Beyond the molecular-sized domain, there is no conceivable entity upon which to tailor architectures that could have programmed cohesive interactions between the individual building blocks. It is at this size region that synthetic chemists have been inherently captivated; however, their fascination is rarely shared by the layperson.” Dr. Tour said. The Broken Windowpane might be adapted for more fantastic molecules, and the NanoCar might be used to deliver targeted drugs to a certain part of the body one day in the future. These molecules show that chemists can make whatever they want, and how magic chemistry is.

The Polymer, PLA: it will be degraded, but our future is not degraded

Did you know that less than 11% of plastics are recycled in Canada since 1950? Many plastics, such as water bottles, bags, and takeaway coffee cups, are buried in landfills and are disposed into the ocean. Over a long period of exposure to air, sunlight, and moisture, they eventually become invisible. Are they degradable? We may be able to use the word “degradation”, but they do not disappear at all. The invisible ones exist as microplastics, thereby polluting our ecosystem.

 

YouTube Preview Image

Video: plastics in the ocean

To resolve the further pollution, chemists have made an effort to develop biodegradable polymers that can be applied to produce commercial plastics. In modern polymer chemistry, considerable attention has been paid to polylactic acid, so-called PLA. Polylactic acid is produced from lactide which is derived from renewable resources such as corn and potato starch.

Figure 2. Chemical structures of lactide (monomer) and polylactic acid (polymer)  . ROP stands for ring-opening polymerization (a type of polymerization). DOI:10.1021/acs.accounts.7b00447

Unlike petroleum-based polymers used in plastics, for example, polyethylene (PE), polyethylene terephthalate (PET), and polypropylene (PP), PLA has biodegradability and biocompatibility. The enriched oxygen atoms in PLA and its structural flexibility make it undergo hydrolytic and enzymatic degradations, regenerating monomers and oligomers. The degraded substances are further broken down to water and carbon dioxide, precluding the formation of micro plastics. Therefore, PLA is a great candidate to substitute for plastics derived from petroleum sources

Although there are general issues to resolve in the economical perspective, the environmentally friendly outcomes and industrial applications have made PLA more attractive research area. PLA certainly has the potential to save our future!

-Young Cho