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.

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New Method of Water Purification can Clean Out Mercury and Other Harmful Metals

Carbon nanostructures have the potential to be used as a new form of water purification. A team of researches out of the Indian Institute of Technology Bombay have shown the potential to clean out Mercury, Cadmium, and Chromium ions safely from drinking water.

The study, which came out at the end of December 2019, shows that three-dimensional nanostructured carbon florets (NCFs) are tightly packed enough to inhibit heavy metal ions such as Hg2+ and Cd2+ from passing through, while allowing the much smaller H2O molecules to pass though easily. This material is particularly good at adsorbing out multiple heavy metal ions simultaneously, making it uniquely qualified for practical use in water filtration systems.

Ease of Implementation

The most interesting aspect of this discovery how easy it is to use. No energy is required to enable these filters, the water source simply passes through and between 80% to 90% of the ions are instantly trapped.  The study further shows that NCFs are easy to reclaim after use and have long lifespans. These structures, while being nanostructures, act very simply as a filter for harmful meta ions.

Furthermore, these NCFS work on a range of pH 2-13, with no significant drop across this large range. This means it can perform well on most all samples of water, and effectively decontaminate water safely. NCFs are also synthesized in a very simple fashion, requiring only minor modifications to an already common nanomaterial known as DFNS (dendritic fibrous nanosilica). 

While there is certainly room for expansion into purification of other heavy metals that pollute water supplies, such as lead, this is a very promising step forwards!

-Griffin Bare

 

Engineered bacteria is capable of feeding through atmospheric CO2

A study led by a team of researchers from the Weizmann Institute of Science in Israel has confirmed a recently developed fully autotrophic E.coli strain whose generated biomass is solely derived from a greenhouse gas.

E. coli bacteria cells. Source: Livescience

CO2 accumulates in our atmosphere and it is commonly used by plants to generate sugars for their sustainable growth.This promising strain could be used as a renewable food source and energy storage.

Hacking Metabolism

An originally heterotrophic bacterium was successfully converted into an autotrophic organism. Scientists rewired their core metabolic pathway, introduced heterologous (non-native) genes and Formate as an accessible electron donor, providing such organism with the required enzymatic machinery to effectively convert inorganic carbon into biomass under physiological conditions. Furthermore, the carbon source of nearly all biomass produced was confirmed to atmospheric CO2 with isotopic labeling techniques.

Summary of photosynthetic pathway from an engineered bacterium cell. Source: Cell

Photosynthesis is a process common to plants and some microorganisms, and it is the first step in the food chain. Evolutionarily speaking, this transformation is considered a major accomplishment since these two metabolic pathways are very distinct. Autotrophs and heterotrophs diverged millions of years ago, although some organisms with both metabolic routes are known to exist.

Summary of transformation. Source: technologyandus.com

 

Next Steps

Regulation of CO2 in our atmosphere has become one of the most important challenges in today’s era.  We are constantly looking for sustainable ways of producing food, fuel and biochemicals, and this study presents a new yet promising approach to reduced carbon emitting food sources with a broad spectrum of fields in which this technology can be applied.

There is great diversity in the compounds that can be synthesized through this process and its deep understanding may have a large impact in the future of a new carbon neutral world.

This finding also denotes the flexibility of metabolic processes to support life as mentioned by the authors:

– “This rapid trophic mode transformation showcases the outstanding plasticity of metabolism and demonstrates the power of the framework described here for designing and implementing the rewiring of cellular metabolism.”

-Aron Engelhard

Xenobots: World’s First Living ‘Flesh Robot’ was Created from Frog Cells

Scientists have created the world’s first living, self-healing robots using stem cells from frogs. Published on  PNAS, a team of scientists from the University of Tufts and the University of Vermont created the first living robot named Xenobots without using any metals or plastics.Those flesh robots constructed from frog cells can manipulate objects, move as directed and even interact with each other. The success of Xenobots promises advances in safe drug delivery, environmental remediation and understanding origins of life.

A New Star in Robotics

“They’re neither a traditional robot nor a known species of animal. It’s a new class of artefact: a living, programmable organism.”

explained by computer scientist Joshua Bongard, a collaborator of this project. Before Xenobots, genetic modifications on a single cell or 3D printing tissues have been attempted to construct living systems. Despite the success in simulating biological structures, those methods cannot predict any behaviors. So the question became how to construct a biological system that ‘knows’ what to behave.

A behavioral goal (e.g., maximize displacement), along with structural building blocks designed by computer. The blue and red regions indicate two types of cells. Source: PNAS

The Birth of Xenbots

Thanks to computer scientists, a method called ‘evolutionary algorism’ has been developed to achieve this goal. During the robot design process, scientists first input some behavioural goals, for example, maximizing the moving area or leaving a hole in the centre to carry drug molecules. The computer would then explore different building blocks with the assistance of evolutionary algorism. There are two types of frog cells for the building block, and by cleverly combining those cells, the robot may move as expected.

Xenobot under the microscope. The diameter is less than 1mm. Source: PNAS

Finally, from thousands of building block combinations, less than ten designs were selected for the experiment in vivo. The robots were manufactured under microscopy through a series of steps and tested in real conditions. The result is surprising. Those robots can live for weeks in the water environment without additional energy. Once the energy dissipated, the cells die naturally and degrade as common organisms. Although they lack a nervous system, the robots can still change their motion regularly, and different individuals tend to exhibit various moving patterns.

YouTube Preview Image                                             Video from the University of Vermont

Will The Terminator Come True?

The incredible character of the living robot is the ability to self-repair in the face of damage. This feature is reflected in the Terminator, in which robots dominate the world.Sam Kriegman, the first author of the study, admitted the moral issues brought by this project: the living robot variations may develop cognitive ability in the future. He also pointed out that, because this study is open to the public, society can discuss the topic and regulators should also formulate applicable policies. However, in the short term, this study is more likely to inspire future robotics and help us understand the innate creativity in life.

-Bokang Hou

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.

 

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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

These Ingredients in Sunscreen Might Promote Breast Cancer

Breast cancer is the most diagnosed cancer with an estimated diagnosis of 331,530 women and 2670 men this year in the US alone. Cancer is a incredibly dangerous illness, caused by the unfiltered division of cells in the body. It is predicted that this year 41,760 women and 500 men will die of breast cancer in the US. Research by the University of Massachusetts Amherst published on January 15 2020 found that benzophenone-3 (BP-3) and propylparaben (PP) can increase the chances of breast cancer.

Because of this, the estimations may now have to take into consideration the dangers of common everyday items that include the chemicals BP-3 and PP. BP-3 is commonly found in sunscreen as it helps to block harmful UV light that may cause damage to the skin. PP is a chemical widely used in the cosmetics industry and can be found in items such as makeup, hair products and moisturisers.

Previous research into the effects of BP-3 had shown that only extremely high concentrations could promote cancer growth. Since these concentrations were far beyond the normal levels of exposure to women, there was no cause for concern. However, this new research shows that cells containing oestrogen receptors, important for regulating gene activity, require only a fraction of the cancer promoting concentration of BP-3 to cause damage to the DNA of the cell. “There may be a risk at lower levels than we would have previously understood,” says professor of Veterinary & animal Sciences at the University of Massachusetts Amherst, science director of Pioneer Valley Institute, and co-director of Rays of Hope Centre for Breast Cancer Research, Dr. Joseph Jerry.

The study shows that DNA damage only occurs in cells containing oestrogen receptors, and that all other cells show no adverse effects.

It might be time to take a look at the ingredients in your everyday items!

 

– Chantell Jansz

 

CHEM 300 Course Blog

Welcome to the CHEM 300 course blog! You’ll use this site as a vehicle for practicing chemistry communication.

Here are few things to make note of before you get started with your posts. First of all, you should read the blogging resources page under the Create menu. This will help you out a lot if you are brand new to using WordPress (the software that runs this site). On this page you will find video tutorials about writing posts on this blog, adding media to your posts, tagging, and categorizing. The course Canvas site has information about the blogging assignments and how they are graded.

There are a few important things to keep in mind when blogging. Please do not assume that just because something is online, it is OK for you to use it. For example, unless it is explicitly stated, an image on the internet cannot just be copied, saved, and used in your own post without permission to do so. We’ll provided you with more details about properly using online content, but if you have questions, please ask.

Under the Explore menu, you will find links that may be of interest or assistance, a list of groups and associations related to communicating chemistry/science as well as a list of local museums and science centres. The Explore menu also contains a library resources page, which you should definitely have a look at. Finally, there is a bookshelf that lists relevant books that should be available for you in Woodward Library.

Let me know if you have any questions about the blog or would like to see any other resources made available. Or, if you find something that you think would be useful to the rest of the class, tell us, and we can add it to the resources. Better yet — write a post about it!

Happy blogging!

Richard Kil