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Can you see molecular bonds? IBM says yes.

IBM is mostly interested in finding new ways to build a processor or a storage medium instead just pure physics knowledge. They were able to image the bonds that can be seen in molecules and were also able to steal electrons from the molecule in order to change its type.

In the papaer publicshed in Nature Cemistry under DOI: 10.1038/NCHEM.2438 IBM researchers, in collaboration with CiQUS at the University of Santiago de Compostela, have observed the rearrangement reaction known as a Bergman cyclisation – which was first described in 1972 by American chemist Robert George Bergman.

The abstract says:

“Here we demonstrate a reversible Bergman cyclization for the first time. We induced the on-surface transformation of an individual aromatic diradical into a highly strained ten-membered diyne using atomic manipulation and verified the products by non-contact atomic force microscopy with atomic resolution.”

Which simply means that they were able to manipulate atoms in order to change the configuration of a molecule. Simply put, this is awesome. It is not the first time, but it has one of the simplest explanatory videos out there. Good on you, IBM.

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5 most dangerous chemicals on Earth

Hank Green, from SciShow, presents a list of top 5 dangerous chemicals int he world. Some of these were so dangerous that not even the nazis would dare touch or use them.

What 5 chemicals is it about then? Here they are:
1. ClF3, chlorine trifluoride, also called “substance N” by the nazis – blows up when exposed to air, lethal when inhaled, burns at 2400 degrees Celsius. It can burn bricks or asbestos or concrete and 1 meter or dirt beneath that too. It is a better oxidizer than oxygen.

2. C2N14, azidoazide azide – the most explosive chemical compound ever created. It explodes even when left alone. The researchers left azidoazide azide in a dark room undisturbed and it still exploded.

3. Ch3CdCh3, dimethylcadmium – the most toxic chemical in the world. A few micrograms/cubic meter are enough to kill you. Friction, water, and any movement will make it explode.

4. C3H6S, thioacetone – the worlds smelliest chemical. You can smell a drop of thioacetone from half a kilometer away. In 1989 the whole city of Freiburg was evacuated due to the accidental release of this substance at a factory in that city.

5. H2FsbF6, fluoroantimonic acid – the strongest corrosive agent in the world and the most dangerous acid ever invented. It is 10 million billions times stronger than sulfuric acid. You can only store fluoroantimonic acid in teflon containers because teflon contains bonds of C-F, carbon-fluorine, the strongest bond in the organic chemistry chemical. It eats glass like it is being nothing.

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Exploring the Universe: we’re made of star stuff

Crash Course Big History #2, with John Green, takes us from the time of Big Bang and up until now, and tells us that we are made of star stuff. Actually, Carl Sagan was the first to put it that way in these exact words.

In any case, the heavy elements we see in our bodies come from supernovae as regular stars only have hydrogen, helium up to iron. It is amazing to think that the atoms that make us could be from several different stars that exploded billions of years ago. Cool, eh?

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Why do leaves turn brown or yellow in fall?

Leaves have a lot of chlorophyll and thus they have a greenish color due to this substance. This substance takes carbon dioxide from the air and with the help of light generates oxygen and glucose. When fall comes there isn’t that much light around and trees start to generate less chlorophyll. Also, by this time a compund from inside chlorophyll called porphyrin breaks down in smaller chunks and thus chlorophyll also breaks down and loses its color.

When the chlorophyll breaks down it allows two other types of pigments to take control of the leaves coloring: carotenoids and flavonoids, which make the leaves turn yellow, brownish or read altogether. These pigments are actually created with the help of glucose stored in the leaves: red is given off by anthocyanin, yellow by carotenoids, and brown by tannins.

Also, since we’re at the chemistry lesson here, let’s learn something about raspberriesThe-Chemistry-of-Raspberries:

Raspberry smell is given off by raspberry ketone, which has the chemical name 4-(4-hydroxyphenyl)butan-2-one), but they also have a ton of other substances in them and along those substance is ethyl formate, which gives off a smell of rum. Yummy.

About raspberry ketone: around 1-4mg of raspberry ketone can be extracted from a kilogram of raspberries and the study done onf mice that indicated that mice that eat this substance f=lose fat was never tested on humans, so don’t fall into the trap of buying any crap supplements that tell you the raspberry ketones will help losing fat. simply don’t.

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CompoundChem mega infusion: chemistry of honey, cosmetics chemistry, antibiotics, insect venoms, aminoacids

The guys at Compound Chem do a great work with their chemistry articles. You don’t need to be a chemistry minor or the sorts to understand what is it about. Once you read what they are posting you are getting one step ahead of crazies that believe that vaccinations are bad or that GMOs will kill you or the sorts.

The infographics from below will teach you way more than you have learned in the high school. Have fun.

1. What is the chemistry of honey. Why won’t it spoil?

Well, honey won’t spoil because it has gluconic acid and hydrogen peroxide and it draws water from its surrounding and killing this way bacteria. Those bacteria being killed honey will not be able to spoil.


2. What chemical compounds can you find in cosmetics?

In lipstick, for example, you can find castor oil, bees wax, lanolin, dyes, perfumes.

3. Organic chemistry: what are benzene derivatives?

Benzene is composed of 6 carbon atoms and each one is connected with a hydrogen atom. Benzene derivatives, where a hydrogen atom is replaced with a functional group are called aromatic compounds as they smell nicely. Example of benzene derivatives: polystyrene, paracetamol.


4. How many antibiotics are there?
Antibiotics are substances used to kill off bacteria. They won’t work on viruses. You need anti-viral stuff for that. Antibiotics were first discovered in 1930 and we now have antibiotic resistant bacteria due to improper use: don’t take antibiotics if you’re cold. Cold is generated by a virus, not a bacteria. Also, if your physician told you to take 20 pills then take them all, not 18 or 19.


5. What is the chemical composition of insect venoms?

Bee venom contains mellitin, apamin, hyaluronidase, mcd peptide, dopamine, histamine, serotonin, phospholipase A, noradrenaline. In order for the bee venom to kill someone you need 2.8 mg/kh of venom in someone’s blood.


6. 20 common amino acids

Amino acids are building blocks of proteins in living beings. From over 500 such substances in the nature the human DNA encodes the genetic information to generate about 20 of these. Essential amino acids need to be taken from the diet while non-essential will be created by our body.


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4 new chemistry lifehacks to rule your day

The guys at Reactions have saved the day once again. They explain 4 new lifehacks and the chemistry behind them. It is not often that we get to understand why we need to do something that might help us in the future.

Here are the 4 lifehacks we should test right now:
– if you want to cool your beer faster, then insert salt in the water and then put ice cubes in it. The water will then be able to freeze well below the 0 degrees Celsius and the beer will cool off faster. The water cools below 0 degrees if there are impurities in it.
– fruit flies can be caught if you use a dish with vinegar in it and then put a plastic bag with holes over it. Fruit flies love vinegar and they will be caught in the trap.
– when you fry hamburgers make sure to crack a hole in the middle so that the entire meat will be cooked evenly
– avoid having stinky sponges by using 2, one in the morning and one in the after-noon.

Case solved 😀

Also, I’d suggest you buy a great book I bought in February, 2014: The Wise Book of Whys
. You will understand why some things are done in a certain way, but you will also see the historic or scientific background of many concepts, terms, processes. A great read. Example: if you want your fruits to ripen faster, simply put a ripen fruit in the same bag as those other green fruits. They all will ripen faster. Why? A ripen fruit gives off ethylene and, if other fruits sense that chemical, they will accelerate the rate at which they ripen.

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Science – what are polymers?

Polymers are substances formed from many basic compounds called monomers. If you have a given molecule and are able to insert many such molecules to form a fully functional bigger molecule, then you have a monomer in place.

The DNA, RNA, tons of types of plastics and cellulose are polymers. They all are build from many smaller chunks and fitted together to work as a whole. Learn more from the video from above.

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Plastic from air? Not so fast

Thunderf00t has his chemistry sniper rifle aimed at the plastic from air hype that claims that a company called Newlight can create plastic from air. Since there is enough carbon dioxide in the air you could theoretically trap it, add water and then burn it to obtain CH2, a base molecule in plastics.

But Thunderf00t asks: if this were true, at what costs? He thinks that these guys don’t even get the carbon from the air int he first place. Most interestingly if they would get it from air, then the energy costs to obtain 1 kg of air plastic would lead to the consumption of 100 kg of fossil fuel used to generate the electricity to make the pump run.

Since we generate over 1kg of carbon each day, Thunderf00t asks why do they obtain so little amounts of plastic in the first place? Even if you would use methane from air, you would still consume way more energy than usual petrochemical processes to obtain that 1 kg of plastic.

If something sound too good to be true, then probably it is.

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Water: it shouldn’t even be a liquid [strange water facts]

Water has been the subject of countless studies and people are still wondering how on Earth could it exist and behave the way it does? I started learning a bit more about water when I stumbled upon Trends in bond angles for H2O and other substances on Chemistry Stack Exchange. The question begs and answer and it is best that we learn a bit of chemistry before falling into the traps of many sharlatans who sell you miraculous alkaline water that cures cancer and such.

Reading about water I spent a bit of time on Steve Lower’s website where you are taught about some basic chemistry things. In order to understand those things you may need a Table of Elements and a basic knowledge of electron orbitals or configurations.

Knowing that Oxygen has 8 electrons you then know how to calculate the orbitals: 1s2 2s2 2p4. Since the p suborbital should have 6 electrons, you can see that Oxygen can accept 2 new electrons from Hygron who is missing one from the s suborbital (it has 1s1 instead of 1s2).

Basic arithmetic for orbial levels (shells) and sublevels (subshells).
– there are 7 main orbitals : K, L, M, O, P, Q and each can have a max of 2n^2 electrons (n= 1,2,3…)
– there are 5 suborbitals: s, p, d, f, g and each suborbital can have a max of 2(2l+1) electrons (l= 0,1,2,…)

Oxygen has 8 electrons and that means that:
– it will have 2 electrons in the K orbital (2*1^2= 2) and 6 electrons in the L orbital (L has a max of 2*2^2 = 8 )
– it will have 2 electrons in the s subshell (1s2, s = 2 (2*0+1) = 2 ) and then 2 in the second s subshell of L shell 2s2 and then 4 electrons in the p subshell of the L shell 2p4 (p = 2(2*1+1)= 6 )

Now, some water facts:
– the bond angles in water should have been 109 degrees, but they are 104.5 degress and can never be changed. Read more on Stack Exchange and from Harvard PDF. The angles in bonds are calculates using a formula like cos( angle) = -1/ sqrt(li*lj), where li, lj are the number of outermost electrons in the hybrid molecular orbital. Like for sp3 there are 3 such electrons. The pdf will make that clearer, search for the Coulson’s Theorem.
– water should have been a vapour at room temperature as it should have become a gas at -70 degrees. See here more. The Hydrogen bonds which show up between the atoms of Hydrogen of one molecule and the Oxygen from another molecule. These bond last only for some picoseconds.
– from the same link above you will learn that water increases volume when is frozen below zero degrees
– water has the highest density at 4 degrees Celsius
– inserting salt into water will get the boiling point upper and the freezing point lower
– surface tension will keep a paper clip on the water
– you cannot get pure water, there will always be some forms of it depending on what type of Hydrogen you have in it (regular, deuterium, tritium)
– we lose about 1.5 litres of water per day from our bodies and most of it (800 mL) from breathing ( Loss through breath: 800 mL, Minimal sweat loss: 100 mL, Fecal loss: 200 mL, Minimal urine loss: 500 mL, Total: 1600 mL)
– water does NOT have memory and it does not get clustered
– the blue color is given by the hydrogen bonds

Read more about the strange properties of water from Martin Chaplin, Water structure and science and from Steve Lower, Water and its structure.

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Chemistry: what makes beer well… beer?

Compound Chem has created a great infographic about beer and the chemical substances that gives beer its bitterness and flavor. Since I am a fan of beer there was a matter of time before I would publish another blog post about beer 😀

How is a beer created, in steps:
1. milling – dried barley is put together and ground
2. mashing – water is added and then it will produce wort
3. brewing – hops are added and then the mixture is boiled
4. cooling – mixture is cooled to under 10 degrees Celsius
5. fermenting – yeast is added and then alcohol is produces
6. maturing – left to mature, filtered and then bottled

Now you know how beer is created.

With 800 different substances int he beer the most known chemical substances found in it are:
– alpha acids found in hops, add bitterness: humulone, cohumulone, adhumulone, posthumulone, prehumulone
– beta acids, also found in hops and add bitterness
– essential oils from hops, add aroma and flavor: caryophyllene, humulene, myrcene
– esthers, add fruity flavors: isoamyl acetate, ethyl hexoanoate.

Read more on Compound Chem.