Indeed, oxygen is one of the most abundant chemical elements on the planet, and it has been baffling scientists since its official discovery in 1773 by Carl Wilhelm Scheele and Joseph Priestley, independently. You will know why I said official when we get to the some facts about oxygen later.

Associated with the chalcogen group, molecular oxygen, dioxygen, or O2, is an extremely volatile covalent compound.

As obvious as it may seem, the discovery of oxygen was key for the development of chemical science: In fact, the process of abstracting electrons from a molecule, known as the chemical process of oxidation, takes its name from this element. This is due to the fact that elemental oxygen has the capacity of forming “oxides” with most chemical elements.

Technically, it is also the third most abundant element in the universe, trailing behind hydrogen and helium, respectively. 

Hence, in this article, you will learn several facts about this fascinating chemical element. We want to get into its photochemical properties (i.e. its color). But also, you will hopefully discover new things to add up to your knowledge. Let’s get started. 

General Properties of Oxygen

First off, we will take a look into molecular oxygen’s physical and chemical properties.

Oxygen is a colorless and tasteless gas at normal circumstances. This chemical compound is virtually odorless. People have stated, however, that it is actually possible to distinguish between air or pure oxygen. If the odor of oxygen does exist, we may not smell it because of olfactory fatigue.

Os we already mentioned, the most common form of that the element oxygen takes is that of molecular oxygen, dioxygen, or simply O2.

Dioxygen molecules, which are found in gas form under standard conditions, are composed by two atoms of oxygen which are bound through a covalent bond to one another.

However, oxygen is not always in a gas form.

Like most chemical compounds, under certain conditions, which we are about to discuss, it can also transition to different states of matter.

Liquid Oxygen

Liquid oxygen is the condensed form of dioxygen. Nowadays, liquid oxygen is used in many industries such as submarine, and aerospace, or in medicine.

In 1877, liquid oxygen was first discovered by Louis Paul Cailletet (France) and Raoul Pictet (Switzerland). This was after Michael Faraday had liquefied most gases known by 1845, but failed to do so with 6 of them which were known as “permanent gases” at the time. Oxygen was one of those gases.

Slightly denser than water in a liquid state, liquid O2 has a density of precisely 1.141 g/cm3. At its freezing point of 54.36 K (−361.82 °F or −218.79 °C), it becomes a solid.

Furthermore, liquefied oxygen is paramagnetic, a special type of magnetism. Paramagnetic materials (such as liquid oxygen) become weakly attracted to an external magnetic field. Check out the experiment on this video:

Oxygen is also an oxidizing agent as it can readily oxidize organic or inorganic (such as metals) materials. It is in fact used as oxidizing agent in liquid-fueled rockets, since its invention in 1926 by Robert Goddard.

Solid Oxygen

Under standard atmospheric pressure, and at temperatures below 54.36 K (−361.82 °F, −218.79 °C), dioxygen transitions from gas to solid, forming a spin-lattice crystal. Also in this state, diatomic oxygen is one of the few small molecules that carry a magnetic dipole moment.

Color and Properties of Oxygen in Different States

Now the question is:

What is the color of oxygen? Well, gaseous oxygen is colorless. However, when in liquid form, it comes in a shade of pale sky-blue.

The color of solid oxygen, on the other hand, ranges from light blue, pink-to-faint blue, faint-blue, orange, dark-red-to-black, and metallic in six of its different possible phases.

You basically can have solid dioxygen in 6 different phases. And each of them display a particular color.

Why Is Liquid Oxygen Blue?

Similarly to what happens to water (which is also blue, by the way!), the energetic transitions of the electrons in oxygen (which are also the cause of its para magnetism) absorb light on the red spectrum. So red light is absorbed to some extent, giving the substance its complementary color: blue.

If you want more info, this paper in the Journal of Chemical Education gets you covered.

Other Facts About Oxygen

Oxygen is a fascinating chemical element. Apart from its physical and chemical properties, it also has a fascinating history. Add more to your new knowledge and digest some of the following facts below.

If you are hungry for even more, make sure to check our explanations to 100 chemistry facts!

Who Discovered Oxygen?

The question of “who” only brings confusion as sources may vary.

The earliest mention of oxygen is in Michael Sendivogius’s 1604 study. A Polish philosopher, physician, and alchemist, he motioned that air contains a substance called ‘cibus vitae,’ which translates as the food of life.

However, most scholars say that the real discoverer of oxygen is Carl Wilhelm Scheele, a Swedish pharmacist. Between the years 1771 and 72, Scheele experimented with various metal salts, including several nitrates. Scheele discovered the release of a then-unknown combustible agent.

Scheele wrote in his manuscript, Treatise on Air and Fire, his observations about a so-called ‘fire gas’ that is released from heating nitrates. He submitted his findings in 1775 and had them published two years later.

During that same time, though, Joseph Priestley, an aptly named British clergyman, observed that mercuric oxide in a glass tube released a gas he called ‘dephlogisticated air’ after sunlight exposure. He further noted that candles burned brighter in ‘dephlogisticated air’ and that a mouse lived longer even after being exposed to it. He also tried breathing it in and noted that it was like breathing regular air. Priestley published these findings in his 1775 paper called An Account of Further Discoveries in Air.

On a different note, Antoine Lavoisier, also made claims that he independently discovered this substance. Both Lavoisier and Priestley exchanged correspondence and shared ideas. However, the former denied having received any letter from Carl Wilhelm Scheele.

Where Did Oxygen Originate on Earth?

Oxygen comes in third as the most abundant element across the whole universe. However this only accounts for about 1% of oxygen, since the two main constituents, hydrogen and helium, account for 75% and 23% of the entire universe, respectively.

But it was relatively scarce during the formation of Earth.

Accordingly to theories, early forms of cyanobacteria have produced oxygen and added it into the atmosphere of our then-prehistoric planet. Like plants of today, these organisms used photosynthesis as a form of sustenance. For millions of years, they took in carbon dioxide and released oxygen — a grand event dubbed as the Great Oxidation Event.  

What Is the Effect of O2 in the Blood?

Oxygen is crucial to our bodily functions. Without it, we would not last long. Oxygen is not only the basic source of energy that fuels the activity of all cells in our body, but also has several other secondary functions such as serving as a buffering agent – keeping our pH levels in check.

The average blood O2 level is around 75-100 mm Hg or millimeters of mercury. When it drops below normal, we may experience shortness of breath. Likewise, our blood will become acidic because of an increase in blood carbon dioxide or CO2.

Now, what if blood O2 increases? We will experience hyperoxia, which, when aggravated, may lead to oxygen toxicity. This condition may also cause severe damage to your body.

Why Do We Turn Blue When Blood O2 Decreases?

Bright red is the color of oxygenated blood because of the protein, hemoglobin. However, when a person experiences hypoxia, hemoglobin will not bind with the red blood cells, resulting in a darker hue, making us appear as bluish.

Basically, oxygen forms a coordination complex with the ‘heme’ group on hemoglobin. This complex is red-colored, whereas free hemoglobin is actually blue.

Why Are Oxygen Atoms Usually Depicted in Red Color?

If you are familiar with molecular models (and you should!), for sure you know that oxygen atoms are usually red-colored.

Considering that these colors (CPK coloring system) are usually inspired by the color of the elements themselves (hydrogen is white since its always colorless, carbon is black because of charcoal, sulfur powder is yellow…) his seems counter-intuitive after everything we have just explained.

The inspiration for traditionally coloring oxygen atoms in red is not that clear. It probably has to do with oxygen being required for combustion (and fire is red), or due to the previous fact that we covered: oxygen makes hemoglobin look bright red!

To Sum Up

And that concludes our discussion on this element.

So what is the color of oxygen, you say? Well, the answer is: it depends on its physical and chemical state. It is colorless when in gas form; pale or sky blue when in liquid, and shades of blue, red, and black-metallic when in solid state.

The post What Is the Color of Oxygen: Properties and Exciting Facts appeared first on Chemistry Hall.

Some other students find are more intimidated by organic chemistry. However, most chemistry students are not incredibly fluent in maths, so all those physical chemistry equations can seem a bit overwhelming.

Physical chemistry isn’t the easiest subject to learn; it might frustrate you at times. Very basic and important concepts such as thermodynamics and kinetics are often overlooked in basic chemistry courses. However, if you have the right tools, in this case, the right books, you will have no problem whatsoever studying and passing exams. 

For this review, we will look at some of the best physical chemistry textbooks. For better or worse, it doesn’t seem to be a huge variety to choose from, in contrast with what happens with organic chemistry or general chemistry textbooks. So this comparison review will be quite concise, focused on the three most recommended physical chemistry reference books.

In any case, it does not matter if you are a college professor with a physical chemistry course to teach, or a student who is looking for a solid book to study from, either way, you are covered.

Our Top Pick: Which Book Is the Absolute Best?

After having used all the reviewed books, it didn’t take us long to choose McQuarrie’s Physical Chemistry: A Molecular Approach as the absolute best way to study, learn or teach physical chemistry.

Physical Chemistry: A Molecular Approach

McQuarrie is definitely the king. The red book, even being still on it’s first edition, is undefeated as the best book to learn physical chem. I know many students that had another books defined as course assignment text, but turned to McQuarrie’s to really be able to grasp everything and ace the courses.

McQuarrie’s is just the way to go in most situations, you cannot go wrong with it.

The Best Physical Chemistry Books Reviewed

And now we jump right into the entire reviews!

1. Physical Chemistry: A Molecular Approach

Authored by Donald A. McQuarrie and John D. Simon, this chemistry book is, without a doubt, the most logical and best physical chemistry book you will find anywhere. If you are a beginner, and you plan on getting your feet wet in physical chemistry, this book is an excellent choice.

Physical Chemistry: A Molecular Approach

The book is logically organized, and its concepts are clear and very easy to follow. The math, which is also clear and easy to follow, comes before the physical chemistry chapters. For beginners, I find this helpful because rather than assuming you learned the math elsewhere, the book explains it to you. And there are adequate mathematical reviews at the end of each math section that you can go over. 

For more advanced students or courses, you aren’t left out. This book is the go-to textbook in the area of Thermodynamics and Quantum. I have never seen quantum chemistry explained in any other book as beautifully and enjoyably.

There are many problems on each chapter. You can grab a copy of the problems and solutions manual for McQuarrie here. Many say it is a must if you are interested in focusing on solving problems (which are the main part of courses and exams), or if you are an instructor.

What Makes McQuarrie’s Physical Chemistry the Best?

After explaining the mathematical equations in the math chapters, the book then introduces the fundamentals of quantum theory with explanations. And then base everything else on a microscopic, atomic/molecular standpoint. And this is revolutionary because it helps students to see the subject in a unified and logical fashion, not leaving them confused. As you are probably aware, quantum chemistry and thermodynamics cover many concepts which are difficult to grasp. But not so much with this book. It takes an approach which I feel is the easiest way to learn these concepts.

All in all, I’d say that this book is a must-have physical chemistry textbook that most students of chemistry or college professors and should have on their book shelf. 

I’ve even hear a story of a non-chemist science enthusiast that grabbed a copy of this book and found it to be highly entertaining and instructive! It leaves you with a great feeling on how chemistry works from a (sub)atomic point of view.

To finish, the only drawback is the fact that the book hasn’t been updated since first release, so the figures can be a bit ugly and sometimes not easy to understand.

2. Atkin’s Physical Chemistry

Next runner up is Physical Chemistry by Peter Atkins, Julio de Paula and James Keeler. Now, here’s an updated and nicely illustrated textbook.

It comes in two volumes. The first one covers thermodynamics and kinetics. On my case, I studied quantum at college before thermodynamics and kinetics, so it seemed to me a bit counterintuitive. But I guess the two-volumes distribution was established for exactly this kind of situations.

This is nice, so you only have to buy and handle a 450 pages book for your thermodynamics and kinetics courses.

Atkins’ Physical Chemistry Volume 1: Thermodynamics and Kinetics

The second volume covers quantum chemistry and spectroscopy. It goes on for a little less than 400 pages, and focuses on the physical chemistry itself, not too much in the math behind. it gives just enough to be understandable with a solid base. But you’d better be equipped with that skillset!

Atkins’ Physical Chemistry Volume 2: Quantum Chemistry, Spectroscopy, and Statistical Thermodynamics

Atkins’ books excel in probably being a bit easier to read than McQuarrie’s. It reads pretty much like a novel, and the well illustrated modern figures definitely help. Besides, the book was updated in 2018 with its 11th edition. These are probably the facts that make Atkins’ the most ubiquitous textbook as part university courses syllabus. It’s a great primary resource.

It goes less in depth than McQuarrie’s, but it is arguably easier to read and a bit less dry.

The corresponding Student Solutions Manual also makes Atkin’s text complete.

3. Levine’s Physical Chemistry

I would say that Physical Chemistry by Ira N. Levine is the third most widely used physical chemistry book over the world. This book aims at making the learning process as easy as possible.

Levine’s Physical Chemistry

It comes with stepwise derivations and all maths quite carefully explained. Does a better job than Atkins’ but still not at the level of McQuarrie’s.

This book is on its 6th edition, but this update was released in 2008. It is written on a more formal or more dry manner than Atkins’, but this also makes it pretty specific and concise most of the times.

However, I would not recommend this text over the other two. It does a good job, but Atkins’ and McQuarrie’s do it better.

Closing Up

In summary, whatever textbook you select for guarding you from mighty physical chemistry, be aware that these courses can be a real challenge.

Just put enough time into studying and you will be fine. Also, make sure to have a decent base on maths (especially calculus) before taking physical chem courses. If you put time, have a good base, and one of these great textbooks, you will do fine.

In terms of comparison, we have already stated how McQuarrie’s Physical Chemistry: A Molecular Approach is the winner of the race. It is simply the best book for learning the subject from scratch, since even the math is explained carefully. It is particularly wonderful for quantum mechanics and statistical mechanics.

Even if your course ask you to follow Atkin’s or Levine’s, McQuarrie’s makes up for the best supplement.

On the other hand, Atkins’ can be arguably considered as the best “starting point” book out of the three. That is probably why it is the most recommended one for university courses.

This is all from our side. Make sure to check our general guide for learning chemistry. You can find there plenty of other resources that we have published or updated recently.

And also, please, if you have any comment or suggestion, or another book that you would like to see reviewed, go ahead and hit the comments section!

The post What Is The Best Physical Chemistry Textbook? appeared first on Chemistry Hall.

The answer to this question is especially relevant to the younger generations. Will I be able to find a job in 20 years doing exactly what I do now? Am I focusing on a branch of science that will be important in a couple of decades?

For now, it is impossible to predict the future of chemistry. However, it seems very likely that any field of science will evolve significantly with the advances on artificial intelligence.

And this is most likely not avoidable. Computers and robots are here to stay, and they are only getting better. But how much better can they become in our lifespan?

Artificial Intelligence and Machine Learning

Probably one of the biggest revolutions in science is the appearance of computers. Something that today we take for granted, has pushed the speed of scientific discovery for the past decades.

Today we almost cannot conceive synthetic chemistry without tools such as SciFinder or Reaxys. But how long until you can input a molecule that has never been made before in a search box, and you get exactly the steps you need to take to make it in a lab? Artificial intelligence (AI) and machine learning might be behind this through the future of chemistry.

If you are not familiar with those terms take two minutes to watch the video below:

You can teach a computer how to differentiate a cat from a dog.

Using AI to solve this problem is not very useful, since humans are already pretty good at it. However, when it comes to analyzing hundreds or thousands of data points at the same time, human beings are drastically outperformed by computers.

And, in a way, chemistry is a lot about this.

How Can the Future of Chemistry Be Defined by AI?

When you want to optimize a new synthetic step, or the properties of a new material, what do you usually do?

Dive into SciFinder, download a couple of reviews and 10 research papers, skim over the schemes, and from that, extrapolate the conditions you want to test in the lab.

Seeing it from an AI perspective, this procedure is extremely rudimentary, to say the least. And yet it’s what >90% of experimental chemists (as myself) do on a daily basis. And computers will eventually be better at it, no doubt about that.

Obviously there is a significant creativity component of a research jobs. And identifying or dealing with unknown results. At the early stage of AI and machine learning in which we are at, humans still outperform machines. It is difficult to know how long it will stay this way. Honestly, I’d be surprised if it took more than 10–15 years.

The Future of Chemistry Now

AI has been around for several decades. Getting better and better every day.

Computer-assisted chemical synthesis was pioneered by E. J. Corey as back as 1985, when he reported in Science a very basic system for synthetic analysis in organic chemistry. This was 5 years before being awarded his Nobel prize, in 1990, but there was not a big follow up on this kind of chemistry until more recently.

However, in the past couple of years, an explosion in computer-assisted chemistry is only getting started. This has been commented by F. Peiretti and J. M. Brunel in 2018, but even since that day, many more recent works have seen the light of day. This might indeed define the future of chemistry.

Some of the key players on this approaches are Abigail Doyle, Matt Sigman, Lee Cronin, or the MIT team led by Timothy Jamison and Klavs Jensen. We will try to briefly review some of the very last years.

We apologize in advance in case we missed some important work. This is not intended to be a comprehensive review, but rather just a collection of some examples to illustrate the idea.

Parameterization and Prediction

The research group led by Matthew Sigman at the University of Utah has plenty of collaborative projects based upon parameterization and prediction.

This method is based on applying predictive statistical analysis to chemical reactions. They part from MM and DFT calculations to abstract properties or parameters of ligands or catalysis. Then they run statistics comparing these parameters to the experimental results obtained with each ligand or catalyst. They come up with models that allow predicting how other ligands, catalysts or substrates would behave.

It apparently it works!

A recent example is a collaboration with Mark Biscoe, in which they show how ligand parameterization allows finding the best ligands to perform a enantiodivergent (you can choose the enantiomer you want as product just by tuning the ligand) Pd-catalyzed C–C cross coupling reaction.

Holistic Predictions of Enantioselectivity

In 2019, Reid and Sigman reported a ground-breaking report on a model for holistic predictions of enantioselectivity in asymmetric catalysis.

As we stated in the introduction, a big part of a synthetic chemist job is to scan the literature to select some reaction conditions to test on a new substrate. This is clearly a job that a well-programmed computer should do better than a human being, especially when there are hundreds or thousands of possible conditions available.

This is a field that Sigman is pioneering, and awesome trends which allow for very significant predictions have already resulted from their efforts.

Many say that statistics, AI and machine learning could be the future of chemistry.

Machine Learning for Predicting Chemical Reactions

As Doyle group explains on their website, machine learning (which is basically statistics and computer science) can be the tool that will solve the problems of multidimensionality (which makes complex problems impossible for humans to analyze) inherent to chemical reactivity and structure.

In early 2018, Doyle reported in Science a collaborative work with Merck in which they developed a chemical model based on machine learning. They used a random forest model to predict the outcome of C–N cross coupling reactions.

Studying the Influence of Additive by Machine Learning

They mainly studied the influence of an additive (a family of isoxazoles) in one of the most useful reactions out there, the Buchwald-Hartwig amination.

A set of 15 different isoxazoles were used as “training set” (to obtain the linear regressions), and then another 8 of them were used as “test set”. Some examples are shown below, together with the corresponding regressions. As you can see, the data obtained with the test set correlates well with the “training regression”. Meaning that a good level of prediction is achieved.

Teaching Computers How to Do Fluorination

A similar concept was reported later that year by the same group, in which an awesome combination of HTS (high throughput screening) experiments and machine learning allowed developing a predictive model for the fluorination of alcohols with PyFluor. This resulted in a great expansion of the scope previously reported by Doyle and co-workers.

In the left, a schematic example of the type of HTS experiments run is displayed, showing how changes on the fluoride source and the base drastically affect the reaction yields.

The right graph shows all the results of observed yield vs. predicted yields. Very good correlations are obtained.

Are Robots Going to Take Our Jobs?

If by “our jobs” you mean by exclusively technical lab work as a chemist, the answer most likely.

But don’t get me wrong, I am nothing but optimistic about the future of chemistry. We need to embrace tools such as AI or robotics. They are here to free us from the most boring routine part of research, so we can focus in creativity to solve important problems.

On this particular matter, several research groups have been working on designing and constructing a chemical robot.

The Chemistry of the Future: Merging AI Planning with Robotic Synthesis

Timothy F. Jamison and Klavs F. Jensen from the Department of Chemistry of the Massachusetts Institute of Technology (MIT).

In 2018, they presented in Science their first version of a chemical synthesis robot. The basic idea of this machine is a complex flow chemistry system controlled by a software that allows optimizing multiple variables. So you can literally input the parameters that you want to optimize, feed the reagents, and wait until your optimization is complete. Then in a matter of days the scope of your transformation is also done.

This is how this synthesis robot looks like:

Fast-forward only one year, and this beast is where they are at:

The same MIT team published a couple of days ago a completely next-generation version of this chemical robot.

Now it is not just about chemical optimization. The synthetic system is fully integrated with an AI planning software.

This AI software is based in what we discussing over the entire article: taking data points out of thousands of published reactions, feeding them to complex algorithms, and getting optimal synthetic routes for a new or relevant target compound.

One can imagine that the third-generation of this system might even come up with its own ideas of what to synthesize. Who knows how far away we are from that…

The Future of Chemistry: Discovery Supported by Chemical Robots

The last example is mainly based upon flow chemistry systems. But some reactions are not suitable for flow. Traditional lab-scale organic synthesis is something that the Cronin group wanted to “digitalize”.

Leroy Cronin and co-workers have published in 2018 their views on howcan we use algorithms to aid discovery by using chemical robots. Not long after, in early 2019, this group working at The University of Glasgow reported some of their efforts on making such robot.

Cronin’s “Chemputer” is a modular robotic platform that allows carrying out the four basic steps of organic chemistry: reaction, work-up, isolation and purification.

For this purpose, it is equipped with pumps, reactors, filtering systems, automated separatory funnels, a rotavap, and of course, software to control all the process.

The following video allows getting an idea on how this system works:

This new system based on a “chemical programming language” allowed the synthesis of several medically relevant molecules, such as sildenafil or rufinamide.

Computer-assisted Total Synthesis of Complex Natural Products

You can argue that the targets selected to test the synthetic systems described above are not of very high complexity. Typical natural product synthetic problems tackled by the big groups are much more challenging.

But computers can also assist us with those! It is just a matter of how well can we integrate DFT-based high level computations with the methods described above. This kind of integration will be relevant in the future of chemistry.

An example of such prediction is the recent synthesis of Paspaline A and Emindole PB by Timothy Newhouse and co-workers.

In this work, the authors envisioned a biosynthetic approach to those natural structures, and though of 3 possible potential intermediates. All these 3 intermediates could in principle lead to the desired natural products.

But the chosen intermediate would have to cyclize with the appropriate selectivity. In case it didn’t, the synthesis of the corresponding intermediate would have been in vain (a problem that every chemist working on natural products synthesis has encountered).

As you can see below, the proposed structures are fairly similar, it would be almost gambling for a human being to predict the outcome of each cyclization. But the structural differences make them difficult to synthesize from a common intermediate.

First Steps on the Natural Products Chemistry of the Future

To tackle this problem, Newhouse’s group predicted via DFT calculation which of the three would cyclize the way they wanted. Once they had their theoretical answer, they prepared only that intermediate precursor (saving 2/3 of the synthetic efforts required). It ended up behaving as predicted, and they completed the total synthesis.

Before Newhouse, the group of Richmond Sarpong and co-workers had already applied a similar concept. They reported in 2015 the use of network-analysis to guide the retrosynthesis of very complex natural products.

Sarpong’s group applied network-analysis iteratively at the early stages of the synthetic planning of weisaconitine D and liljestrandinine, published in Nature. This allowed to come up with efficient disconnection

Even more recently, the same group of researchers published in J. Am. Chem. Soc. the total synthesis of the diterpenoid alkaloid arcutinidine.

This synthesis was also aided by this network-analysis, which is inspired by the initial work already performed by E. J. Corey back in the 80s.

I wanted to close with this last set of examples, because they are a great demonstration of what, in my opinion, would be the ideal future of AI and computing in organic chemistry.

“As scientists, AI should not replace us, but rather free us from routine and boring tasks, letting us focus on what is important: solving more complex and more important problems.” Click to Tweet This

I would love to hear from your opinion on AI and computers, and how they are going to affect how we see and approach chemistry (and science in general). After all, the future of chemistry is in our hands.

Feel free to post in the comment sections below!

The post What Is the Future of Chemistry? [Artificial Intelligence in Science] appeared first on Chemistry Hall.

Scientists have been working tirelessly to answer this question for hundreds of years ever since the first element, phosphorus, was discovered using scientific means by Hennig Brand in 1669. While Hennig’s initial intention wasn’t to discover a new element (he was actually trying to obtain gold from urine), his discovery was a jump-start to the scientific search for more elements.

The discovery of the majority of the elements on the periodic table over the course of the past 300 years has helped scientists to understand a great deal more about the composition of the universe (we are always trying to see and comprehend what’s making everything up).

However, these elements only represent a small percentage of what we actually know is out there. What makes up the rest of it? 

What is the Composition of the Universe?

So what is the universe made of?

What if I told you that an incredible 95% of the universe was made up of “stuff” that’s invisible to scientists with the current means at their disposal?

And because of this, they aren’t able to fully understand it or study it and can only work off of what they have theorized from observing the various parts of the universe that they CAN see. 

The Composition of the Universe: Dark Energy

Of this 95% of “stuff,” dark energy makes up a large portion of it. It accounts for 68% of the universe, to be exact. But what is dark energy, and why is there so much of it? 

Dark energy is an unknown form of energy that scientists believe is causing the universe to expand at an increasing rate. Scientists had originally hypothesized that the expansion of the universe would be decelerating due to the combined gravitational pull of objects on one another, but the exact opposite has been found. 

This video sums it up in great way:

Thanks to studies done by the Hubble space telescope on the expansion rate of the universe, they believe that this is happening due to an immense amount of dark energy working against the pull of gravity. These studies have led scientists to believe that dark energy far outweighs regular matter and dark matter, and this is how they determined the large percentage of the universe it makes up. 

Sixty-eight percent of the total universe is an incredible amount of energy to have out there expanding an already massive universe. Since it’s such a large and mysterious part of our universe, it’s no surprise that scientists have a variety of explanations for dark energy. 

The Composition of the Universe: Dark Matter

Now, what makes up the other 27% of the universe? While the name may be similar, dark matter is not related to dark energy except for the fact that it can’t be seen or studied by scientists, as it neither emits nor absorbs light. 

While dark energy is a force that is expanding the universe, dark matter is similar to regular matter in that it has an effect on gravity but it doesn’t exist in the form of matter that we are used to. 

If we can’t see it, how do we know it’s there? 

When they look at the motion of objects in space, they see gravitational effects too strong to be explained by the matter we see. Thus, scientists have determined that there must be some sort of dark matter out there. Since dark matter can’t be seen, it is simpler for scientists to look at it in terms of what it isn’t than what it is. NASA has determined that it can’t be normal matter in the form of dark clouds, as we would be able to detect the absorption of radiation passing through them. Nor can it be antimatter, since no gamma rays are produced from annihilating with matter. They also ruled out galaxy-sized black holes, as no gravitational lenses were noticed when encountering light. 

Weakly Interacting Massive Particles (WIMPs)

A common theory among scientists is that dark matter is made up of more exotic material, such as Weakly Interacting Massive Particles (WIMPs). 

A WIMP is an electromagnetically neutral subatomic particle. They are thought to be heavy and slow moving, and they don’t bump into each other like regular particles do, hence the “weakly interacting” name. Although WIMPs have been the best candidate for what makes up dark matter, some believe that the hopes for this to prove true have been dashed. 

The Small Part of the Universe That We Do Understand

Now that we’ve taken a look at the part of the universe that is, for all intents and purposes, invisible and far more mysterious than scientists would like, it’s time to explore the small portion of the universe that we are able to understand. 

The last 5% of the universe is made up of matter, which is defined as the substance or substances of which any physical object consists. 

To put it more simply, everything we know is made up of matter. From the computer you’re reading this on to the air you’re breathing to the food you’re about to have for dinner, all of it is made up of matter. 

What Makes Up Matter?

Matter can come in the form of a solid, gas, liquid, or plasma and is made up of atoms. These atoms make up the elements on the periodic table, which then combine into compounds to create everything we know. 

Now, let’s explore how much of this 5% of the universe the most common elements make up. 

The four most common elements that matter is composed of are hydrogen, helium, oxygen, and carbon. As we covered in our list of 100 chemistry facts, hydrogen accounts for an incredible 75% of all matter, with helium accounting for 23%, oxygen for 1%, and carbon for just 0.5%. The abundance of the rest of the elements begins to drop off after that, with many accounting for just <0.0001% of the of the small amount of matter in the universe. 

All these elements make up everything we see or touch. From our human body to all of the most dangerous chemicals in the world.

Why are hydrogen and helium the most abundant elements in the universe? 

That question can be answered by the Big Bang, which is what led to the formation of the universe. During this time, the lightest elements, hydrogen and helium, were created. Lithium and beryllium were made as well, but only in trace amounts. As stars formed and came together into galaxies, the rest of the elements were created through nuclear reactions and stellar explosions.

Stars begin as thin clouds of hydrogen gas that turn into large, dense spheres. Once the star reaches a certain size, nuclear fusion begins and creates the star’s incredible amount of energy. When hydrogen atoms are fused together, they transform into heavier elements like helium, oxygen, and carbon. 

However, Earth’s composition is quite different from that of the rest of the universe. While hydrogen and helium make up 98% of all the matter in the universe, their combined mass only accounts for less than 1% of Earth’s crust. The most abundant element on Earth is oxygen, which makes up 47% of Earth’s mass. Eight different elements account for 98.5% of Earth’s crust; the composition of the mantle and core will need more advanced research to be determined. 

So for now, much of the composition of the universe remains a mystery. But with the many advances in science, we can only hope that there will come a day when scientists are finally able to “see” the dark energy and dark matter that have confounded us for so long. 

About the author

Alan Bernau Jr. is the owner of Alan’s Factory Outlet, a family business he inherited from his father. When not running the business, he enjoys creating educational resources that touch on a variety of topics, such as science, nature, history, and space. You can find Alan on Twitter at @abernaujr. 

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Some of the most well-known forms of carbon are diamond (a) or graphite (b). Other allotropes are fullerenes (d, e, f), amorphous carbon (g) or carbon nanotubes (h).

But until today, it was not possible to characterize a cyclic molecular all-carbon ring. Researchers at University of Oxford teamed up with scientists at IBM, and resurrected this long-forgotten challenge.

The result is spectacular: a circle of 18 sp-hybridized carbon atoms, held together by alternating single and triple bonds.

The challenge of building such molecule is actually not new. In fact, the basis for this recent work were already established in 1990.

Initial Work Towards Cyclocarbon

At that time, while pursuing the synthesis of the same kind of cyclic carbon allotrope, cyclo[18]carbon, the group of François Diederich reported in the Journal of the American Chemical Society the synthesis of and characterization of a stable hexacobalt complex of this cyclic material.

This structurally peculiar coordination complex may seem to be really close to the desired all-carbon cyclic molecule, but this couldn’t be further from the truth.

In fact, almost 30 years passed since Diederich and his team made the initial steps towards this target, until today.

Synthesis and Characterization of the First Cyclic Carbon Allotrope

Fast-forward to 2019, P. Gawel, H. L. Anderson (Oxford University), L. Gross (IBM) and co-workers finally completed this challenge.

How did they do it? Basically they made a great use of Scanning Tunneling Microscopy (STM).

STM is a technique based in quantum tunneling. In STM, you usually deposit the molecule you want to study in a metal surface. Then a voltage is applied through a very small conducting tip, which allows electrons to “tunnel”, generating a current. Analyzing changes in the system, you can extract information and display it as images.

Thanks to the most recent advances in STM and atomic force microscopy (ATM), it is possible to obtain and see images of molecules with great resoluion.

Diederich group had developed the synthesis of several cyclocarbon oxides (shown as precursors in the pictures below).

Cyclocarbon oxide (C24O6), a triangular oxygenated molecule, was deposited on a bilayer of NaCl on a Cu(111) surface. Then it was submitted to low-temperature STM-AFM.

Under these conditions, the starting molecule loses CO as carbon monoxide. This process can occur multiple times, until the all-carbon 18-membered ring, cyclocarbon, is obtained. The molecule can be imaged in-situ (and therefore, characterized) at the same time. In this manner, the first cyclic allotrope of carbon was finally prepared.

The decarbonylation process takes place step by step (one molecule of CO at a time). This allows not only to see images of the final cyclocarbon, but also of several decarbonylated intermediates.

It is hard to tell if the resulting structure is “aromatic”, since classical Hückel rules cannot be applied to such complex systems. In fact, one could argue that this product is borderline between inorganic and organic chemistry.

Many scientist had tried before to make and observe this elusive structure. But why?

The Significance of the First Cyclic Carbon Allotrope

Well, for starters, initial studies on cyclo[18]carbon suggest that this new material can act as a semiconductor, which is the main appeal for the synthesis of new carbon allotropes, or other compounds such as polyaromatic hydrocarbons.

From a purely academic point of view, this specific structure is significantly less stable than any other of the well-known carbon allotropes. Therefore, it was a significant scientific challenge to overcome. It took 30 years and mastering modern techniques such as STM-AFM to actually see a molecule that many didn’t think we would see any time soon.

This discovery also allowed scientist to solve an old mistery. Are cyclic all-carbon molecules polyynic (alternating double and triple bonds) or cummulenic (consecutive double bonds)?

As you can see in the image below, the experimental image of the cyclic allotrope of carbon, perfectly matches with a predicted polyyne, made of alternating triple and single bonds.

So far this is very fundamental research, since these techniques only allow making “one molecule at a time”, and at under very specific conditions. This doesn’t allow actually preparing enough amount of material to test potential applications. However, this is a big leap forward in nanomaterials chemistry, and for sure this discovery will lead the scientific community to many relevant findings.

All credit to:

An sp-hybridized molecular carbon allotrope, cyclo[18]carbon. K. Kaiser, L. M. Scriven, F. Schulz, P. Gawel, L. Gross, H. L. Anderson Science 2019, doi: 10.1126/science.aay1914

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Confirming the actual structure of a molecule, is still a big challenge now-a-days. The advances in techniques such as NMR (Nuclear Magnetic Resonance) spectroscopy, or single-crystal X-ray diffraction have significantly helped speeding up this problem.

Molecular structure determination

Every month we get reports of chemical structures whose structures have to be reassigned or revised after some study (either synthetic or just based on characterization techniques) is carried out. On this regard, it is worth remarking the difference between scientific models and reality.

Truth is, even today, the methods for the characterization of molecules available to use routinely (which are explained in the most basic chemical bibliography), can be consider rather rudimentary, and of difficult interpretation for non-experts. Let me be honest, I am a trained PhD organic chemist and if I had to take a look at the NMR spectra of a complex natural product such as maitotoxin, I would probably have no clue what I am looking at.

Single crystal X-ray diffraction is probably the closest method to easily visualize the structure of a molecule in 3D. However, this is not a bulletproof method. The sample preparation (growing single crystals) required for this indirect technique, renders it useless for a wide variety of chemical compounds.

Can we actually see real molecules or atoms?

Accordingly, I would say that by today, there should already be a method that allows taking a direct microscopic “picture” of any compound you like, and immediately visualizing its structure in a screen. Apparently we are not quite there yet (in regards to “any compound”, keep reading). However, the answer may come under the name of atomic microscopy, and all of its variations.

Atomic force microscopy (AFM) or scanning force microscopy (SFM) is a very high resolution probe-microscopy technique. It allows us to actually “see” or “take real pictures” at the nanometer-scale, in which the molecular realm lies. A picture is worth 1000 words. In the example below, scientists make use of this technique to get pictures of a compound called naphthalenetetracarboxylic diimide. We can actually see a real molecule.

Much more recently, researchers at Oxford and IBM used STM-AFM to generate and visualize in situ the first cyclic allotrope of carbon, cyclo[18]carbon.

Seeing atoms in motion

The world of visualizing at the atomic level took a leap more than ten years ago. In 2008, a research group reported the imaging for the first time of light atoms and molecules on graphene. Subsequently, the same team managed to observe for the first time the actual movement of insolated graphene atoms in real time. The following movie from the Berkeley team shows the growth of a hole in a graphene sheet. For this experiment, a beam of electrons is focused to a specific spot on the graphene sheet, blowing out the focused carbon atoms making a hole. Besides, it can also be observed how the carbon atoms rearrange themselves (edge reconstruction) to adapt a more stable configuration.

The Boy And His Atom: The World’s Smallest Movie

The Guinness World Record for the “Smallest Stop-Motion Film” is held by a movie recorded by IBM scientists. Sometimes, nanophysicists also need to have a bit of fun, and what they decided is to “film” a movie by using scanning tunneling microscopy, a the result is in the following video:

By the use of this technique, the scientists managed to move a lot of molecules of carbon dioxide following their will. The result is a movie you can only see using a microscope that magnifies one hundred million times.

Direct observation of chemical reactions

Obviously, taking real pictures of molecules and atoms was just not enough for the scientific community. If we fast-forward to year 2013, atomic microscopy, more specifically, non-contact atomic force microscopy, allowed the direct imaging of molecular structures during a chemical reaction. Some results of these experiments published in the journal Science are displayed below. We cannot only see actual atoms molecules, we can observe directly chemical reactions!

AFM in structural determination

This field started as a cluster of isolated cases, but as the years went by, more and more examples of the application of this set of physical techniques are being constantly reported. The level at which the studied molecules can be observed is rather impressive. A recent example is the actual structural determination of a natural compound, breitfussin A. Several functional groups of the molecule were derived from classical spectroscopic data (a). Then, an AFM image (c) allowed observing the real structure of the molecule, placing each piece of the puzzle (a) in the correct spot. This established the previously unknown structure of the molecule (b).

Taking real pictures of complex chemical reactions

On the reactivity side of things, much more recently, it was possible to directly image the course of a reaction called the Bergman cyclization. This is one of the most fascinating rearrangements in chemistry. The chemical transformation is directly induced in the metal surface in which the atomic microscopy procedure is carried out.

However, as stated at the end of the introduction, not every molecule or reaction can be a candidate for a STM study as these. Several conditions need to be met. One of them (which might have already called your attention) is that the analyzed compounds need to be near-planar. These techniques rely on depositing the molecules of the compound in a planar metal surface, so planar molecules are the ones that give more interpretable data.

The search for the “Holy Grail” of structural determination

To finish this short essay that does not make justice to the whole field of molecular imaging, a recent application of what is called micro-electron diffraction (MicroED) will be discussed. This brilliant application of electron diffraction, allows overcoming probably the biggest problem on classical X-ray diffraction methods: the requirement of crystalline material of the molecule which structure wants to be elucidated.

This technique allows taking simple powder of any non-crystalline solid, without almost any sample preparation, and getting 3D structures of the powder nano-crystals in a matter of minutes, with extremely high resolutions. The structure of molecules with very high complexity, as thiostrepton, could be obtained unequivocally.

Is this the future of chemistry?

Can we see real atoms and molecules at this point? I would say that we definitely can. All the results that have been described in this article were published only over the last decade. Atomic microscopy seems to be here to stay, and it might be one of the tools that finally allows chemists to stop relying in rudimentary techniques for the determination of molecular structures. Only time will tell.

Stay tuned for more posts about the future of chemistry, share, and post your thoughts in the comment section!

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