Tag Archives: chemical reaction

Coldest chemical reaction reveals intermediate molecules in slow motion

When you chill things close to absolute zero, everything slows down to the point that even the vibration of atoms can come to a grinding halt. This is what researchers at Harvard achieved during an experiment in which they’ve generated the slowest chemical reaction yet. This allowed them to buy enough time to image intermediate chemical compounds that would have otherwise assembled into something else too fast for even our most advanced instruments to follow.

The coldest bonds in the history of molecular chemistry

A diagram showing the transformation of potassium-rubidium molecules (left) into potassium and rubidium molecules (right). Normally the intermediate (middle) step occurs too fast to see but new tech demonstrated by Harvard researchers managed to capture it for the first time. Credit: Ming-Guang Hu.

Absolute zero — the coldest possible temperature — is set at -273.15 °C or -459.67 °F. In experiments closer to room temperature, chemical reactions tend to slow down as the temperature decreases. As you cross into the ultra-cold realm, you’d expect no chemistry at all to happen — but that’s just not true.

Researchers at Harvard University chilled a gas made of potassium and rubidium atoms to just 500 nanoKelvin. For reference, this is millions of times colder than interstellar space.

Even at such frigid temperature, atoms and molecules still react — and they do so slowly enough for scientists to see everything. When the potassium and rubidium molecules interacted, researchers were able to image for the first time the four-atom molecule that was created in an intermediate step.

At room temperature, chemical reactions occur in just a thousandth of a billionth of a second. Previously, scientists used ultrafast lasers like fast-action cameras to snap images of the reactions as they occur. However, because the reaction time is so fast, this method cannot image the many intermediate steps involved in a typical chemical reaction.

“Most of the time,” said Ming-Guang Hu, a post-doc researcher at the department of chemistry and chemical biology at Harvard University and first author of the new study. “you just see that the reactants disappear and the products appear in a time that you can measure. There was no direct measurement of what actually happened in the middle.” 

In the future, scientists will be able to use a similar method to study other chemical reactions in minute detail. Observations aside, such a technique may also enable researchers to tamper with chemical reactions in a more controlled manner, with potential applications in the pharmaceutical, energy, and household product industries.

The findings were reported in the journal Science.

What’s the difference between ionic and covalent bonds

Every bit of matter around you is held together by chemical bonds. Sometimes, chemical bonds are broken, such as during a chemical reaction, only for atoms to bond again to form different molecules. Energy is always released to generate bonds and, likewise, energy is always required to break bonds.

There are two main types of chemical bonds: ionic and covalent.

What are ionic and covalent bonds?

Atoms bond together to form compounds because in doing so they attain lower energies than they possess as individual atoms, becoming more stable in the process. By the Law of Conservation of Energy, when a new chemical bond is formed, the chemical reaction releases an amount of energy (usually as heat) almost equal to the difference in the amounts of stored chemical energy between the products and the reactants. This stored chemical energy of the system, or heat content, is known as its enthalpy.

An ionic bond forms when two ions of opposite charges exchange electrons between them, where an ion is an atom that has either lost or gained an electron. Ions that loss one or more electrons have more protons than electrons, which means they have a positive charge. Such ions are called cations (metals). On the other hand, gaining electrons grants the ion a negative charge. Chemists refer to such ions as anions (non-metals).

Ionic compounds are typically neutral. Therefore, ions combine in ways that neutralize their charges.

A textbook example of an ionic compound is sodium chloride, also known as table salt. A single sodium atom has 11 protons and 11 electrons, but only a single electron in its outer shell (or valence shell). Chlorine is made up of 17 protons and 17 electrons, and has 7 electrons in its outer shell. When the two atoms react, sodium (electropositive) loses its valence electron to chlorine (electronegative). Now, in the resulting crystal structure, each sodium ion is surrounded by six chloride ions and each chloride ion is surrounded by six sodium ions. What’s more, each ion has a complete electron shell that corresponds to the nearest inert gas; neon for a sodium ion, argon for a chloride ion

Covalent bonds form when atoms or ions share electrons such that their outer shells become occupied. Covalent bonds, also called molecular bonds, only form between nonmetal atoms with identical or relatively close electronegativity value.  Electronegativity, denoted by the symbol χ, is a chemical property that describes the tendency of an atom to attract a shared pair of electrons (or electron density) towards itself.

The number of covalent bonds an atom can form is called the valence of the atom. This property represents the electrons of an atom that can participate in the formation of chemical bonds with other atoms. They are the furthest electrons from the nucleus.

A prime example of a covalent bond is the hydrogen molecule, which forms from two hydrogen atoms, each with one electron in their outer shell. Bond formation releases heat; therefore, it is exothermic. For the hydrogen molecule, the heat released during its formation, also known as the standard enthalpy change (ΔH°),  is −435 kJ per mole. The reverse process, breaking the H—H bond, requires 435 kJ per mole, a quantity called the bond strength.

Another classic example of a covalent bond is hydrogen chloride (HCl), which is a hydrogen halide. The chlorine atom has 7 atoms in its outer shell while hydrogen has 1 electron in its outer shell. Both combine perfectly so each atom fills their valence shells, forming a highly stable molecule. Now, the HCl molecule will not react further with other chlorine or hydrogen atoms.

Differences between ionic and covalent bonds

  • Covalent bonds are much more common in organic chemistry than ionic bonds.
  • In covalent bonds, atoms share electrons, whereas in ionic bonds atoms transfer electrons.
  • The reaction components of covalent bonds are electrically neutral, whereas for ionic bonds they are both charged. This explains why sodium chloride (salt) conducts electricity when dissolved — its components are charged.
  • Ionic bonds are much stronger than covalent bonds.
  • Covalent bonds are far more common in nature than ionic bonds. Most molecules in living things are covalently bonded, for instance.
  • Covalent bonds can form between atoms of the same elements (i.e. H2). However, ionic bonds cannot do this.
  • Covalent bonds are formed between two non-metals, whereas ionic bonds are formed between a metal and non-metal.
  • Molecules formed by covalent bonds have a low melting point, whereas those with ionic bonds have a high melting point. The same relationship exists for boiling point.
  • At room temperature, covalently bonded molecules are in the vast majority of cases liquids or gases, whereas ionic compounds are solid.

Similarities between ionic and covalent bonds

  • Both types of bonds lead to the formation of stable chemical compounds.
  • It takes exothermic reactions (i.e. that release heat) in order to create ionic and covalent bonds.
  • Valence electrons are involved in both bonding processes.
  • It doesn’t matter whether a molecule is formed through ionic or covalent bonding as far as its electrical charge is concerned: the result is always electrically neutral.

Scientists image chemical reactions to improve industrial chemistry

It can be quite difficult to visualize chemical reactions in real life, but modern science is here to help us once again. Alexander Riss, a chemist from the Max Planck Institute for the Structure and Dynamics of Matter, and his team managed to image several organic reactions, in an attempt to improve our understanding of chemical reactions used in industrial processes.

Visualizing a chemical reaction. Credits: Riss et al, 2016.

Visualizing a chemical reaction. Credits: Riss et al, 2016.

Organic chemistry is the bane of many high school students but it’s one of the cornerstones of our modern society. The chemical industry converts into raw materials more than 70,000 different products.

“Chemical transformations at the interface between solid/liquid or  solid/gaseous phases of matter lie at the heart of key industrial-scale manufacturing processes,” researchers write in the paper.

Understanding the microscopic mechanisms of these reactions is a great challenge, but could provide great improvements to the chemical industry. With that in mind, they employed a special microscopy technique called non-contact atomic force microscopy (nc-AFM).

“To obtain a better understanding of the different reaction pathways observed on the substrate surface, we determined the precise chemical structures of the adsorbates through high-resolution nc-AFM imaging.”

As microscopy techniques continue to develop, we’re getting a better and better look of these processes and being able to actually see a chemical reaction is simply mind blowing.

Journal Reference: Imaging single-molecule reaction intermediates stabilized by surface dissipation and entropy.

Chemists see molecule bond breaking and forming

Chemical bonds – the bane of all high school students. Many see chemistry as an abstract way of describing the world, but for some chemists, it’s a very practical thing. Using a special type of microscopy, researchers triggered and visualized a chemical reaction at the atomic level.

AFM (colorized images, top) visualizes the starting material, radical intermediates, and product from an STM-driven reaction (bottom). Image credits: Nature, via C&EN.

The team studied a version of the Bergman cyclization – an organic reaction and more specifically a rearrangement reaction taking place when an enediyne is heated in presence of a suitable hydrogen donor. Leo Gross of IBM Research Zurich and coworkers there and at the University of Santiago de Compostela used scanning tunneling microscopy (STM), a technique for nudging things at an atomic level taking advantage of a phenomenon called quantum tunneling. They then used atomic force microscopy (AFM) to image atomic-level details of that molecule as it formed. They managed to see its stages of formation as well as the final product.

The study “is a real breakthrough,” says Wolfram Sander of Ruhr University Bochum, a chemist who studies reaction intermediates. The ability to visualize and push the system in both reaction directions “is a great achievement,” he says.

The fact that they managed to both create and reverse is important. The technique could be applied to “initiate radical reactions by manipulating molecules at an atomic level” with potential applications in molecular electronics and subsequently electronic or medical devices.

Peter Chen of the Swiss Federal Institute of Technology (ETH) Zurich, also a reactive intermediates expert, notes that the technique also praised the results.

[It] “allows the chemist to initiate the reaction of a single molecule and then see the bonding changes in that very same molecule—not quite directly, but as close to directly as one can possibly imagine. This corresponds to the state of the art of what can be achieved” he said, referring to probe microscopy.

Journal Reference [open access]: Reversible Bergman cyclization by atomic manipulation.

The improved AFM developed at MIT. (c) MIT

New Atomic Force Microscope is x2,000 faster, images chemical reactions almost real time

MIT researchers made a huge upgrade to an instrument that’s indispensable in research today: the atomic force microscope (AFM).

The improved AFM developed at MIT. (c) MIT

The improved AFM developed at MIT. (c) MIT

The AFM is one of the most versatile and powerful microscopy technology for studying samples at nanoscale or million times smaller than the width of a human hair. Despite it can zoom in and a capture even the tinniest and subtlest details of a surface, its main limitation is that it takes too long to scan. As such, it can only be used for static shots. Dynamic events, like chemical reactions, can’t be imaged with AFM. I mean, they can, but just like when you use a DSLR on high exposure to take a picture of a moving car, it will all be a mess.

That’s set to change, as an upgraded version can scan samples 2,000 times faster — enough to image chemical reactions close to real time at 8 to 10 frames per second (real time is considered 30fps). The new instrument is based on the work of Iman Soltani Bozchalooi, now a postdoc at MIT’s Mechanical Engineering department, while still in his PhD days.

A classical AFM works by measuring force between a probe (a sort of needle) and the sample. The probe skims past the probe slowly tracing its topography nanometer by nanometer, like a blind person might read Braille by using his fingers to feel embossed patterns and surfaces. To scan the sample, the AFM moves it across a platform laterally and vertically beneath the probe. The platform or scanner as it’s called has to move slowly, line by line, to image the whole surface of the sample.

“If the sample is static, it’s ok to take eight to 10 minutes to get a picture,” says Kamal Youcef-Toumi, a professor of mechanical engineering at MIT. “But if it’s something that’s changing, then imagine if you start scanning from the top very slowly. By the time you get to the bottom, the sample has changed, and so the information in the image is not correct, since it has been stretched over time.”

The new upgrade makes use of smaller platforms that image samples over a smaller area, but makes up in speed. The main innovation centers on a multiactuated scanner and its control: a sample platform incorporates a smaller, speedier scanner as well as a larger, slower scanner for every direction, which work together as one system to scan a wide 3D region at high speed. Of course, such attempts were made before but scientists couldn’t sync multiple scanners working together, so a single platform AFM that slowly, but steadily works has remained the norm for years.

chemical reaction AFM

The MIT researchers solved this challenge by developing control algorithms that take into account the effect of one scanner on the other.

“Our controller can move the little scanner in a way that it doesn’t excite the big scanner, because we know what sort of motion triggers this scanner, and vice versa,” Bozchalooi says. “In the end, they’re working in synchrony, so from the perspective of the scientist, this scanner looks like a single, high-speed, large-range scanner that does not add any complexity to the operation of the instrument.”

MIT researchers demonstrated the new AFM by scanning a  70- by-70-micron sample of calcite as it was first immersed in deionized water and later exposed to sulfuric acid. Scientists could see the acid eating away at the calcite, expanding existing nanometer-sized pits in the material that quickly merged and led to a layer-by-layer removal of calcite along the material’s crystal pattern, over a period of several seconds. You couldn’t had possibly see this kind of chemical interaction with a simple AFM.

“People can see, for example, condensation, nucleation, dissolution, or deposition of material, and how these happen in real-time — things that people have never seen before,” Youcef-Toumi says. “This is fantastic to see these details emerging. And it will open great opportunities to explore all of this world that is at the nanoscale.”

The device could help researchers visualize chemical reactions and trigger breakthroughs in fields like battery research, medicine and material science. MIT is thinking about speeding up the AFM even further. “We want to go to real video, which is at least 30 frames per second, Youcef-Toumi says.

Chemical reaction

Chemistry doesn’t suck, Chemistry is Beautiful! [Incredible reactions shot with 4K UltraHD resolution]

The Tsinghua University Press and University of Science and Technology of China partnered to release an amazing video which zooms on various chemical reactions  at ultraHD resolution. Using  advanced computer graphics and state-of-the-art interactive technology, a group of 3D artists in Shanghai created this extraordinary short animation to express their impression of chemical structures. Check out the result in the embedded video below and find out more at the “Chemistry is Beautiful” project website.

Chemical reaction

chemical reaction

chemical reactions


This scanning tunnelling microscopy image shows how iron atoms and organic molecules become ordered in patterns on a gold substrate. (c) Nature Comm

Cheap and easy to make catalyst could replace platinum in fuel cells

Fuel cells are absolute wonders of technology – electrochemical systems that directly convert the chemical energy of a fuel (hydrogen and oxygen) into electricity and heat. There’s no combustion, and consequently fuel cells aren’t limited by the same thermodynamic cycles as a typical heat engine. A theoretical efficiency of 70% is thus reached – which is staggering compared to burning fossil fuels. There are numerous hurdles that have prevented so far the hydrogen economy via fuel cells from booming. One such difficulty is the expensive use of platinum as catalysts in the fuel cell.

Researchers at the Max Planck Institute for Solid State Research in Stuttgart report they’ve made a new type of catalyst based on earth-abundant metals (iron and manganese) embedded into organic molecules. The researchers hope the catalyst may be employed as a substitute to platinum, the expensive noble metal.

[ALSO READ] New, affordable fuel cells could spark micro-grid revolution 

A new catalyst for fuel cells

This scanning tunnelling microscopy image shows how iron atoms and organic molecules become ordered in patterns on a gold substrate. (c) Nature Comm

Iron atoms and organic molecules become ordered in patterns on a gold substrate. (c) Nature Comm

Platinum has proven to be essential in driving the key oxygen reduction reaction at the anode side of the fuel cell. Here, oxygen molecules combine cu hydrogen ions and electrons to form water and heat, while an external circuit funnels electrons to an fro the two electrodes, driving an electrical current in the process. Typically, oxygen can combine with either two or four electrons, depending on whether it reacts directly with hydrogen or via an intermediate hydrogen peroxide molecule to form water.

The type of electrochemical conversion we see in fuel cells is far from being an unique man-made wonder. The process can be seen in nature, employed by various biological entities including inside us, humans. As we breath in fresh air, enzymes – which are basically natural catalysts – help drive a combination reaction between oxygen and hydrogen producing energy. The researchers at Max Planck sought inspiration from similar enzymes to replicate in an artificial system of their own.

Such oxygen-reducing enzymes contain metals like iron and manganese, while organic molecules act like sort of anchors for the metals, holding them tight for oxygen to easily bind with them. Klaus Kern and his staff member Doris Grumelli from the Max Planck Institute for Solid State Research vaporized iron and manganese atoms together with organic molecules, in a high vacuum environment, and deposited these on a gold substrate. The resulted molecules auto-assembled and became ordered in patterns that strongly resemble the functional centres of enzymes.

Reducing oxygen – the key

Schematic shows how iron atoms (blue) and the organic molecules (green, black) form a lattice pattern on the gold substrate. (c) Nature Comm

Schematic shows how iron atoms (blue) and the organic molecules (green, black) form a lattice pattern on the gold substrate. (c) Nature Comm

After a bit of toying around for a solution to move the samples into a liquid (transferring samples from high vacuum can be tricky), the researchers eventually landed these on an electrodes surface. It turned out that the catalytic activity depended of the kind of metallic centre, while, on the other hand, the stability of the structure depended on the type of organic molecules that form the network. Iron atoms led to a two-level reaction via the intermediate hydrogen peroxide molecule, while manganese atoms produced a direct reaction of oxygen to water. The reactions took place in an alkaline medium.

Scientists are more interested in a direct reaction, since it’s more efficient, however a hydrogen peroxide reaction could be useful in other applications rather than fuel cells, like biosensors. In any even, the researchers pride themselves with having made a nano-catalyst that is easy to make (vapor deposition is a heavily employed method in the industry) and cheap (readily available metals and organics).

Findings were reported in the journal Nature Communications.

Diagram illustrates the newly-discovered reaction that transforms molecules of ketohydroperoxide into acids and carbonyl molecules, after going through intermediate stages. ILLUSTRATION COURTESY OF JALAN ET AL

New type of oxidation chemical reaction revealed

Since the study of modern chemistry was initiated, only 36 basic types of chemical reactions have been fully described. Recently, researchers at MIT, building on the work of another study published 30 years ago, have fully described the mechanisms of a 37th reaction –  a low-temperature oxidation that results in the decomposition of complex organic molecules known as gamma-ketohydroperoxides. The reaction is an important part of atmospheric reactions that lead to the formation of climate-affecting aerosols; biochemical reactions that may be important for human physiology; and combustion reactions in engines.

Stephen Klippenstein, a senior scientist at the Argonne National Laboratory in Illinois who was not involved in this research, says, “I think this may be the best paper I have read this year. It uses a multitude of theoretical methods … to explore multiple aspects of a novel discovery that has important ramifications in atmospheric chemistry, combustion kinetics and biology.”

Diagram illustrates the newly-discovered reaction that transforms molecules of ketohydroperoxide into acids and carbonyl molecules, after going through intermediate stages.  ILLUSTRATION COURTESY OF JALAN ET AL

Diagram illustrates the newly-discovered reaction that transforms molecules of ketohydroperoxide into acids and carbonyl molecules, after going through intermediate stages.

Stefan Korcek, and engineer for Ford Motor Company, first described the reaction some 30 years ago, prompted by the need to better understand  how engine oils break down through oxidation – a major factor that contributes to oil waste. Since waste oil is among the largest hazardous waste streams in the United States, understanding the chemical mechanisms that lead to its degradation is very important. In his paper, Korcek outlined an unusually complex multipart reaction, whose products included carboxylic acids and ketones, and made some predictions on how the reaction takes place step-by-step. Nobody took the interest, however, to verify these findings. Not until MIT graduate student Amrit Jalan, chemical engineering professor William Green, and six other researchers decided to take a thorough look.

Jalan says that the MIT researchers’ analysis came about almost by accident. “I was looking at that paper for a different study,” he says, “and I came across [Korcek’s] work, which hadn’t been verified either theoretically or experimentally. … [We] decided to see if we could explain his observations by throwing quantum mechanical tools at the problem.”

The researchers’s through analysis revealed in detail how the reaction takes place. Remarkably, Korcek’s predictions were on par, albeit  part of the process differs slightly from Korcek’s original hypothesis. Green points out that because this is an entirely new type of reaction, it opens the door to research on other variations.

“Once you discover a new type of reaction, there must be many similar ones,” he says.

“It’s very odd to have so many reactions at once in such a small molecule,” Green adds. “Now that we know that can happen, we’re searching for other cases.”

What’s so special about this reaction? First of all, it’s a newly fully described chemical reaction. Understanding in full detail what goes on at a molecular level in a compound subjected to various environmental stimuli is paramount to science. Regarding practical applications, biofuel technology might be the first to benefit from the new findings. Various kinds of biofuels oxidize differently — sometimes producing toxic or corrosive byproducts —  and by applying this new found understanding of degradation following oxidation might help scientists pin down the best fuel types worth pursuing.

Like all organic matter, the human body suffers oxidation as well contributing to the tissue damage and aging.

Anthony Dean, dean of the College of Applied Science and Engineering at the Colorado School of Mines, who was not involved in this work, says, “A particularly nice aspect of this work is to then consider how this finding might be applicable to other systems. In a broader context, this combined effort by two very prominent research groups illustrates the power and potential for electronic structure calculations [in] quantitatively important problems in chemical kinetics.”

Klippenstein adds, “As a result of this clear exposition and the high level of theory that was applied, I believe this work will be widely accepted immediately. I certainly am already convinced by their conclusions.”

J. Am. Chem. Soc., 2013, 135 (30), pp 11100–11114 , DOI: 10.1021/ja4034439