What are Molecules?


For millennia, scientists have pondered the mystery of life – namely, what goes into making it? According to most ancient cultures, life and all existence was made up of the basic elements of nature – i.e. Earth, Air, Wind, Water, and Fire. However, in time, many philosophers began to put forth the notion that all things were composed of tiny, indivisible things that could neither be created nor destroyed (i.e. particles).

However, this was a largely philosophical notion, and it was not until the emergence of atomic theory and modern chemistry that scientists began to postulate that particles, when taken in combination, produced the basic building blocks of all things. Molecules, they called them, taken from the Latin “moles” (which means “mass” or “barrier”). But used in the context of modern particle theory, the term refers to small units of mass.


By its classical definition, a molecule is the smallest particle of a substance that retains the chemical and physical properties of that substance. They are composed of two or more atoms, a group of like or different atoms held together by chemical forces.

Both simple and complex organic (carbon-containing) molecules have been found in space. Carbon is formed in the cores of red giant stars, where it gets cycled to the surface and dispensed into space. Credit: IAC; original image of the Helix Nebula (NASA, NOAO, ESA, the Hubble Helix Nebula Team, M. Meixner, STScI, & T.A. Rector, NRAO
Artist’s impression of simple and complex organic (carbon-containing) molecules that have been found in space. Credit: IAC/NASA/NOAO/ESA/Hubble Helix Nebula Team/M. Meixner/STScI/T.A. Rector/NRAO

It may consist of atoms of a single chemical element, as with oxygen (O2), or of different elements, as with water (H2O). As components of matter, molecules are common in organic substances (and therefore biochemistry) and are what allow for life-giving elements, like liquid water and breathable atmospheres.

Types of Bonds:

Molecules are held together by one of two types of bonds – covalent bonds or ionic bonds. A covalent bond is a chemical bond that involves the sharing of electron pairs between atoms. And the bond they form, which is the result of a stable balance of attractive and repulsive forces between atoms, is known as covalent bonding.

Ionic bonding, by contrast, is a type of chemical bond that involves the electrostatic attraction between oppositely charged ions. The ions involved in this kind of bond are atoms that have lost one or more electrons (called cations), and those that have gained one or more electrons (called anions). In contrast to covalence, this transfer is termed electrovalance.

In the simplest of forms, covelant bonds take place between a metal atom (as the cation) and a nonmetal atom (the anion), leading to compounds like Sodium Chloride (NaCl) or Iron Oxide (Fe²O³) – aka. salt and rust. However, more complex arrangements can be made too, such as ammonium (NH4+) or hydrocarbons like methane (CH4) and ethane (H³CCH³).

Diagram of a water molecule, which is made up of two hydrogen atoms and one oxygen atom. Credit: britannica.com
Diagram of a water molecule, which is made up of two hydrogen atoms and one oxygen atom. Credit: britannica.com

History of Study

Historically, molecular theory and atomic theory are intertwined. The first recorded mention of matter being made up of “discreet units” began in ancient India where practitioners of Jainism espoused the notion that all things were composed of small indivisible elements that combined to form more complex objects.

In ancient Greece, philosophers Leucippus and Democritus coined the term “atomos” when referring to the “smallest indivisible parts of matter”, from which we derive the modern term atom.

Then in 1661, naturalist Robert Boyle argued in a treatise on chemistry – titled “The Sceptical Chymist“- that matter was composed of various combinations of “corpuscules”, rather than earth, air, wind, water and fire. However. these observations were confined to the field of philosophy.

It was not until the late 18th and early 19th century when Antoine Lavoisier’s Law of Conservation of Mass and Dalton’s Law of Multiple Proportions brought atoms and molecules into the field of hard science. The former proposed that elements are basic substances that cannot be broken down further while the latter proposed that each element consists of a single, unique type, of atom and that these can join together to form chemical compounds.

Various atoms and molecules as depicted in John Dalton's A New System of Chemical Philosophy (1808). Credit: Public Domain
Various atoms and molecules as depicted in John Dalton’s A New System of Chemical Philosophy (1808). Credit: Public Domain

A further boon came in 1865 when Johann Josef Loschmidt measured the size of the molecules that make up air, thus giving a sense of scale to molecules. The invention of the Scanning Tunneling Microscope (STM) in 1981 allowed for atoms and molecules to be observed directly for the first time as well.

Today, our concept of molecules is being refined further thanks to ongoing research in the fields of quantum physics, organic chemistry and biochemistry. And when it comes to the search for life on other worlds, an understanding of what organic molecules need in order to emerge from the combination of chemical building blocks, is essential.

We have written many interesting articles about molecules for Universe Today. Here’s Molecules From Space May Have Affected Life On Earth, Prebiotic Molecules May Form in Exoplanet Atmospheres, Organic Molecules Found Outside our Solar System, ‘Ultimate’ Prebiotic Molecules Found in Interstellar Space.

For more information, check out Encyclopaedia Britannica‘s page on molecules.

We’ve also recorded an entire episode of Astronomy Cast all about Molecules in Space. Listen here, Episode 116: Molecules in Space.


What Is John Dalton’s Atomic Model?

Atomic theory – that is, the belief that all matter is composed of tiny, indivisible elements – has very deep roots. Initially, the theory appeared in thousands of years ago in Greek and Indian texts as a philosophical idea. However, it was not embraced scientifically until the 19th century, when an evidence-based approach began to reveal what the atomic model looked like.

It was at this time that John Dalton, an English chemist, meteorologist and physicist, began a series of experiments which would culminate in him proposing the theory of atomic compositions – which thereafter would be known as Dalton’s Atomic Theory – that would become one of the cornerstones of modern physics and chemistry.

Continue reading “What Is John Dalton’s Atomic Model?”

Cool Infographic Compares the Chemistry of Planetary Atmospheres

Here on Earth we enjoy the nitrogen-oxygen atmosphere we’ve all come to know and love with each of the approximately 24,000 breaths we take each day (not to mention the surprisingly comfortable 14.7 pounds per square inch of pressure it exerts on our bodies every moment.) But every breath we take would be impossible (or at least quickly prove to be deadly) on any of the other planets in our Solar System due to their specific compositions. The infographic above, created by UK chemistry teacher Andy Brunning for his blog Compound Interest, breaks down — graphically, that is; not chemically — the makeup of atmospheres for each of the planets. Very cool!

In addition to the main elements found in each planet’s atmosphere, Andy includes brief notes of some of the conditions present.

“Practically every other planet in our solar system can be considered to have an atmosphere, apart from perhaps the extremely thin, transient atmosphere of Mercury, with the compositions varying from planet to planet. Different conditions on different planets can also give rise to particular effects.”

– Andy Brunning, Compound Interest

And if you’re thinking “hey wait, what about Pluto?” don’t worry — Andy has included a sort of postscript graphic that breaks down Pluto’s on-again, off-again atmosphere as well. See this and more descriptions of the atmospheres of the planets on the Compound Interest blog here.

Source: Compound Interest on Twitter

Where Should We Look for Life in the Solar System?

Emily Lakdawalla is the senior editor and planetary evangelist for the Planetary Society. She’s also one of the most knowledgeable people I know about everything that’s going on in the Solar System. From Curiosity’s exploration of Mars to the search for life in the icy outer reaches of the Solar System, Emily can give you the inside scoop.

In this short interview, Emily describes where she thinks we should be looking for life in the Solar System.

Follow Emily’s blog at the Planetary Society here.
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Continue reading “Where Should We Look for Life in the Solar System?”

Intelligent Alien Dinosaurs?

I for one welcome our alien dinosaur overlords…maybe.

Dinosaurs once roamed and ruled the Earth. Is it possible that similar humongous creatures may have evolved on another planet – a world that DIDN’T get smacked by an asteroid – and later they developed to have human-like, intelligent brains? A recent paper discussing why the biochemical signature of life on Earth is so consistent in orientation somehow segued into the possibility that advanced versions of T. Rex and other dinosaurs may be the life forms that live on other worlds. The conclusion? “We would be better off not meeting them,” said scientist Ronald Breslow, author of the paper.

The building blocks of terrestrial amino acids, sugars, and the genetic materials DNA and RNA have two possible orientations, left or right, which mirror each other in what is called chirality. On Earth, with the exception of a few bacteria, amino acids have the left-handed orientation. Most sugars have a right-handed orientation. How did that homochirality happen?

If meteorites carried specific types of amino acids to Earth about 4 billion years, that could have set the pattern the left-handed chirality in terrestial proteins.

“Of course,” Breslow said in a press release, “showing that it could have happened this way is not the same as showing that it did. An implication from this work is that elsewhere in the universe there could be life forms based on D-amino acids and L-sugars. Such life forms could well be advanced versions of dinosaurs, if mammals did not have the good fortune to have the dinosaurs wiped out by an asteroidal collision, as on Earth.”

But not everyone was impressed with the notion of dinosaurs from space. “None of this has anything to do with dinosaurs,” wrote science author Brian Switek in the Smithsonian blog Dinosaur Tracking. “As much as I’m charmed by the idea of alien dinosaurs, Breslow’s conjecture makes my brain ache. Our planet’s fossil record has intricately detailed the fact that evolution is not a linear march of progress from one predestined waypoint to another. Dinosaurs were never destined to be. The history of life on earth has been greatly influenced by chance and contingency, and dinosaurs are a perfect example of this fact.”

For further reading:
American Chemical Society paper
ACS press release
Dinosaur Tracking blog

Honoring Copernicus – Three New Elements Added To The Periodic Table


Today, November 4, 2011, the General Assembly of the International Union of Pure and Applied Physics (IUPAP) is meeting at the Institute of Physics in London, to approve the names of three new elements… one of which will honor the great Copernicus. Their names are: Element 110, darmstadtium (Ds), Element111, roentgenium (Rg) and Element 112. copernicium (Cn).

Are these new elements? Probably not. All the new ones were discovered long ago, but groups like IUPAC elect names to be used in scientific endeavors. Not only does this include the element, but new molecules which belong to it. As a general rule, these “new elements” are given names by their discoverer – which also leads to international debate. The elements can be named after a mythological concept, a mineral, a place or a country, a property or a very known scientist… even an astronomer!

As for element 112, this extremely radioactive synthetic element can only be created in a laboratory. Copernicium was created on February 9, 1996 by the Gesellschaft für Schwerionenforschung, but its original name – ununbium – didn’t get changed until almost two years ago when a German team of scientists provided enough information to prove its existence. When it was time to give it a moniker, the rules were that it had to end in “ium” and it couldn’t be named for a living person. On February 19, 2010, the 537th anniversary of Copernicus’ birth, IUPAC officially accepted the proposed name and symbol.

This “name calling” process comes from the Joint Working Party on the Discovery of Elements, which is a joint body of IUPAP and the International Union of Pure and Applied Chemistry (IUPAC). From there it is given to the General Assembly for approval. Dr. Robert Kirby-Harris, Chief Executive at IOP and Secretary-General of IUPAP, said, “The naming of these elements has been agreed in consultation with physicists around the world and we’re delighted to see them now being introduced to the Periodic Table.”

The General Assembly consists of 60 members from different countries. These delegates are elected from national academies and physical societies around the world. The five day meeting, which started session on Monday, October 31 will end today. The meeting included presentations from leading UK physicists, and the inauguration of IUPAP’s first female President, Professor Cecilia Jarlskog from the Division of Mathematical Physics at Lund University in Sweden.

Original Story Source: Institute of Physics News Release.

Atomic number

Fine Structure Constant


Ever wonder why the periodic table of elements is organized the way it is? Why, for example, does Hydrogen come first? And just what are these numbers that are used to sort them all? They are known as the element’s atomic number, and in the periodic table of elements, the atomic number of an element is the same as the number of protons contained within its nucleus. For example, Hydrogen atoms, which have one proton in their nucleuses, are given an atomic number of one. All carbon atoms contain six protons and therefore have an atomic number of 6. Oxygen atoms contain 8 protons and have an atomic number of 8, and so on. The atomic number of an element never changes, meaning that the number of protons in the nucleus of every atom in an element is always the same.

Arranging elements based on their atomic weight began with Ernest Rutherford in 1911. It was he who first suggested the model for an atom where the majority of its mass and positive charge was contained in a core. This central charge would be roughly equal to half of the atoms total atomic weight. Antonius van den Broek added to this by formerly suggesting that the central charge and number of electrons were equal. Two years later, Henry Moseley and Niels Bohr made further contributions that helped to confirm this. The Bohr model of the atom had the central charge contained in its core, with its electrons circulating it in orbit, much like how the planet in the solar system orbit the sun. Moseley was able to confirm these two hypotheses through experimentation, measuring the wavelengths of photon transitions of various elements while they were inside an x-ray tube. Working with elements from aluminum (which has an atomic number thirteen) to gold (seventy nine), he was able to show that the frequency of these transitions increased with each element studied.

In short, the higher the atomic number (aka. the higher the number of protons), the heavier the element is and the lower it appears on the periodic table. The atomic number of an element is conventionally represented by the symbol Z in physics and chemistry. This is presumably derived from the German word Atomzahl, which means atomic number in English. It is not to be confused with the mass number, which is represented by A. This corresponds to the combined mass of protons and neutrons in the element.

We have written many articles about the atomic number for Universe Today. Here’s an article about the atomic nucleus, and here’s an article about the Atom Models.

If you’d like more info on the Atomic Number, check out NASA’s Atoms and Light Energy Page, and here’s a link to NASA’s Atomic Numbers and Multiplying Factors Page.

We’ve also recorded an entire episode of Astronomy Cast all about the Atom. Listen here, Episode 164: Inside the Atom.

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Jefferson Lab
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What Is Atomic Mass

Faraday's Constant


The answer to ‘what is atomic mass’ is this: the total mass of the protons, neutrons, and electrons in a single atom when it is at rest. This is not to be associated or mistaken for atomic weight. Atomic mass is measured by mass spectrometry. You can figure the molecular mass of an compound by adding the atomic mass of its atoms.

Until the 1960’s chemists and physicists used different atomic mass scales. Chemists used a scale that showed that the natural mixture of oxygen isotopes had an atomic mass 16. Physicists assigned 16 to the atomic mass of the most common oxygen isotope. Problems and inconsistencies arose because oxygen 17 and oxygen 18 are also present in natural oxygen. This created two different tables of atomic mass. A unified scale based on carbon-12 is used to meet the physicists’ need to base the scale on a pure isotope and is numerically close to the chemists’ scale.

Standard atomic weight is the average relative atomic mass of an element in the crust of Earth and its atmosphere. This is what is included in standard periodic tables. Atomic weight is being phased out slowly and being replaced by relative atomic mass. This shift in wording dates back to the 1960’s. It has been the source of much debate largely surrounding the adoption of the unified atomic mass unit and the realization that ‘weight’ can be an inappropriate term. Atomic weight is different from atomic mass in that it refers to the most abundant isotope in an element and atomic mass directly addresses a single atom or isotope.

Atomic mass and standard atomic weight can be so close, in elements with a single dominant isotope, that there is little difference when considering bulk calculations. Large variations can occur in elements with many common isotopes. Both have their place in science today. With advances in our knowledge, even these terms may become obsolete in the future.

We have written many articles about atomic mass for Universe Today. Here’s an article about the atomic nucleus, and here’s an article about the atomic models.

If you’d like more info on the Atomic Mass, check out NASA’s Article on Analyzing Tiny Samples, and here’s a link to NASA’s Article about Atoms, Elements, and Isotopes.

We’ve also recorded an entire episode of Astronomy Cast all about the Atom. Listen here, Episode 164: Inside the Atom.

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What Is An Electron

Faraday's Constant


What is an electron? Easily put, an electron is a subatomic particle that carries a negative electric charge. There are no known components, so it is believed to be an elementary particle(basic building block of the universe). The mass of an electron is 1/1836 of its proton. Electrons have an antiparticle called a positron. Positrons are identical to electrons except that all of its properties are the exact opposite. When electrons and positrons collide, they can be destroyed and will produce a pair (or more) of gamma ray photons. Electrons have gravitational, electromagnetic, and weak interactions.

In 1913, Niels Bohr postulated that electrons resided in quantized energy states, with the energy determined by the spin(angular momentum)of the electron’s orbits and that the electrons could move between these orbits by the emission or absorption of photons. These orbits explained the spectral lines of the hydrogen atom. The Bohr model failed to account for the relative intensities of the spectral lines and it was unsuccessful in explaining the spectra of more complex atom. Gilbert Lewis proposed in 1916 that a ‘covalent bond’ between two atoms is maintained by a pair of shared electrons. In 1919, Irving Langmuir improved on Lewis’ static model and suggested that all electrons were distributed in successive “concentric(nearly) spherical shells, all of equal thickness”. The shells were divided into a number of cells containing one pair of electrons. This model was able to qualitatively explain the chemical properties of all elements in the periodic table.

The invariant mass of an electron is 9.109×10-31 or 5.489×10-4 of the atomic mass unit. According to Einstein’s principle of mass-energy equivalence, this mass corresponds to a rest energy of .511MeV. Electrons have an electric charge of -1.602×10 coulomb. This a standard unit of charge for subatomic particles. The electron charge is identical to the charge of a proton. In addition to spin, the electron has an intrinsic magnetic moment along its spin axis. It is approximately equal to one Bohr magneton. The orientation of the spin with respect to the momentum of the electron defines the property of elementary particles known as helicity. Observing a single electron shows the upper limit of the particle’s radius is 10-22 meters. Some elementary particles decay into less massive particles. But an electron is thought to be stable on the grounds that it is the least massive particle with non-zero electric charge.

Understanding what is an electron is to begin to understand the basic building blocks of the universe. A very elementary understanding, but a building block to great scientific thought.

We have written many articles about the electron for Universe Today. Here’s an article about the Electron Cloud Model, and here’s an article about the charge of electron.

If you’d like more info on the Electron, check out the History of the Electron Page, and here’s a link to the article about Killer Electrons.

We’ve also recorded an entire episode of Astronomy Cast all about the Composition of the Atom. Listen here, Episode 164: Inside the Atom.