Silicon-capped hydrocarbons: Mysterious molecules in space

This graph shows absorption wavelength as a function of the number of carbon atoms in the silicon-terminated carbon chains SiC_(2n+1)H, for the extremely strong pi-pi electronic transitions. 

When the chain contains 13 or more carbon atoms, not significantly longer than carbon chains already known to exist in space, these strong transitions overlap with the spectral region occupied by the elusive diffuse interstellar bands. 

Credit: D. Kokkin, ASU

Over the vast, empty reaches of interstellar space, countless small molecules tumble quietly though the cold vacuum.

Forged in the fusion furnaces of ancient stars and ejected into space when those stars exploded, these lonely molecules account for a significant amount of all the carbon, hydrogen, silicon and other atoms in the universe.

In fact, some 20 percent of all the carbon in the universe is thought to exist as some form of interstellar molecule.

Many astronomers hypothesize that these interstellar molecules are also responsible for an observed phenomenon on Earth known as the "diffuse interstellar bands," spectrographic proof that something out there in the universe is absorbing certain distinct colours of light from stars before it reaches the Earth.

But since we don't know the exact chemical composition and atomic arrangements of these mysterious molecules, it remains unproven whether they are, in fact, responsible for the diffuse interstellar bands.

Now in a paper appearing this week in The Journal of Chemical Physics, from AIP Publishing, a group of scientists led by researchers at the Harvard-Smithsonian Center for Astrophysics (CfA) in Cambridge, Mass. has offered a tantalising new possibility: these mysterious molecules may be silicon-capped hydrocarbons like SiC3H, SiC4H and SiC5H, and they present data and theoretical arguments to back that hypothesis.

At the same time, the group cautions that history has shown that while many possibilities have been proposed as the source of diffuse interstellar bands, none has been proven definitively.

"There have been a number of explanations over the years, and they cover the gamut," said Michael McCarthy a senior physicist at the Harvard-Smithsonian Center for Astrophysics (CfA) who led the study.

Molecules in Space and How We Know They're There
Astronomers have long known that interstellar molecules containing carbon atoms exist and that by their nature they will absorb light shining on them from stars and other luminous bodies.

Because of this, a number of scientists have previously proposed that some type of interstellar molecules are the source of diffuse interstellar bands, the hundreds of dark absorption lines seen in color spectrograms taken from Earth.

In showing nothing, these dark bands reveal everything. The missing colours correspond to photons of given wavelengths that were absorbed as they travelled through the vast reaches of space before reaching us.

More than that, if these photons were filtered by falling on space-based molecules, the wavelengths reveal the exact energies it took to excite the electronic structures of those absorbing molecules in a defined way.

Armed with that information, scientists here on Earth should be able to use spectroscopy to identify those interstellar molecules, by demonstrating which molecules in the laboratory have the same absorptive "fingerprints."

But despite decades of effort, the identity of the molecules that account for the diffuse interstellar bands remains a mystery.

Nobody has been able to reproduce the exact same absorption spectra in laboratories here on Earth.

"Not a single one has been definitively assigned to a specific molecule," said Neil Reilly, a former postdoctoral fellow at Harvard-Smithsonian Center for Astrophysics (CfA) and a co-author of the new paper.

Now Reilly, McCarthy and their colleagues are pointing to an unusual set of molecules, silicon-terminated carbon chain radicals, as a possible source of these mysterious bands.

As they report in their new paper, the team first created silicon-containing carbon chains SiC3H, SiC4H and SiC5H in the laboratory using a jet-cooled silane-acetylene discharge.

They then analysed their spectra and carried out theoretical calculations to predict that longer chains in this family might account for some portion of the diffuse interstellar bands.

However, McCarthy cautioned that the work has not yet revealed the smoking gun source of the diffuse interstellar bands.

To prove that these larger silicon capped hydrocarbon molecules are such a source, more work needs to be done in the laboratory to define the exact types of transitions these molecules undergo, and these would have to be directly related to astronomical observations.

But the study provides a tantalising possibility for finding the elusive source of some of the mystery absorption bands, and it reveals more of the rich molecular diversity of space.

"The interstellar medium is a fascinating environment," McCarthy said. "Many of the things that are quite abundant there are really unknown on Earth."

More information: The Journal of Chemical Physics, July 29, 2014. DOI: 10.1063/1.4883521

Magnifying the Universe - Video

Copyright 2012. Magnifying the Universe by Number Sleuth.

H3+: The Molecule that Made the Universe

The molecule known as H3+ is believed to have had a vital role in cooling down the first stars of the universe, and may still play an important part in the formation of current stars. Above, new stars burst into being in the star-forming nebula Messier 78, imaged by NASA's Spitzer Space Telescope. (Image credit: NASA/JPL-Caltech)

In a study that pushed quantum mechanical theory and research capabilities to the limit, UA researchers have found a way to see the molecule that likely made the universe - or at least the hot and fiery bits of it.

Lurking in the vast, chilly regions between stars, the unassuming molecule known as a triatomic hydrogen ion, or H3+, may hold secrets of the formation of the first stars after the Big Bang.

At the University of Arizona, then doctoral candidate Michele Pavanello spent months doing painstaking calculations to find a way to spot H3+ and unveil its pivotal role in astronomy and spectroscopy, supervised by Ludwik Adamowicz, a professor in the UA's department of chemistry and biochemistry.

The groundbreaking results have been published in a recent edition of Physical Review Letters.

"Most of the universe consists of hydrogen in various forms," said Adamowicz, "but the H3+ ion is the most prevalent molecular ion in interstellar space. It's also one of the most important molecules in existence."

Believed to be critical to the formation of stars in the early days of the universe, H3+ also is the precursor to many types of chemical reactions, said Adamowicz, including those leading to compounds such as water or carbon, which are essential for life.

Early stars would have become hotter and hotter until they exploded before they ever formed, according to Pavanello, unless there was a way to release some of that pent-up energy.

"There wouldn't be any star formation if there weren't molecules that slowly cool down the forming star by emitting light," said Pavanello. Not many molecules can do that, he added, partly because very few molecules existed in the early days of the universe.

"Astronomers think that the only molecule that could cool down a forming star in that particular time is H3+."

A perfect asymmetry
Another molecule, molecular hydrogen, would have been present, but it would have had a much harder time cooling a forming star than H3+. "Hydrogen does not like to emit light, while H3+ can bend and vibrate, and in doing so it is able to emit light." said Pavanello.

H3+ is an electrically charged molecule, called an ion. It consists of three hydrogen atoms with only two, as opposed to a healthy three, electrons to share between them. Lacking a negatively charged electron, the molecule takes on a plus-one positive charge.

H3+ has a triangular shape, explained Adamowicz. "As it is excited it starts to vibrate in various ways."

"One has to involve a large amount of computations at the quantum mechanical level to predict those vibrations," said Adamowicz. "The role of theory is essentially to simulate those vibrations in the computer and then describe how the molecule is swinging or dancing."

Understanding the various vibrations of H3+ could help astronomers deduce to what extent it played a role in the formation of the early stars.

"In the 1990s, H3+ was observed surrounding stars," said Adamowicz. "The stars emit radiation, which not only contributes to the production of H3+ but also excites the molecule to higher energy states. The molecule can also become excited through leftover energy from chemical reactions it was involved in or through collisions with other molecules. In the process of de-excitation the molecule emits photons that are detected by our radio telescopes."

"That can only happen with H3+ because molecular hydrogen is too symmetric," said Pavanello. "And so H3+ has a very important cooling function in the formation of the first stars after the Big Bang."

"The only way we can predict how the stars form is if we know very well what the cooling abilities of H3+ are, and we cannot know its cooling ability until we know its vibrational spectrum. We need to know what these energy levels are," said Pavanello.

"With this paper we have pinpointed the energy levels up to a certain energy threshold that is already good enough to generate accurate predictions of the cooling ability of H3+," said Pavanello.

It happened almost by chance
The group didn't set out to unlock the secrets of H3+, said Pavanello, who graduated from the UA in 2010 with a prestigious Marie Curie post-doctoral fellowship that took him to Leiden University in the Netherlands. He is now an assistant professor of theoretical chemistry at Rutgers University in Newark, N.J.

"It all happened almost by chance," he said. "A friend of the mass-spectrometry facility in the UA's chemistry department happens to be a very good quantum chemist from Hungary. He once visited the department and talked to Ludwik about the possibility to do some H3+ calculations. At the time, I had just started. The code I was writing was almost done, and we thought H3+ could be a good system on which to test this code."

The researchers input a computer code into super computers at the UA's High Performance Computing Center that described the ways in which H3+ vibrates according to quantum mechanical principles. "We couldn't have done this without their support," said Pavanello.

Depending on the level of approximations made in the computer code, said Pavanello, the researchers can develop software that can describe the motion of small molecules very well, or large molecules very approximately.

"We decided to implement something that had essentially no approximations, but of course with the price that we can only apply it to very small molecules," said Pavanello. "Our method simply did not exist before in a mainstream form."

The UA team's results were corroborated by teams from Hungary, France, London and Russia, and also by experiments done at the Max-Planck Institute in Heidelberg, Germany that created H3+ in a laboratory and verified that its spectral lines matched the predictions.

The UA team's contribution allowed the researchers for the first time to assign spectral lines of H3+ to particular types of the vibrational motions as the ion releases photons with near-visible wavelengths. These wavelengths contribute to the color of the light H3+ radiates toward us from interstellar space.

Astrobiologists Discover Sweet Spots For Formation of Complex Organic Molecules

Scientists within the New York Center for Astrobiology at Rensselaer Polytechnic Institute have compiled years of research to help locate areas in outer space that have extreme potential for complex organic molecule formation.

The scientists searched for methanol, a key ingredient in the synthesis of organic molecules that could lead to life.

Their results have implications for determining the origins of molecules that spark life in the cosmos.

The findings will be published in the Nov. 20 edition of The Astrophysical Journal in a paper titled "Observational constraints on methanol production in interstellar and preplanetary ices."

The work is collaboration between researchers at Rensselaer, NASA Ames Research Center, the SETI Institute, and Ohio State University.

"Methanol formation is the major chemical pathway to complex organic molecules in interstellar space," said the lead researcher of the study and director of the NASA-funded center, Douglas Whittet of Rensselaer.

If scientists can identify regions where conditions are right for rich methanol production, they will be better able to understand where and how the complex organic molecules needed to create life are formed.

In other words, follow the methanol and you may be able to follow the chemistry that leads to life.

Using powerful telescopes on Earth, scientists have observed large concentrations of simple molecules such as carbon monoxide in the clouds that give birth to new stars.

To make more complex organic molecules, hydrogen needs to enter the chemical process. The best way for this chemistry to occur is on the surfaces of tiny dust grains in space, according to Whittet.

In the right conditions, carbon monoxide on the surface of interstellar dust can react at low temperatures with hydrogen to create methanol (CH3OH).

Methanol then serves as an important steppingstone to formation of the much more complex organic molecules that are required to create life.

Scientists have known that methanol is out there, but to date there has been limited detail on where it is most readily produced.

What Whittet and his collaborators have discovered is that methanol is most abundant around a very small number of newly formed stars. Not all young stars reach such potential for organic chemistry.

In fact, the range in methanol concentration varies from negligible amounts in some regions of the interstellar medium to approximately 30 percent of the ices around a handful of newly formed stars.

They also discovered methanol for the first time in low concentrations (1 to 2 percent) in the cold clouds that will eventually give birth to new stars.

The scientists conclude in the paper that there is a "sweet spot" in the physical conditions surrounding some stars that accounts for the large discrepancy in methanol formation in the galaxy.

The complexity of the chemistry depends on how fast certain molecules reach the dust grains surrounding new stars, according to Whittet.

The rate of molecule accumulation on the particles can result in an organic boom or a literal dead end.

Ultra high speed film - Femtoseconds

How fast an intense laser pulse can change the electrical properties of solids is revealed by researchers from Kiel University in the current edition of Nature (09.03.2011). Scientists in the team of Professor Michael Bauer, Dr. Kai Roßnagel and Professor Lutz Kipp from the Institute of Experimental and Applied Physics, together with colleagues from the University of Kaiserslautern and the University of Colorado in Boulder, U.S.A., are following the course of electronic switching processes which occur within fractions of a second (femtoseconds).


The results of their research may trigger future developments of custom-made and ultra fast opto-electronic components in order to increase data transmission rates or to accelerate optical switches, to name just one example of potential areas of application.

“These techniques that we have developed enables us to record films of extremely fast processes in a much more comprehensive manner than it was previously possible with similar techniques”, Bauer explains. “We are able to, for example, directly track phase transitions in solids or catalytic reactions on surfaces.”


To record the films, the Kiel scientists used ultra short flashes of light in the soft x-ray spectral region generated with a specific laser system. Bauer: “The amount of information gained from our pictures when played back in slow motion is vast.

We will get completely new insights into most relevant electronic properties of solids which are important for a variety of current and future technologies, for example, in telecommunications.”

The Christian-Albrechts-Universität zu Kiel (CAU) has proven international expertise as a North German research university in the field of nanosciences and surface science, for example, in the German Research Foundation’s Collaborative Research Centre 855 “Magnetoelectric Composites — Future Biomagnetic Interfaces”.

Furthermore, the CAU is applying for the current round of the Excellence Initiative with the excellence cluster “Materials for Life”.

Background information:

Femto means “one part in a thousand million million”. When, for example, molecules react with one another or when the switching states in electronic components change, processes at the atomic length scale are involved which take place on time scales of femtoseconds.

Ultra short laser pulses in the so-called “soft x-ray spectral region” — i.e. light with very short wavelengths — enables one to make snapshots of the electronic states which are transiently formed during a switching process, for example.

The shots are combined in series to deliver a film depicting such switching processes with a level of detail and a temporal resolution which could previously not be achieved.

Original Paper:
www.nature.com/nature under: 10.1038/nature09829

Scientists Create World's First Molecular Transistor

Scientists Create World's First Molecular Transistor

A group of scientists has succeeded in creating the first transistor made from a single molecule. The team, which includes researchers from Yale University and the Gwangju Institute of Science and Technology in South Korea, published their findings in the December 24 issue of the journal Nature.

The team, including Mark Reed, the Harold Hodgkinson Professor of engineering and Applied Science at Yale, showed that a benzene molecule attached to gold contacts could behave just like a silicon transistor.

The researchers were able to manipulate the molecule's different energy states depending on the voltage they applied to it through the contacts. By manipulating the energy states, they were able to control the current passing through the molecule.

"It's like rolling a ball up and over a hill, where the ball represents electrical current and the height of the hill represents the molecule's different energy states," Reed said. "We were able to adjust the height of the hill, allowing current to get through when it was low, and stopping the current when it was high." In this way, the team was able to use the molecule in much the same way as regular transistors are used.

Non-Bees Stinging Tumours

They're called "nanobees," and they're not insects -- they're tiny particles designed to destroy cancer cells by delivering a synthesized version of toxin called melittin that is found in bees.

"Melittin, which would otherwise result in substantial destruction of your red blood cells and other normal tissues if it were delivered intravenously alone, is completely safe when it's on a nanoparticle," said Dr. Samuel Wickline, director of the Siteman Center of Cancer Nanotechnology Excellence at Washington University in St. Louis, Missouri.

Nanobees are one of the latest examples of how nanotechnology may change the way diseases are treated.

Nanotechnology encompasses a wide array of innovations that make use of structures that are 100 nanometers or smaller. That means they generally cannot be seen under a regular microscope, but are larger than individual atoms. For example, a nanobee is less than 10 times diameter of a red blood cell, Wickline said.

Particles on the nanoscale are small enough to enter cells, but big enough to carry large doses of drugs, said Robert Langer, Institute professor at the Massachusetts Institute of Technology and a leader in the nanotech field. Watch MIT researchers talk about nanotechnology

"We are gradually forming a pipeline of nanotechnology-based products," said Piotr Grodzinski, director of the National Cancer Institute's Alliance for Nanotechnology in Cancer, a program that funds eight Centers of Cancer Nanotechnology Excellence in the U.S., including Wickline's and Langer's research initiatives. "These things are happening as we speak."

There have already been two approved cancer treatments on the market that make use of nanoparticles: ovarian cancer drug Doxil, approved in 1995, and breast cancer drug Abraxane, approved in 2005. Both of these involve medication bound with nanoparticles that circulate in the bloodstream for longer than conventional drugs and are expected to migrate to the tumor site, Grodzinski said. These drugs are being tested in some of the eight clinical trials associated with the NCI nano program.