Archive for the ‘Chemistry’ Category

Quantum tunnelling enables ‘impossible’ space chemistry

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Accelerated chemistry in the reaction between the hydroxyl radical and methanol at interstellar temperatures facilitated by tunnelling
Robin J. Shannon, Mark A. Blitz, Andrew Goddard & Dwayne E. Heard
Understanding the abundances of molecules in dense interstellar clouds requires knowledge of the rates of gas-phase reactions between uncharged species.
However, because of the low temperatures within these clouds, reactions with an activation barrier were considered too slow to play an important role.
Here we show that, despite the presence of a barrier, the rate coefficient for the reaction between the hydroxyl radical (OH) and methanol—one of the most abundant organic molecules in space—is almost two orders of magnitude larger at 63 K than previously measured at ∼200 K.
We also observe the formation of the methoxy radical product, which was recently detected in space.
These results are interpreted by the formation of a hydrogen-bonded complex that is sufficiently long-lived to undergo quantum-mechanical tunnelling to form products.
We postulate that this tunnelling mechanism for the oxidation of organic molecules by OH is widespread in low-temperature interstellar environments…

Read also: Quantum mechanics enables ‘impossible’ space chemistry

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July 1, 2013 at 10:25 am

Precise measurements test quantum electrodynamics …

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… constrain possible fifth fundamental force

A schematic layout of the experimental setup. The oscillator cavity is seeded by a cw Ti:Sa laser, the pulsed output of which makes multiple passes in an amplifier stage. The amplified output is frequency up-converted in two frequency doubling stages leading to fourth harmonic generation of ~211 nm. The deep UV radiation is sent to the experiment, where molecules in the X1 Σg+ ν´ = 1 state, populated by electrical discharge, are optically excited in a two-photon Doppler-free configuration . The cw-seed light is compared to a frequency comb while the frequency offset between pulsed and cw-seed light is measured via on-line chirp analysis to obtain an absolute frequency calibration. See text for further details. SHG: second harmonic generation; PMT: photomultiplier tube; and YAG: yttrium-aluminum garnet. Reproduced with permission from G. D. Dickenson et al, Phys. Rev. Lett. 110, 193601 (2013)

A schematic layout of the experimental setup. The oscillator cavity is seeded by a cw Ti:Sa laser, the pulsed output of which makes multiple passes in an amplifier stage. The amplified output is frequency up-converted in two frequency doubling stages leading to fourth harmonic generation of ~211 nm. The deep UV radiation is sent to the experiment, where molecules in the X1 Σg+ ν´ = 1 state, populated by electrical discharge, are optically excited in a two-photon Doppler-free configuration . The cw-seed light is compared to a frequency comb while the frequency offset between pulsed and cw-seed light is measured via on-line chirp analysis to obtain an absolute frequency calibration. See text for further details. SHG: second harmonic generation; PMT: photomultiplier tube; and YAG: yttrium-aluminum garnet. Reproduced with permission from G. D. Dickenson et al, Phys. Rev. Lett. 110, 193601 (2013)

Quantum electrodynamics (QED) – the relativistic quantum field theory of electrodynamics – describes how light and matter interact – achieves full agreement between quantum mechanics and special relativity.
(QED can also be described as a perturbation theory of the electromagnetic quantum vacuum.) QED solves the problem of infinities associated with charged pointlike particles and, perhaps more importantly, includes the effects of spontaneous particle-antiparticle generation from the vacuum.
Recently, scientists at VU University, The Netherlands, published two papers in quick succession that, respectively, tested QED to extreme precision by comparing values for the electromagnetic coupling constant1, and applied these measurements to obtain accurate results from frequency measurements on neutral hydrogen molecules that can be interpreted in terms of constraints on possible fifth-force interactions beyond the Standard Model of physics2.
In addition, the researchers point out that while the Standard Model explains physical phenomena observed at the microscopic scale, so-called dark matter and dark energy at the cosmological scale are considered as unsolved problems that hints at physics beyond the Standard Model.
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Written by physicsgg

June 6, 2013 at 9:55 am

The NEW Periodic Table Song (In Order)

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There’s Hydrogen and Helium Then Lithium, Beryllium Boron, Carbon everywhere Nitrogen all through the air

With Oxygen so you can breathe And Fluorine for your pretty teeth Neon to light up the signs Sodium for salty times

Magnesium, Aluminium, Silicon Phosphorus, then Sulfur, Chlorine and Argon Potassium, and Calcium so you’ll grow strong Scandium, Titanium, Vanadium and Chromium and Manganese

CHORUS This is the Periodic Table Noble gas is stable Halogens and Alkali react agressively Each period will see new outer shells While electrons are added moving to the right

Iron is the 26th Then Cobalt, Nickel coins you get Copper, Zinc and Gallium Germanium and Arsenic

Selenium and Bromine film While Krypton helps light up your room Rubidium and Strontium then Yttrium, Zirconium

Niobium, Molybdenum, Technetium Ruthenium, Rhodium, Palladium Silver-ware then Cadmium and Indium Tin-cans, Antimony then Tellurium and Iodine and Xenon and then Caesium and…

Barium is 56 and this is where the table splits Where Lanthanides have just begun Lanthanum, Cerium and Praseodymium

Neodymium’s next too Promethium, then 62’s Samarium, Europium, Gadolinium and Terbium Dysprosium, Holmium, Erbium, Thulium Ytterbium, Lutetium

Hafnium, Tantalum, Tungsten then we’re on to Rhenium, Osmium and Iridium Platinum, Gold to make you rich till you grow old Mercury to tell you when it’s really cold

Thallium and Lead then Bismuth for your tummy Polonium, Astatine would not be yummy Radon, Francium will last a little time Radium then Actinides at 89


Actinium, Thorium, Protactinium Uranium, Neptunium, Plutonium Americium, Curium, Berkelium Californium, Einsteinium, Fermium Mendelevium, Nobelium, Lawrencium Rutherfordium, Dubnium, Seaborgium Bohrium, Hassium then Meitnerium Darmstadtium, Roentgenium, Copernicium

Ununtrium, Flerovium Ununpentium, Livermorium Ununseptium, Ununoctium And then we’re done!!

Written by physicsgg

May 18, 2013 at 6:18 pm

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Building the Smallest Possible Ice Crystal

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It may sound like a Zen koan, but it’s a serious scientific question: How many molecules of water does it take to make the smallest possible ice crystal? Because crystals are defined by a repeated, three-dimensional arrangement of molecules, you can’t necessarily take any small group of bonded-together molecules and call them a crystal. That’s especially true for water: When it freezes, the weak hydrogen bonds that loosely bind the water molecules together pull the disordered clusters of molecules (left) into a more open—but also more rigid—cagelike arrangement (cross section of cluster at right). This roomy lattice is also why ice is less dense than water (and therefore floats). So to calculate the minimum number of molecules needed to make an ice lattice, a team of researchers shone infrared lasers on clusters of water molecules containing between 80 and 500 molecules. The team paid particular attention to how much energy the clusters absorbed from the lasers between the wavelengths of 2.63 micrometers and 3.57 micrometers—the range in which the oxygen-hydrogen bonds in water continually stretch and shrink. A particular peak of energy absorption occurred at a wavelength of about 3.125 micrometers—denoting the spectral characteristic of ice—and only appeared for clusters containing more than 275 water molecules, the researchers report online today in Science. That number of molecules yields a tiny ice cluster between 1 nanometer and 3 nanometers across—the ultimate in crushed ice.

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Read also: How many water molecules does it take to make ice?

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September 21, 2012 at 12:39 pm

Further proof of extraterrestrial origin of quasicrystals

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Fragment of a 3D icosahedral quasicrystal composed of four types of polyhedral units. (Courtesy: J E S Socolar, P Steinhardt)

An international team of researchers has found nine new samples of naturally occurring quasicrystals. The work also provides further proof that quasicrystals were delivered to the Earth by a meteorite. The team’s discovery challenges our understanding of both crystallography and solar-system formation.
Conventional crystal structures are made of atoms, or clusters of atoms, that repeat periodically. These patterns are normally restricted to two, three, four or sixfold rotational symmetry – the numbers corresponding to how many times the crystal appears the same during a rotation through 360°. For a long time these were considered hard and fast rules, and no crystals that broke these conditions were thought to exist…..
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August 13, 2012 at 6:33 pm

Posted in Chemistry

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New chemical bonds possible in extreme magnetic fields

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Could helium molecules form in very high magnetic fields? (Courtesy: NASA)

In the extreme magnetic fields of white dwarves and neutron stars, a third type of chemical bonding can occur. That is the finding of theoretical chemists in Norway, who have used computer simulations to show that as-yet-unseen molecules could form in magnetic fields much higher than those created here on Earth.
High-school chemistry students are taught that there are two types of chemical bond – ionic bonds, in which one atom donates an electron to another atom; and covalent bonds, in which the electrons are shared. In fact, real chemical bonds usually fall somewhere in between.
When two atoms come together, their atomic orbitals combine to form molecular orbitals. For each two atomic orbitals combined, two molecular orbitals are formed. One of these is lower in energy than either atomic orbital and is called the bonding orbital. The other “anti-bonding” orbital is higher in energy than either atomic orbital. Whether or not the atoms will actually bond is determined by whether the total energy of the electrons in the molecular orbitals is lower than the total energy of the electrons in the original atomic orbitals. If it is, bond formation will be energetically favoured and the bond will be formed.

Bonding and anti-bonding

The Pauli exclusion principle forbids a single orbital from holding more than two electrons (it can hold two if they have opposite spins). If the atomic orbital of each atom contained just one electron, both can go into the bonding orbital when the orbitals combine. Both electrons are therefore lowered in energy and the bond formation is energetically favoured. But if the atomic orbitals contained two electrons each, two of the four electrons would have to go into the anti-bonding molecular orbital. Overall, therefore, two electrons would have their energy lowered by bond formation, while two electrons would have their energy raised.
Under normal circumstances, the anti-bonding orbital is always raised in energy farther above the energy of the higher-energy atomic orbital than the bonding orbital is lowered below the energy of the lower-energy atomic orbital. This means that a chemical bond with both its bonding and its anti-bonding orbitals full would always have a higher energy than the atomic orbitals from which it would be formed. Such a bond would therefore not form. This is why noble-gas atoms, which have full outer atomic orbitals, almost never form molecules on Earth.
But now Kai Lange and colleagues at the University of Oslo have used a computer program developed by their group called LONDON to show this is not always true elsewhere. LONDON creates mathematical models of molecular orbitals under the influence of magnetic fields of about 105 T. This is much stronger than the 30–40 T fields that can be made in laboratories and that have little effect on chemical bonds.

Changing the rules

Large fields could be relevant to those studying astronomical objects such as white dwarves – where magnetic fields can reach 105 T – and neutron stars, where fields could be as high as 1010 T. Under such conditions, the team has shown that the rules of bonding change. In particular, the anti-bonding orbital is lowered in energy when a diatomic molecule is subjected to a strong perpendicular magnetic field. Molecules with full bonding and anti-bonding orbitals, such as diatomic helium, can still be energetically favoured.
Team leader Trygve Helgaker explains the sophistication of LONDON enabled the group to perform calculations that others have found impossible. “We can do accurate calculations with all orientations of the molecule to the magnetic field,” he says. “People have done the same kinds of electronic-structure calculations before, but I believe their calculations were limited to the situation where the field is parallel to the molecular axis.”
The research is published in Science; in an accompanying commentary, Peter Schmelcher of the Institute for Laser Physics at the University of Hamburg, Germany, said “Atoms, molecules and condensed-matter systems exposed to strong magnetic fields represent a fascinating topic, and this work has added a key bonding mechanism.” Interestingly, while he accepts the fields present around a white dwarf will be unachievable in a laboratory in the foreseeable future, he sees an alternative way the group’s models might be tested experimentally. Rydberg atoms are highly excited atoms that can be the size of the dot of an “i”. Because the bond length between Rydberg atoms is so great, the Coulomb interaction is much smaller, and Schmelcher believes it might therefore be possible to use them to produce magnetic fields of comparable strength.
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July 21, 2012 at 7:53 am

Posted in ATOMIC PHYSICS, Chemistry

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‘Olympic rings’ molecule olympicene in striking image

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Olympicene radical AFM Laplace filtered. The black bar corresponds to 0.5 nm. Credit: IBM Research – Zurich, University of Warwick, Royal Society of Chemistry

Scientists have created and imaged the smallest possible five-ringed structure.
A collaboration between the Royal Society of Chemistry (RSC), the University of Warwick and IBM Research – Zurich has allowed the scientists to bring a single molecule to life in a using a combination of clever synthetic chemistry and state-of-the-art imaging techniques

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May 28, 2012 at 1:08 pm

Posted in Chemistry

The Single Theory That Could Explain Emergence

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Organisation And The Origin of Life

An example of an RAF set that was found by the RAF algorithm in an instance of the
binary polymer model. Molecule types are represented by black dots and reactions by white boxes. Solid arrows indicate reactants and products coming in and out of a reaction, while dashed arrows indicate catalysis. The food set is F ={0, 1, 00, 01,10, 11}

Biochemists have long imagined that autocatalytic sets can explain the origin of life. Now a new mathematical approach to these sets has even broader implications

One of the most puzzling questions about the origin of life is how the rich chemical landscape that makes life possible came into existence. 

This landscape would have consisted among other things of amino acids, proteins and complex RNA molecules. What’s more, these molecules must have been part of a rich network of interrelated chemical reactions which generated them in a reliable way.

Clearly, all that must have happened before life itself emerged. But how? 

One idea is that groups of molecules can form autocatalytic sets. These are self-sustaining chemical factories, in which the product of one reaction is the feedstock or catalyst for another. The result is a virtuous, self-contained cycle of chemical creation.

Today, Stuart Kauffman at the University of Vermont in Burlington and a couple of pals take a look at the broader mathematical properties of autocatalytic sets. In examining this bigger picture, they come to an astonishing conclusion that could have remarkable consequences for our understanding of complexity, evolution and the phenomenon of emergence. 

They begin by deriving some general mathematical properties of autocatalytic sets, showing that such a set can be made up of many autocatalytic subsets of different types, some of which can overlap. 

In other words, autocatalytic sets can have a rich complex structure of their own.

They go on to show how evolution can work on a single autocatalytic set, producing new subsets within it that are mutually dependent on each other.  This process sets up an environment in which newer subsets can evolve. 

“In other words, self-sustaining, functionally closed structures can arise at a higher level (an autocatalytic set of autocatalytic sets), i.e., true emergence,” they say.

That’s an interesting view of emergence and certainly seems a sensible approach to the problem of the origin of life. It’s not hard to imagine groups of molecules operating together like this. And indeed, biochemists have recently discovered simple autocatalytic sets that behave in exactly this way.

But what makes the approach so powerful is that the mathematics does not depend on the nature of chemistry–it is substrate independent. So the building blocks in an autocatalytic set need not be molecules at all but any units that can manipulate other units in the required way. 

These units can be complex entities in themselves. “Perhaps it is not too far-fetched to think, for example, of the collection of bacterial species in your gut (several hundreds of them) as one big autocatalytic set,” say Kauffman and co.

And they go even further. They point out that the economy is essentially the process of transforming raw materials into products such as hammers and spades that themselves facilitate further transformation of raw materials and so on. “Perhaps we can also view the economy as an (emergent) autocatalytic set, exhibiting some sort of functional closure,” they speculate.

Could it be that the same idea–the general theory of autocatalytic sets–can help explain the origin of life, the nature of emergence and provide a mathematical foundation for organisation in economics?

As Kauffman and friends say with just a little understatement: “We believe that these ideas are worth pursuing and developing further.”

We’ll look forward to following the work as it progresses.

Ref: The Structure of Autocatalytic Sets: Evolvability, Enablement, and Emergence

Written by physicsgg

May 7, 2012 at 3:46 pm