From Nano to Geo Atoms at Play Neil Allan .

From Nano to Geo

Atoms at Play

Neil Allan

http://www.chm.bris.ac.uk/pt/allan/research

From The Third Policeman (Flann O’Brien) (1939) (published 1967)

-‘Did you ever study the Mollycule Theory when you were a lad?’ he asked. Mick, said no, not in any detail.

-That is very serious defalcation and an an abstruse exacerbation, he said severely…. Everything is composed of small mollycules of itself, and they are flying around in concentric circles and arcs and segments and innumerable various other routes too numerous to mention collectively, never standing still or resting by spinning away and darting hither and thither and back again, all the time on the go…

-They are as lively as twenty punk leprechauns doing a jig on the top of a flat tombstone. Now take a sheep. What is a sheep but only millions bits of sheepness whirling around doing intricate convulsions inside the base?

The nano-world and nanoscience:

Understanding atoms and molecules

How and Why?

What are the atoms doing? Atoms are only 10-10 m in size, i.e., one ten-millionth of a millimetre.

We now have an amazing set of techniques to examine them - from special forms of microscopy to techniques related to MRI.

ChromosomesThe letters IBM written in atoms

• Why are some molecules stable, some unstable? Why do some react quickly, some slowly? Can we predict – from the bottom up - new substances with improved properties for particular applications? How do we make these predicted substances? (Sometimes very difficult – e.g., making carbon nitride which is predicted to be harder than diamond!)

• The new chemistry – rather than trial and error - often tries to understand the atomic behaviour and use this to design new molecules or materials for specific purposes. Self-assembly, molecular organisation are key concepts.

Some important questions

Theoretical Chemistry – Experiments on a Computer

Modern chemistry

Vs.

The caricature! The reality!

Our DIRAC computer

Why and how do atoms form molecules and materials? Why are some stable, some

unstable? Why do they behave as they do? Why do some react quickly, some slowly?

Can we predict new substances with improved properties for particular applications?

A vital tool - unravelling the complexity of materials and minerals.

A source of ideas. It is possible to control and analyse simulations in ways and in detail

that no experiment can reach. Simulation reveals the underlying physics of individual

processes that combine to produce complex experimental effects.

A testbed of possibilities.

Much of chemistry is concerned with finding what information about atoms and

molecules can be obtained from macroscopic data. Here we go in the opposite

direction – wish to obtain macroscopic quantities from calculating atomic properties.

Models – highly useful but must appreciate limitations.

The role of theoretical chemistry and simulation

How can we model atomic behaviour?

• Quantum mechanics: Schrödinger equation

• The input is the set of the electrostatic interactions (repulsions and attractions) in the molecule or solid. Need to make approximations for the electron-electron repulsions and exactly what approximations to make have been hotly debated since the 1920s!

• The output is the energy and the associated wave. Wave-particle duality!

• Limited by computer resources to tens of atoms.

• For solids use periodic symmetry to reduce a problem involving 6x1023 atoms to the repeat unit (the unit cell) hopefully containing tens of atoms or less!

ψψ EH

Quantum Mechanics and Periodic Boundary Conditions (2)

ψψ EH

Calculated electron density (2) in MnS.

M.C. Escher

What about larger systems? Molecular mechanics and dynamics

• We abandon the quantum mechanics and make some savage approximations. Inevitable tradeoff.

• Atoms treated as (interacting) snooker balls.

• We input an approximation for how the atoms interact and then use classical mechanics to see how the atoms arrange themselves, the forces between them and how they will move with time (molecular dynamics).

• Largest simulation we’ve done (molecular dynamics) is 2,000,000 atoms for 3x10-9 s (picoseconds).

How do atoms and molecules interact even when non-bonded?

rij

Vij

0

612 σσε4

rrrVAttraction at large distances,

repulsion at shorter distances.

Most famous approximation is the Lennard-Jones potential.

Simulation - Molecular dynamics

Water at a clay surface – the water molecules both diffuse and rotate much more slowly than in bulk water.

Simulation - Molecular dynamics (2)

Wetting of rough surfaces by nanodroplets

Simulation - high temperature. Negative thermal expansion.

‘All substances expand when heated’ (Abbott, Ordinary Level Physics 1970).

Not so! For example ZrW2O8 contracts on heating from very low temperatures up to 900 K, where it decomposes.

WO4 tetrahedra, ZrO6 octahedra

W green, Zr blue, O red

Free energy molecular mechanics minimisations reproduce the contraction with increasing temperature.

And from the simulations we can see why and how……

This unexpected behaviour is due to the fine details of the vibrations of the lattice. The Zr-O-W transverse vibrations increase in frequency with increasing volume.

Compare the transverse vibrations of a violin string which increase in frequency when it is stretched.

ν1

ν2 > ν1

ν2

Understanding negative thermal expansion

Understanding the nanoscale… ZnO – PREDICTING STRUCTURES

[0001]

[1010]

[1120]

Bulk würtzite structure of ZnO (Zn blue, O red) – but what structure do very thin films prefer and can we explain the observed shape of the crystals?

ZnO – thin films

For ZnO, films of <18 layers optimise to graphite-like (graphene) hexagonal sheets. For >18 layers we revert to würtzite-like structures.

Take-home message – nano-structures are often very different from bulk structures!

Graphene form of ZnO

How does an ion pair move across an oxide surface? Not by a direct hop, but by an exchange mechanism, which was totally unexpected!

Important implications, e.g., the mixing inevitable when this mechanism is present must be considered when attempts are made to grow sharp interfaces in oxide nanostructures!

Ba O O O

BaBa

BaBa

Ba

Simulation reveals the unexpected – atoms moving across surfaces

And for chemistry at unfamiliar conditions

Eagle Nebula

6500 light years away4 light years long

The Earth

Temperature at bottom of mantle 4000 °CPressure 1.4 million atmospheres

Chemistry at high pressure. Journey to the centre of the Earth.

Many substances change their structure at high pressure. We need to understand these phase transitions and the changes in chemical and physical properties that arise from this.

For example NaCl (in which the ions have 6 neighbours) changes at about 300,000 atmospheres to the CsCl structure (ions have 8 neighbours) and the compressibility drops dramatically.

We have carried out many quantum mechanical and molecular mechanics calculations to investigate such changes, which are often controversial!

For NiF2 which changes from the MgF2 to the CaCl2 structure at 100,000 atmospheres, we carried out both experiments and theory!

Low pressure High pressure

Every atom has 8 neighbours

Every atom has 6 neighbours

• H2, HCl, PN, SiO, SiS, HNO, CH4

• CCC, HCN, HNC, CCCO, HN=C=O, HCCH, H2C=C=C, HCCNC, C4Si

• CH+, HCO+, HCS, HCNH+

• OH, CH, CN, NO, HCO, CP, C2O, C3H

• The elements present are those cosmically abundant.

• The physical conditions are far from thermal equilibrium. The preference for unsaturated species can reasonably be understood in terms of the low-pressure environments of interstellar molecules. Theoretical chemistry has been key in the identification of many of these species from their molecular spectra.

And out in space – some interstellar molecules

‘For over three decades efforts to find solutions to the radioactive waste management in the UK have failed.’

Committee on Radioactive Waste Management, Summer 2006.

The good, the bad, the ugly - radiation damage in ceramics

Gas p

lum

e

Study initial damage caused by -particle decay using molecular dynamics – include a U atom in the simulation cell with energy in the keV range. Cell contains 2 million ions! Total timescale 8-12 ps.

We are looking for a ‘self-healing’ material that reforms after damage.

Here is some of the damage caused in Gd2Zr2O7, which is much more resistant to damage than Gd2Ti2O7.

Radiation Damage Cascades

Gas p

lum

e

More from The Third Policeman (Flann O’Brien)

-Mollycules is a very intricate theorem and can be worked out with algebra but you would want to take it by degrees with rulers and cosines and familiar other instruments and then at the wind-up not believe what you had proved at all. If that happened you would have to go back over it till you got a place where you could believe your own facts and figures exactly delineated from Hall and Knight’s Algebra and then go on again from that particular place till you had the whole pancake properly believed and not have bits of it half-believed or a doubt in your head hurting you like when you lose the stud of your shirt in the middle of the bed.

-Very true, Mick decided to say.

And finally… designing the molecular world

The domain in which chemical synthesis exercises its creative power is vaster than that of nature itself.

Marcellin Berthelot

He who understands nothing but chemistry doesn’t even understand chemistry.

Georg Lichtenberg