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The Dynamic Life of Crystals


Professor Kenneth Harris

Cardiff University


April 2023




1. Introduction


A crystal, declared 1938, Nobel prize winner and chemist, Leopold Ruzicka is, ‘….a chemical graveyard’. Certainly, crystal images suggest a stacked mausoleum of chemical constituents, endless in extent, rigidly frozen in time, with no semblance of a beginning nor prospect of an end (to paraphrase another scientist), in effect a dead chemical structure.

In a fascinating presentation, Kenneth, a chemist with a specialism in crystal structures, was able to suggest, if not prove, that crystals are dynamic entities, essential to the world of science. Kenneth hails from Cardiff University and has determined the structure of all 20 amino acid. Of course, the study of crystals extends beyond chemistry. Certain branches of science are big into crystallography, not least geologists, where the crystal structure of rock constituents can definitively inform of past Earth processes.



2. Crystals


The first question is, of course, ‘what is a crystal?’ It is a solid consisting of a range of chemical constituents with a regular repeating structure which propagates infinitely. Its structure exists in 3-dimensions, therefore a flat structure such as graphene does not count. It contrasts with amorphous solid glasses where the molecular order is regularly disrupted. Examples of crystals include graphite, salt, gypsum, sucrose & ice (see Fig.1).




Fig 1: Different minerals have different molecular compositions, repetitiveness of composition makes a crystal


A concept important in crystallography is polymorphism in which a given substance has two or more different crystal structures. This results in substances with identical chemical components, but with very different physical properties, including melting point, solubility, optical properties, conductivity etc. It obviously has crucial implications to industry. In pharmaceuticals, for example, a particular polymorph of a drug needs to be manufactured without contamination by other polymorphs otherwise its effect will not be as intended.


ROY (5-ethyl-2-[(2-nitrophenyl)amino]-3-thiophenecabonitrile) is the chemical compound holding the world record for the number of polymorphs with 22 varieties.




Fig 2: Calcite and aragonite- examples of polymorphs (colour reflects different impurities)



A good example (see Fig. 2) of polymorphic behaviour (and undoubtedly familiar to biologists and Earth Scientists) is calcium carbonate (CaCO3) appearing in shells of molluscs and in limestones. It has two main forms, calcite and aragonite which presents different crystal shapes and different physical properties despite having the same chemical formula. An even more striking example is graphite and diamond, physically poles apart, but chemically both made exclusively of carbon atoms.


The next question, having defined a crystal, is how can we interrogate it to gain an insight into its structure? The answer, is of course, X-Ray diffraction. X-ray crystallography goes back to 1912 when Walter Frederich, Paul Nipping and Max von Laue obtained the first diffraction image (of copper sulphate). It was further developed by the Braggs (both William), father and son Nobel laureates. In fact, the subject area of X-ray crystallography has produced the most Nobel prize winners of any subject, in addition to, possibly, the biggest near miss in the person of Rosalind Franklin who first imaged DNA, revealing its double helix structure. X-rays, with a wavelength of a few Angstroms (10-10m = 1 Å), are conveniently similar in magnitude to crystal structures, meaning the electromagnetic rays interact maximally with the crystal structure. The crystal array splits the beam (diffraction) with the result that when detected on a screen, some of the disrupted X-rays will add too or detract from other ray paths in a process of constructive and destructive interference to produce an image definitive of the crystal under study (see Fig.3).




Fig 3: X-ray diffraction


The same principle can be demonstrated by shining a hand-held laser through a handkerchief onto a wall. The single beam of laser light is split by the weave/weft of the handkerchief into a disparate image reflecting the texture of the handkerchief material.


Commonly used is X-ray Powder Diffraction (XRD), a rapid analytical tool to determine sample composition. The analysed material is finely ground, homogenised and the average bulk composition is determined. It is widely used for identification of unknown crystalline materials- crucial to studies in geology, material science, engineering and biology.


Whilst a crystal may be a pretty obvious entity, less clear is how a crystal initially forms. This might be inter alia by hanging drop, vapour diffusion (e.g. snowflakes), free interface diffusion or mechano-chemical micro grinding.



3. The Life of Crystals



For Kenneth, a study of crystals can be best described in terms of the four stages of crystal life, namely, birth, adolescence, maturity and life changing events:



i) BIRTH


The beginning of a crystal starts with nucleation, but the point at which atoms become crystals can be analysed in terms of energy (Fig. 4). Nucleation and growth are of uttermost importance for crystallization since they determine the structure, shape, and properties of a crystal. The classical crystallization theory is based on the balance of the energy gain by formation of a new phase after nucleation and the energy loss by the development of a new interface. In consequence, an energy barrier for growth (ΔG) needs to be overcome.


Nucleation is simply defined as the first random formation of a distinct, new thermodynamic phase (daughter phase) that has the ability to irreversibly grow into a larger sized nucleus within the body of a metastable parent phase.

Free energy ΔG

Nucleus size, r

Fig: 4 Energy dynamics of crystallisation. GS > 0 → creating an interface “costs energy GV < 0 → forming a new phase decreases energy (natural transformation). Note ∆G=GS +GV

It is difficult to study transient nucleation events but these can be modelled with clathrate hydrates. In nature, these form typically in the deep ocean where cold temperature and a pressurised environment allow ice molecules to capture and retain methane molecules into a stable crystalline structure.


ii) ADOLESCENCE


This phase involves crystal growth and polymorphic transformations. With crystals having very regular shapes, it is the underlying atomic/molecular structure which control crystal shape. At the simplified level, iron sulphide consists of iron and sulphur atoms in a cubic lattice which reflects the very cubic shape of the crystal. There are additional complications, hex-shape crystals, for example, can exist in several forms, plate, prism or needle (see Fig. 5), each reflecting the hex-symmetry but distinctly different in appearance. The final shape reflects the relative rate of growth in the 3 dimensions of the crystal.




Fig 5: Different physical shapes of hex-shaped crystal


Snowflakes are a wonderful example of hex-symmetry crystal growth which was first recognised in 1611 by Johann Kepler in the book ‘Strena, seu de Nive Sexangula’. In the atmosphere, water molecules are exposed to a wide range of atmospheric conditions, most notable, temperature and super saturation, and these vary for any given snowflake over time as convection currents move it about resulting in the development of complex shapes reflecting different conditions of formation and growth.




Fig: 6 Differing and changing temperature and supersaturation constraints, as the snowflake moves within a cloud, will give rise to differing crystal appearances


Formation of crystals during adolescence can also be manipulated. As noted in Fig 5, the final shape of a molecule can be determined by the relative rate of growth in each of the three dimensions. In certain cases, inhibitory molecules can manipulate the final shape. Urea compounds form long needle shaped crystals, but inhibitory molecules, locking into the end points of the urea molecule will slow vertical growth, allowing greater horizontal enlargement resulting in a prism or plate crystal than the usual needle shape (see Fig. 7).





Fig 7: Use of additives as growth inhibitors to produce altered crystal shape


In unusual circumstances, exotic crystal shapes can be formed, including twisted and curved crystals by using appropriate additives to mediate crystal growth.


Polymorphic transformation at this stage is important. Crystallisation from solution often starts is such a way that the thermodynamically unstable phase(s) appear first followed by recrystallisation into thermodynamically stable phases at a later point in time. In a compound with two crystal structures these are the D (metastable) and G (stable) polymorphs respectively. Knowing these polymorphs is important. A drug, which has a specified intended shelf life, could exhibit different effects if, while it was manufacturer in the desired less stable polymorph it changed within its expected shelf life to the stable form. This is known as Ostwald's rule of stages where the phase that nucleates first is not necessarily the most thermodynamically stable, rather it is the one closest to the free energy of the mother phase.



iii) MATURITY


Crystals in maturity have reached a stable state and do not change with time. Such crystals exhibit either:


· the stable polymorph (thermodynamic stability); or

· the long lived, metastable polymorph (kinetic stability).


Crystals in the mature state can be confidently used, within reason, in a wide range of applications and devices.


iv) LIFE CHANGING EVENTS


Keeping with the theme of successive life stages, Kenneth noted crystals can be affected by major events, in much the same way that a human life span could be impacted by unexpected challenges and sudden turns of fate. Such events in crystals involve responses by the structure of the crystal to external events. These responses are particularly interesting to the scientific community because they have potential practical applicability in many fields such as actuators, biomimetic materials and sensors.


Discovered in 1983, some crystals are noted to jump over 10,000 times their length when exposed to light or heat. This includes the cobalt complex [Co(NH3)5 (NO2)]Cl(NO3) or pentaamminenitrocobalt (III) chloride. When photons hit the complex, it undergoes isomerisation – the nitrite ligand changes from being bonded through a nitrogen atom to being bonded through an oxygen atom. There is a build-up of the reaction product perpendicular to the irradiated face and this causes an increase of extreme stress in the solid, causing constituent layers to bend and crack, and the crystals to jump and break apart.


Some crystals also demonstrate mechanical change (bending/deformation) in response to stimuli. As noted previously, crystals generally consist of a rigid arrangement of molecules that are fixed and are therefore brittle. Of great interest are soft crystalline materials adaptable to mechanical forces. Such characteristics have been discovered in several crystals including hexachlorobenzene (see Fig.8).




Fig:8 Hexachlorobenzene crystal bent on (001) face and packing diagram and propagation of bend through the crystal on continuous stress application (indicated by arrows)



When stress is applied to the crystals, weak halogen-halogen and N-N interactions between the 2D planes are broken and reformed, thereby keeping the overall packing structure and causing permanent deformation.


Other crystals, in addition to jumping crystals, respond mechanically to light. DSP (2,5, distyrylpyrazine) is a representative molecule that undergoes a photopolymerisation reaction in a chemical phase in UV light. The crystal bends away from the light due to a change of shape along its axes. If a light is shone from the other side, it straightens up. The molecular stacking structure is affected due to lattice movement (lattice slipping). Other types of photo-induced crystal deformation include the formation of a twisted shape from a ribbon.



4) Conclusion


Crystals and crystallography provide a fascinating glimpse into the world of structural molecular relationships. It is clear that crystals of some organic molecules offer attractive physical properties that are different from the thermal, mechanical, optical, and electronic properties of conventional solids because of the presence of weak intermolecular interactions and the interplay between inter-and intramolecular degrees of freedom. During the last decade, understanding the physics and mechanical behaviour of crystals has become a major objective of researchers exploring and exploiting them for various technological applications such as molecular electronics and pharmaceutics, and nano-engineering.












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