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John Desmond Bernal: his contributions to crystallography

Christine SlingsbyPaul Barnes, John FinneyVincent Casey
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The 50th anniversary of John Desmond Bernal’s death (15 September 1971) seems an appropriate occasion to look at his fundamental role in the development and exploitation of crystallography. The following three articles explore his influence on structural biology, material science and our understanding of liquid structure (including water). The final article describes his recent scientific legacy in Ireland (the country of his birth), which is helping to realise his concern that science should be used for the benefit of society. These articles were originally published in the June 2021 issue of Crystallography News, and are reproduced with permission.

Bernal’s early influence on biomolecular structure, and on protein crystallography

Christine Slingsby, Birkbeck College, University of London, UK

Bernal had the satisfaction of determining the atomic structure of graphite in the early days of X-ray crystallography under the guidance of William H. Bragg while at the Davy–Faraday Laboratory at the Royal Institution in London (1923–1927). Bernal was less enchanted with the tedium of indexing the diffraction spots, and so he devised ways of aiding the interpretation of single-crystal rotation photographs by inventing Bernal charts. His first two papers published in 1924 and 1926 brought him early recognition as a leader in X-ray crystallography. However, recognising even then the potential of the technique, he wanted to extend the reach of X-ray structure analysis to the biological world. As both he and his colleague Bill Astbury wanted to tackle proteins, they divided the field between them, Astbury taking on the fibres, Bernal the soluble globular proteins.

In 1927 Bernal moved back to Cambridge as a Lecturer in Structural Crystallography in the Department of Mineralogy next door to the Cavendish. In his quest to understand the biological world he took advantage of the proximity of the biochemistry laboratory, led by Frederick Gowland Hopkins, who considered that enzymatic activity was responsible for the biological activity of living cells. Although little was known of protein structure at the time, it was known that chemically they were chains of amino acids. In the summer of 1928 Bernal travelled around European laboratories to catch up on progress in protein research. He began work on amino acids and related compounds using crystals prepared by A. Leese in Biochemistry. Atomic resolution structures of these molecules were beyond reach at that time, but Bernal had shown from his Cambridge student days that he had the kind of geometric mind that could independently derive all 230 space groups (see Paul Barnes’s article below). He therefore embarked on optical and X-ray characterisation of the unit cells to reveal likely models of the amino acids and how they packed together in the crystals. The final paragraph of the survey published in 1931 reads: “A detailed account of the crystallographic investigation with a discussion of its chemical implications will be published at a later date. In the meanwhile, in view of the difficulty of obtaining crystals of these compounds the author would be very grateful if anyone possessing such crystals of a magnitude of 0.01 mm or over would send a few mgms of them to him for examination”.

In the early 1930s Solly Zuckerman and J. B. S. Haldane steered Bernal towards new crystals of the sex hormone oestrin. He was able to figure out from unit-cell dimensions, symmetry and optical properties that all steroids were likely to have a similar structure, which was not in agreement with the ideas of the leading chemists of the day. Bernal’s observations led to a rapid reappraisal of sterol chemistry. The sterol success boosted Bernal’s reputation among chemists and filled his desk with samples. In 1932 an Oxford graduate Dorothy Crowfoot joined him as a PhD student. He invited her to sort out his desk and she became his principal photographer of biological samples.

Protein crystallography begins

The key experiment performed by Bernal in 1934 that started protein crystallography is described in Nature, with an opening sentence that reads like a diary entry: “Four weeks ago, Dr G. Millikan brought us some crystals of pepsin prepared by Dr Philpot in the laboratory of Prof. The Svedberg, Uppsala.” On exposure to air the crystal birefringence diminished and X-ray photographs taken in the usual way showed nothing but a vague blackening. So Bernal drew a new pepsin crystal into a fine glass tube, surrounded by its mother liquor. To his delight this time there was a pattern of spots extending all over the film that sent him wandering the streets of Cambridge through the night. From the intensity of the spots near the centre, he proposed that protein molecules are relatively dense globular bodies, separated by relatively large spaces which contain water. From the intensity of the more distant spots, he inferred that the arrangement of atoms inside the protein molecule is of a perfectly definite kind, although without the periodicities characterising the fibrous proteins, as determined by Astbury. Several more pepsin photographs were taken by Dorothy, but further interpretation was abandoned. The molecular basis of the activity of the enzyme pepsin was within grasp, but not yet.

[Figure1]Figure 1. Dorothy Hodgkin discussing things with Bernal. Courtesy of S. Jane Bernal.

Although Dorothy was not in Cambridge the day the first photo was taken, her name was on the publication. She remained in close contact with Bernal when she moved to Oxford later that year and acquired some insulin crystals. He mentored her through the X-ray work and pushed her to publish a single-author paper in Nature in 1935 on her early results on dry insulin crystals. In 1935 in correspondence with Bernal on insulin she says: “It was clear that Bernal was thinking of the possibilities of changing zinc in the crystal for heavier metals and using the change to find the phase angles necessary for the direct calculation of an electron density map of insulin – the method of isomorphous replacement.” Bernal’s steering allowed her at a young age to be in a position to pursue independent research. Her subsequent application of X-ray crystallography to solve penicillin, vitamin B12 and insulin changed the way chemists approached the development of medical therapeutics.

Viruses and haemoglobin

Isidor Fankuchen came to work with Bernal in 1935, ostensibly to work on sterols, having been trained in crystallography by W. Lawrence Bragg in Manchester. Instead Bernal had him work on plant virus particles, such as tobacco mosaic virus (TMV), in collaboration with N. W. Pirie, who had purified a ‘crystalline protein’ from infected tobacco leaf sap. Bernal was keen to define the nature of the crystallinity. By measuring diffraction data from wet and dry gels and solutions, they showed that the sample was in fact liquid crystalline. They deduced that the virus particles formed long rods that probably contained some RNA. Most of the diffraction peaks originated in the internal structure of each rod, for which Bernal, typically, had this to say: “A complete interpretation of this intramolecular pattern has not yet been possible; but a rough survey indicates that the molecule is made of piles of sub-molecules of dimensions 22 Å x 20 Å x 20 Å, somewhat smaller than the normal protein molecule, and themselves divided into nearly identical units with half these dimensions.” But there was little interest in the substance, other than it was possible to follow the wake of a goldfish swimming in a solution of it when viewed under polarised light.

Bernal and Fankuchen were also intrigued by spherical viruses, and X-rayed crystals of tomato bushy stunt virus (TBSV). In Dorothy Hodgkin’s Royal Society Biographical Memoir of Bernal, she tells us that: “The photograph was necessarily a powder photograph, though of wet crystals, and showed at first only two lines. With a pair of dividers and a ruler on the wet film, in great excitement, Bernal measured these lines and, assuming as was likely from the form of the crystal, that the lattice was cubic body-centred, deduced a cubic unit cell of edge 390 Å, containing two particles of diameter 340 Å and a molecular mass of the order of 10 000 000.” However, the more reflections they recorded, the less good the fit with any symmetrical model, so the work was paused.

When Max Perutz arrived in Bernal’s lab in 1936, he wanted to work on a biological molecule. With enthusiastic support from Bernal, he used his own initiative to get crystals of horse methaemoglobin, with the first diffraction photographs taken in late 1937. With help from Fankuchen, a Nature paper was rapidly published in March 1938. Wet crystals of both haemoglobin (and chymotrypsin) diffracted X-rays to high resolution with perfectly definite reflections at spacings as low as 2 Å, proving the internal regularity of the protein molecules down to atomic dimensions. Furthermore, controlled dehydration of the crystals caused variation in the intensities which Bernal saw may make possible the direct Fourier analysis of the molecular structure once complete sets of reflections became available in different states of hydration.

Birkbeck College

Bernal had ambitions to form an Institute of Biomolecular Research that would be organised at the boundaries of classical disciplines, but as he was disliked by the Head of the Cavendish, Ernest Rutherford, and out of favour with the University establishment, he could not progress his career in Cambridge. Early in 1938 Bernal was appointed Professor of Physics at Birkbeck College, University of London, taking over from Patrick Blackett. Formerly the London Mechanics’ Institution, Birkbeck was organised so that working people could study for degrees in the evening, and so was more aligned with Bernal’s politics.

The department was housed in the ancient Bream’s Buildings, close to Chancery Lane. W. L. Bragg moved to Cambridge in 1938, having been appointed Cavendish Professor in succession to Rutherford who had died unexpectedly. Bragg and Bernal shared out the Cambridge apparatus and students. Max Perutz wished to stay in Cambridge with his crystals and Bragg was keen to keep him. Fankuchen went with Bernal to Birkbeck with the virus projects, soon to be joined by Harry Carlisle, a student from Burma.

Bernal summarised his thinking on proteins at a Friday evening discourse at the Royal Institution in January 1939, which was published the following April in Nature. He proclaimed that the phase problem can only be resolved by some physical artifice, such as the introduction of a heavy atom, or the observation of intensity changes on dehydration. The paper also includes his thoughts on “how the behaviour of the hydrophobe groups of the protein must be such as to hold it together… a force of association is provided which is not so much that of attraction between hydrophobe groups, which is always weak, but that of repulsion of the groups out of the water medium”. Charles Tanford judged this overview as “a pioneering and prophetic paper, a glimpse into a rare moment when one man’s insight was able to encompass simultaneously all the strands of a complex problem, much of which the rest of the protein community would not understand for another twenty years”.

What Bernal – or anyone else – did not foresee at the time, was that a polypeptide chain could form a regular helix with a non-integral number of amino acids per turn. In the early 1950s Linus Pauling proposed the alpha helix which respected the planarity of the peptide bond, had around 3.7 amino acid residues per turn, with a predicted distance repeat of 5.4 Å, close to, but not exactly matching, the 5.15 Å repeat measured by Astbury in unstretched keratins.

In the summer of 1939 Bernal undertook an extensive trip to the US, visiting labs and giving lectures, including to the Rockefeller Institute. He made contact with Moses Kunitz, who specialised in crystallising enzymes, and this may have been the occasion at which he gave Bernal a tube of ribonuclease crystals. Bernal cut short the trip to return to the UK as war was coming. He evacuated his students and equipment to Dorothy in Oxford. (Harry Carlisle took his aging cholesteryl iodide crystals to her lab and she guided him through the calculation of a 3D map phased from the heavy atom. The structure, announced in Cambridge in 1943, was the first time a complex, asymmetrical biological molecule was visualised directly by X-ray analysis and opened a new path to determining unknown chemical structures.) Bernal feared that outbreak of war would stop all work on proteins in Europe, so he dispatched Fankuchen to the US with most of his materials in the hope he could continue there. At the start of the London Blitz, Fankuchen submitted a paper (from MIT, Cambridge) on X-ray diffraction of dry crystals of ribonuclease, while in the early hours of 25 September 1940 Birkbeck College was hit by incendiary bombs.

The war interlude

In 1939 Bernal suspended his direct academic activities. He joined the Civil Defence Research Group, and in spite of his MI5 dossier, was recruited by a member of Chamberlain’s cabinet, Sir John Anderson, who is quoted as saying “even if he is as red as the flames in hell, I want him”. In 1942 Bernal became Scientific Adviser to Combined Operations under Lord Louis Mountbatten.

As an Austrian, Perutz became a refugee in 1938. He was arrested in Cambridge as an enemy alien in May 1940 and transported under appalling conditions to Canada where he was interned in a camp. He was able to return to his red crystals in Cambridge at the start of 1941, but was desperate to join the war effort. Bernal recruited him onto the doomed Habbakuk floating ice strip project (see Paul Barnes’s article below), based under Smithfield Market, a role which required Perutz to travel to the US for demonstrations. The Home Office was pressed in 1943 to grant Perutz naturalisation, issuing him a British passport with a US visa. Max was soon able to network with US protein scientists like John Edsall at Harvard and Martin Buerger at MIT, and to showcase his successful haemoglobin work. Meanwhile Bernal told Pauling he had “left the field myself for the duration to spend my time being an engineer, architect and explosives expert”. However, Bernal went on to make more charts, this time for the landing beaches of Normandy. After D-Day, Bernal was sent to Ceylon. While testing bombs for jungle use alongside Wing Commander John Kendrew, he convinced Kendrew of the central importance of protein structure to understand the biology of living systems and directed him to Perutz in Cambridge.

The ‘new’ lab in a (very) old building

In 1947 the MRC agreed to support Perutz, Kendrew and a small team in a Unit within the Cavendish for five years. Francis Crick joined in 1949. Meanwhile Bernal’s group was dispersed in temporary accommodation until his Biomolecular Research Laboratory, at 21–22 Torrington Square, was opened in July 1948 by W. L. Bragg. The research strategy was to exploit and enhance physical methods to understand the structure and function of soluble proteins and viruses, as well as to pursue research into materials and liquids (see articles by Paul Barnes and John Finney below) in conjunction with the development of computing methods. Bernal was looking for a link between long-range interactions of proteins and biological systems, though was pessimistic about being able to buy the newly invented electron microscope. All this was expected to take place in a pair of partially repaired bomb-damaged Georgian houses in Bloomsbury that was supposedly temporary, but lasted for 20 years.

[Figure2]Figure 2. The Birkbeck Laboratory from 1948 to 1966.

Although Bernal, like most scientists in the early 1940s, considered genes might be proteins, he recognised that chromosomes and viruses share a similar chemical composition. In his post-war Birkbeck lab, he directed Harry Carlisle to supervise PhD student Sven Furberg, who solved the structure of a nucleoside, cytidine. The puckered pentose ring was perpendicular to the flat base ring, an observation noted by Watson and Crick in their DNA double-helix paper.

Getting a biological crystalline sample from an outside laboratory inside a well-equipped X-ray lab and into the hands of a brilliant investigator was the recipe for advancement in the early days of biological structure analysis. In 1953 Bernal invited Rosalind Franklin to bring her fellowship to Birkbeck to follow up his pre-war studies of the rod-shaped TMV. Her X-ray diffraction photographs of oriented gels of TMV, which showed evidence of helical diffraction, enticed Aaron Klug to join her team in early 1954. They established the helical symmetry of TMV, showing it had 49 subunits per three turns of the helix. In 1955 Don Caspar, an American biophysicist on a fellowship in MRC Cambridge, came to work in Franklin’s lab. They showed from a comparison of X-ray fibre diagrams of oriented gels of intact TMV and the reassembled isolated protein labelled with heavy atoms that the RNA was inside the helical protein shell, embedded in the protein subunits. Shortly before her early death in 1958, Franklin began work on poliomyelitis virus, sourced from Wendell Stanley, Berkeley. Klug and Caspar continued the polio work and raided the fridge for Bernal’s old samples of spherical viruses. Caspar took the TBSV crystals while Klug and John Finch worked on the turnip yellow mosaic virus (TYMV). All turned out to have icosahedral symmetry, with 180 subunits. Caspar and Klug wrote their classic paper in 1962 on quasi-equivalence, taking inspiration from Buckminster–Fuller’s construction of geodesic domes. This paper brought new ways of thinking about loosening regularity in modular protein assemblies, as well as a basis for the interpretation of virus electron micrographs. In 1962 Klug with John Finch and Ken Holmes, who had both gained their PhDs at Birkbeck in 1959, moved to the newly opened MRC Laboratory of Molecular Biology (LMB) in Cambridge.

 

Bernal, Booth and the double helix

During the Birkbeck 2004 degree ceremony, Andrew Booth, a Bernal protégée, and a founder of computer science, whose multiplication algorithm sits in many contemporary laptops, was being made an honorary fellow. In his acceptance speech, Booth reported a story involving himself, Bernal, Rosalind Franklin and the Nobel laureates Crick and Watson.

When Rosalind Franklin was at King’s College before she moved to Birkbeck, Bernal arranged a meeting of these five to discuss the state of knowledge of the structure of DNA. The meeting was friendly and relaxed, and the participants were fully aware of the possibility of DNA assuming a double-helix shape, since this was openly discussed at the meeting. Crick and Watson published their DNA double-helix theory shortly afterwards. If this account is true, and I have no reason to think it is not, it may not rewrite history, but it adds to our knowledge of the timeline that led to the double-helix discovery.

Paul Barnes

 

The phase problem was solved by Perutz in 1953, not by dehydrating crystals, but by introducing the physical artifice of a heavy-atom derivative into haemoglobin enabling him to calculate the first two-dimensional electron density projection of haemoglobin. Kendrew was the first in 1960 to calculate a high-resolution tertiary structure of a protein, monomeric myoglobin, showing rather unexpectedly that the alpha helices were not lying in an orderly parallel fashion. Perutz’s team calculated the quaternary tetrameric structure of haemoglobin in 1968.

In 1950 David Harker accepted the challenge of building a team to solve a protein structure for USD 1 million. The Protein Structure Project was set up at the Polytechnic Institute in Brooklyn, following successful lobbying by Fankuchen, with ribonuclease as its target. A 2 Å structure was published in Nature in 1967. Without the luxury of such a large budget, Bernal and Carlisle started work on ribonuclease in the post-war years, trudging the painful path of searching for heavy-atom derivatives. The structure was published in 1974.

Bernal had a mission to establish crystallography as a distinct branch of science. In 1951 he began his difficult campaign with Birkbeck to extricate crystallography from physics into a separate department. In 1963 Bernal got his Chair in Crystallography, but the splitting of the two departments was delayed until 1967. Bernal’s first stroke, which he largely recovered from, was in the summer of 1963. In late summer 1965 he suffered a disabling stroke, but his brain remained highly active, and he could, though with difficulty, communicate with colleagues, give lectures and write papers and books. He retired in 1966, just as the new crystallography laboratories were opened, and Harry Carlisle took the Chair. A couple of years later, Bernal had a heart attack and suffered a further stroke that left him essentially speechless for two years until his death on 15 September 1971. Carlisle continued protein research on ribonuclease, and new projects on plasma transferrins and eye lens crystallins were begun. Protein crystallography underwent rapid expansion when Tom Blundell, a former colleague of Dorothy Hodgkin, joined the department in 1976, taking the Bernal Chair in 1978.

Concluding comments

Bernal was clearly a – if not the – major driving force in the genesis and early development of biomolecular crystallography. The work he himself did in the 1920s and 1930s laid much of the foundations that have been built on by others. And his legacy can also be seen through the achievements of those he collaborated with and inspired – an impressive list that includes Caspar, Fankuchen, Finch, Franklin, Hodgkin, Holmes, Kendrew, Klug and Perutz. You can count the Nobel Prizes yourself.

Bibliography

Brown, A. (2005). J. D. Bernal: The Sage of Science. Oxford University Press.

Ferry, G. (1998). Dorothy Hodgkin: a Life. Granta Books London.

Ferry, G. (2008). Max Perutz and the Secret of Life. Cold Spring Harbor Laboratory Press.

Hodgkin, D. M. C. (1980). Biogr. Mem. Fellows R. Soc. 26, 17.

Maddox, B. (2002). Rosalind Franklin: the Dark Lady of DNA. HarperCollins Publishers.

Tanford, C. (1997). Protein Sci. 6, 1358–1366.

Tulinsky, A. (1999). Rigaku J. 16, 1.

Swann, B. & Aprahamian, F. (1999). Editors. J.D. Bernal: A Life in Science and Politics. Verso. 

 

Bernal, material science and problem solving

Paul Barnes, Birkbeck College, University of London, UK

I first met Sage, as Bernal had been known since his undergraduate days, in his house, in 1968, after joining his Liquids Group as a postdoctoral researcher. There is a record of that first meeting in Andrew Brown’s biography (Brown, 2005), a book I recommend to anyone interested in Bernal. Though my meetings with Bernal were, due to his deteriorating health, intermittent over the three remaining years of his life, I drew inspiration from them and felt that I had touched greatness.

In my opinion he was one of the most powerful scientific thinkers of the 20th century, an intellectual giant within the vast field of structural science. He possessed a natural curiosity, endless enthusiasm, prodigious knowledge and brilliance with which he could explore the more remote regions of a subject outside the conventional boundaries of science. These are lofty claims so if any reader suspects exaggeration, a quick glance at the informed comments of eight Nobel laureates (see box) should surely set the record straight.

 

Comments on Bernal by eight Nobel laureates (from Brown, 2005)
Aaron Klug (1982) “...was one of the most influential scientists of the 20th century.”
James Watson (1962) “...the extraordinary Irishman whose genius inspired the birth of molecular biology.”
Francis Crick (1962) “I regarded Bernal as a genius.”
Linus Pauling (1954)  “...one of the greatest intellectuals of the 20th century.”
Dorothy Hodgkin (1964) “His greatest gift was his power to inspire others.”
Hermann Muller (1946) “One of the best, if not the best scientific mind in the world.”
Lawrence Bragg (1915) “He has been the pioneer who pushed the frontier forward.”
John Kendrew (1962) “It seems to me you’ve fathered 5 Nobel Prizes this year alone.”

 

In this article, I take a quick look at some relevant events during his formative years, his search for research positions that complemented his skills and the turning points in his development. I am intrigued to see whether we can learn anything new from his choice of research projects or the open manner in which he carried them out.

The early days

While the boy Bernal showed clear signs of exceptional promise, his stellar potential only became fully recognised during his first year at Emmanuel College, Cambridge. There he would be able to sample the full Cambridge educational package comprising not only the necessary science components but also the essentials of a fully rounded academic life with activities such as political discussion, debating, networking and meeting influential thinkers. Bernal thrived in such an environment which in turn brought out the very best in him, accelerating his transition towards the later accomplished version that we would eventually recognize.

Bernal enjoyed listening to lectures that explored the dimensionality of a given topic and was clearly developing a flair for solving geometrical problems. In 1921 he set himself the challenging project of deriving the 230 crystallographic space groups using the quaternion mathematical representation. His wife to be, Eileen Sprague, assisted by typing the 80-page document which was then shortened to a 60-page version full of densely packed mathematics with no diagrams. It won him a shared first prize of £30 from Emmanuel College but the effort and time that he devoted to it may have cost him the first class honours he wanted so badly.

Bernal's next task was to find a post that fitted in with his areas of expertise in crystallography and that could provide him with a salary. The Cavendish could not help him. However, he did succeed in getting some temporary support from his old college, Emmanuel, which kept him and Eileen alive until he was able to join W. H. Bragg at the Royal Institution (RI).

Bernal at the Royal Institution

Bernal’s stay at the RI from 1923 to 1927 comes across as a happy period despite a clumsy start. The laboratory exuded a friendly informal atmosphere which encouraged cooperation. In addition, Bernal and Eileen melded effortlessly into the London social and political scene which in turn was well-suited to the Bernals’ unconventional lifestyle. Bernal started slowly in the lab, but then excelled himself by making significant improvements to the X-ray equipment and production of crystallographic manuals and charts and teaching aids. However, these endeavours were all over-shadowed by one single Bernal breakthrough, the determination of the structure of graphite. This was hugely significant for several reasons:

  • Several big names in crystallography had tried to solve its structure, but all had failed. Bernal, however, demonstrated he had the patience to succeed and even constructed a home-made X-ray diffraction camera from various discarded objects (brass tubing, bicycle clips, alarm clock, bent nail – see Fig. 1). Needless to say, he had to perform all his calculations by hand!
  • There was a long-standing paradox regarding diamond and graphite. Both are made from carbon alone, yet diamond was the hardest material known to man while graphite is a very soft material. Bernal’s explanation resolved the paradox on the basis of the differences in structure: diamond has strong covalent bonds in a tetrahedral arrangement, thereby imparting strong interactions in all directions, whereas the graphite structure consists of hexagonal layers that can slide over each other like cards in a deck, resulting in softness and a tendency to smear. Obvious now to us as we accept that properties are related to structure (hence crystallography!), but this was not realised before Bernal explained it.
[Figure3]Figure 1. Bernal’s prototype rotation camera!

Following his four years at the RI, Bernal held a lectureship in Mineralogy and Crystallography at Cambridge until he moved to Birkbeck College in 1938, where he was to remain until his death.

Bernal, Birkbeck and World War II

With the likelihood of war against Hitler’s Germany, Bernal felt compelled to voice his protest at the lack of preparation for mounting any form of response against an initial attack. He and Solly Zuckerman, a medic turned bio-scientist and anthropologist, became an effective duo in challenging the politicians’ official lines. Perhaps in line with US President Lyndon Johnson’s infamous remark about preferring his antagonists to be inside rather than outside his tent, Lord Louis Mountbatten in April 1942 invited Bernal to become his scientific advisor in Combined Operations. Bernal accepted and set about designing arrangements that would enable him to work on Combined Operations while remaining in contact with Birkbeck and crystallography via some kind of partial leave of absence. The complex arrangements, formal and informal, considerable deputising, delegation and shuffling of duties eventually brought about a successful arrangement, but not without heavy negotiations and quite a few headaches.

Bernal’s scientific interests were extremely broad, both with respect to science itself and the use to which science could be put. His Birkbeck department reflected this broad range, with research groups focussing on Structures of Biological Systems (see article by Christine Slingsby above), Materials Science Structures (initially headed by Helen Megaw, and which I took over following the retirement of Jim Jeffery), Structures of Liquids (see article by John Finney below) (the group which I originally joined) and Generalised Crystallography (in which Alan Mackay was a major collaborator).

This eclecticism is reflected not only in the strictly structural problems of, for example, graphite, bronze, metals and alloys, proteins, viruses and liquids, but also in the application of scientific methodology to ‘real’ issues exampled by many of the problems he was concerned with during the war.

 

Some war-related projects of Bernal’s

  • Efficacy of gas masks with respect to poisonous gases
  • Action of incendiary bombs on building top floors
  • Design of effective shelters
  • Blast management
  • Physics of explosions
  • Biological effects of explosions
  • Resistance of concrete and other materials to explosions
  • Handling of unexploded bombs (Bernal risked his life many times by defusing real unexploded bombs)
  • Physics of air raids
  • Statistical analysis of bombing raids
  • Effects of breakwaters in sinking boats
  • Properties of pykrete
  • A synthetic iceberg as an airstrip for bomber operations

 

While much of what Bernal accomplished was not crystallographic – even within his wide interpretation of the subject – I give below an example of his non-crystallographic war work, followed by one war project which certainly did relate to materials and their functionality. Finally I say something about the work that involved me – the polywater story.

(a) Statistical analysis of bombing raids

If there was one area of science above all others in which Bernal, as scientific advisor, had left his distinctive mark it would, I believe, be on his use of statistical analysis; one might call it Bernal's war-time legacy. Bernal took its implementation to a new level, in terms of both the surveying and the interpretation of the raw data. This was particularly so for assessing the effectiveness of bombing raids of both sides in causing both physical and psychological damage.

An assortment of volunteers and students, as well as professional statisticians, were used to establish relationships between damage, tonnage of bombs deployed, type of environment ascertained from observation, previous conflicts and accurate maps. Similar methodology was used to measure loss of morale using medicinal changes and increased alcohol consumption as indicators of population morale. Interestingly, the loss of morale in the affected population was generally less than expected. The rigour and neutrality behind the data from the statisticians were a breath of fresh air compared with the unverified and sometimes exaggerated claims made by those carrying out the ‘work’, such as flight crews. One issue of great irritation to the statisticians was the ignoring of their predictions, meaning the lives of pilots were sometimes being put in danger unnecessarily as they carried out bombing missions that statisticians had already shown to be of little value.

I close this section with an anti-intuitive statistical gem: more damage was inflicted on RAF aircraft parked on the ground than during aerial combat.

(b) Habakkuk

Habakkuk was an Old Testament prophet who invited the heathen to look upon his unbelievable works in fear (“I will work a work in your days which ye will not believe, though it be told you”); Brown (2005) also suggests the name might have been chosen after a character in Voltaire’s Candide “who was, like Mountbatten, capable of anything”. So, it was perhaps appropriate that Habakkuk was used as the name for one of the most imaginative and ambitious projects of World War II: to produce man-made icebergs to serve as gigantic aircraft carriers. The reasons for Habakkuk were not obvious, nor was it obviously feasible. However, consider the following remarkable attributes:

  • The cost of the building materials is virtually zero.
  • The breakup cost is virtually zero since the main component simply melts away.
  • The project is ecologically 'green'. 
  • The project is economically independent of how long the structure operates.
  • The structure is mobile with a range of thousands of miles, and so can be positioned to match war requirements.
  • The structure would need to last for only a few years, unlike a commercial equivalent.

With these points taken into account the project does appear attractive. The iceberg would be powered by a number of propelling units, and steered by a combination of those units and a gigantic rudder. Inside the structure would be refrigerator units supplementing the natural environmental chill, keeping it at sub-zero temperatures. To give some idea of the feasibility of staying cool, a scaled-down model was built that took two years to melt naturally.

The icebergs were to be built using pykrete – a mixture of 15% wood shavings and 85% ice. This material, named after its inventor Geoffrey Pyke, has remarkable strength, and melts very slowly. The plan was to make each of these icebergs the size of 25 conventional aircraft carriers.

If correctly constructed, pykrete blocks are stronger than concrete by weight and their thermal conductivity is lower than ordinary ice by an order of magnitude – the wood shavings behave as thermo-mechanical barriers. It was what we now know as a composite material; then, it was 40 years ahead of its time.

It was a controversial project. Some believed it was outlandish. Others including Churchill thought it had sufficient merits to be worth a try. The pykrete block was tested by Max Perutz (see article by Christine Slingsby above) – the same Perutz who went on to win with John Kendrew the Nobel Prize for his work on haemoglobin.

A somewhat amusing scene took place in a briefing session on board the Queen Mary (see Fig. 2). A block of pykrete and a block of ordinary ice were presented to an audience, which we believe included Churchill. One General Arnold attempted to break the ice block with an axe. He succeeded easily. When trying to break the pykrete block, not only did the axe fail to cause any damage, but also the resulting shock-wave travelling up Arnold's arm caused him to gasp in pain.

[Figure4]Figure 2. The pykrete test!

In typical dramatic style, Lord Mountbatten decided to repeat the experiment, but with a revolver. The ordinary ice shattered. In contrast, the pykrete block suffered little damage. Moreover, the bullet ricocheted off, narrowly missing one of the observing officers. It is said that pykrete was demonstrated by Churchill at dinner parties. He would present two apparently similar blocks of ice, but one of them would appear not to melt, or would melt only very slowly, presumably amazing his guests.

Despite these positives, the project was turned down after the requirements expanded. The required travelling range grew to 7,000 miles, the required lifetime expanded to 3–5 years, and the weight to be carried grew from that of fighter planes only to bombers and fighters. These increases in requirements, and the increase in distances that aircraft could fly without refuelling, combined to result in the project's cancellation.

(c) Polywater

Polywater was the name given to an allegedly new structural form of water being worked on by the Russian group of Boris Deryaguin, and was being followed up by various international groups. I was aware of the work of Deryaguin mainly because of his classic publication on the DLVO theory of surface interactions. He had a high reputation in the scientific world, so when he made the surprising claims regarding the existence of a new from of water, he was given the benefit of the doubt. He claimed that water could be persuaded to condense onto confined silicate surfaces (e.g. glass or quartz capillaries) in a form that exhibited significant changes in its physical properties, such as boiling point, freezing point and density–temperature profile. Deryaguin's claims went further: he said that when ordinary and polywater droplets co-existed in proximity but with no physical contact, the polywater droplets could grow at the expense of the ‘ordinary’ water droplets. He was saying ordinary water could transform easily into polywater, implying polywater was a more stable form of H2O.

When I was a postdoctoral researcher in Cambridge in 1968, I attended a lecture on polywater given by Deryaguin who was visiting the UK. I then wrote to Bernal at Birkbeck and asked if I could join his team which I had heard was to start research into polywater. Thus my four decade career at Birkbeck began. So in some ways Deryaguin was responsible for my association with Birkbeck. This is somewhat ironic, since he later tried to get me – and the rest of the team (including John Finney, current editor of Crystallography News) – sacked.

At the time I joined Birkbeck, the scientific community was full of polywater rumours and counter-rumours, and these extended into the wider academic world, industry and government. The issue started to feature in mainstream newspapers and TV. I was even interviewed about polywater, along with some of my Birkbeck colleagues, by the BBC.

Several ad hoc scientific meetings were arranged to address the issue. I remember one in particular in 1969, attended by about 40 physicists and chemists. The morning session consisted of everyone having an opportunity to describe their experiences making or using the alleged polywater. Reports fell into three categories:

  1. I am trying hard but cannot make any polywater.
  2. I can make polywater, and I am trying to measure some property (e.g. X-ray spectra, boiling point, freezing point).
  3. Beware of the misleading effects of surface chemistry.

At the end of that meeting, various follow-up meetings were arranged to take place depending on the outcomes of further work. It may be that none ever took place...

Further communications on the subject became progressively quieter and less frequent when the Birkbeck group decided it was time we went public with the results of our work on the problem: that all such ‘sightings’ were nothing more than surface effects and contamination. And there was no real danger to our planet, as there would have been had ‘polywater’ indeed been a more stable form of H2O as claimed by some polywater adherents. We said polywater did not exist; what others had found were just ‘polypollutants’ (Bernal et al., 1969; Barnes et al., 1971).

After publication we waited for the response which we expected would be an onslaught of invective against anything found carrying the name of Birkbeck. In the event it was the opposite: near-silence except for a letter from Deryaguin to Bernal urging that the Birkbeck team should be sacked for incompetence! Communications on polywater then appeared to vanish altogether, its champions seeming to have given up and moved onto other projects. Polywater was dead, killed by a deafening silence.

I think Deryaguin had been reporting what he believed to be true, based on information given to him by his experimental colleagues. He himself was more of a theoretician. A few years after our paper, Deryaguin, to his credit, retracted his previous claims in print.

A final comment

A question about Bernal: one long mission or multiple short-term solutions?

While waiting for a bus I sometimes play my mind game Categorize in which I try to place all members of a chosen group into the lowest possible number of categories. For example if the group comprised all famous crystallographers, dead or alive, known by me, I might try to sub-divide the members into two categories: those who are driven or inspired in their research as part of a life-long mission (e.g. seeking a cure for cancer; developing a new quantum theory) and those who are driven by the repeated thrill of solving many short-term problems (e.g. regularly solving the Times crossword). I can usually make an informed choice between the two but when the case of Bernal comes up, clarity disappears, as I uncover signs in his history that can apply to either of the two forms of inspiration. This ambiguity might in turn be related to another of Bernal’s renowned abilities, that of multi-tasking, evident long before the modern use of the term had been invented.

So the answer to the above question is that Bernal was in both categories.

Concluding remarks

In my opinion, Bernal was one of the greats, both for who he was and for what he did. His abilities included an amazing memory, a fertile imagination and a determination to make science work for the benefit of mankind.

I rate him as one of the four founding pillars of X-ray crystallography. Röntgen discovered X-rays; von Laue confirmed X-ray diffraction; the Braggs used X-rays to reveal crystal structure. For me, the fourth pillar is Bernal, since he linked the above discoveries and systematised X-ray crystallography.

A case could be made that Bernal should have been awarded whole or part of four Nobel Prizes: a share in the one awarded to Dorothy Hodgkin, a share in the one awarded to Max Perutz and John Kendrew, and two prizes that were never awarded; one for his founding work linking X-ray diffraction with the structure, properties and function of crystalline material, and another for his founding work on liquids, water and hydrogen bonding. As to why Bernal was never a Nobel laureate, the reasons offered range from political forces to being active in too many different areas of science. These reasons are still debated now, 50 years after his death.

One final remark. Over the last 18 months we have seen scientists around the world work together for the benefit of mankind as they delivered vaccines effective against COVID-19. The level of cooperation and the speed with which life-saving results have been delivered has been unprecedented and remarkable. This is exactly the role that Bernal wanted for science. If had lived to see this, he would have been very happy.

Acknowledgements

This article is derived from my own experience plus a host of discussions and written sources too numerous to mention, with the exception of Andrew Brown’s excellent biography (Brown, 2005), which has been my main written source. Special thanks are due to Michael O’Callaghan, friend and colleague, who has been a huge help in the research and writing of this article.

References

Barnes, P., Cherry, I. A., Finney J. L. & Peterson. S. (1971). Nature, 230, 351.

Bernal, J. D., Barnes, P., Cherry, I. A. & Finney, J. L. (1969). Nature, 224, 393–394.

Brown, A. (2005). J. D. Bernal: The Sage of Science. Oxford University Press.

 

Bernal, water and liquids

John Finney, University College London, UK

Though Bernal threw out ideas for others to develop, he kept the development of his approach to liquids for himself. Initially, his interest was sparked by the biological relevance of water, saying “My interest in the subject... came about... through my biochemical interests, in that all living structures are mostly composed of water” (Bernal, 1964). This interest was to lead to a landmark paper in 1933 published in the first number of the Journal of Chemical Physics (Bernal & Fowler, 1933). Bearing in mind that this was only 20 years since X-rays were first diffracted from a crystal, and barely a decade since the first methods of working back from a diffraction pattern to a crystal structure were successful, to tackle the much more difficult problem of liquids, where there was inadequate understanding of how to interpret the broad diffraction patterns that liquids gave, was ambitious to say the least.

Arguing that the charge distribution on a water molecule was near-tetrahedral, Bernal proposed that as opposite charges would attract, the local molecular structure should be essentially tetrahedral (see Fig. 1).

[Figure5]Figure 1. The ideal local tetrahedral arrangement of water molecules as first envisaged by Bernal in 1933. Two of the four molecules surrounding the central one are in the plane of the paper, while one is above and one is below.

Noting that silica (SiO2) also forms similar local structures, he developed ‘disordered’ versions of two silica structures (quartz and tridymite) to fit the X-ray data. With this model, he was able to explain a wide range of the properties of water and ionic solutions, as listed in the short summary heading that paper shown in Fig. 2.

[Figure8]Figure 2. The ‘Short summary’ of Bernal’s classic 1933 water paper.

It is also worth noting that the not-quite tetrahedral charge distribution he used is essentially the father of the effective pair potentials used today in simulations of water and aqueous systems.

In Birkbeck, he returned to the water problem in the 1950s, when he recognised that his 1933 approach “was, frankly, one of crystal structure, trying to picture water structure as that of a mixture of the analogous four co-ordinated structures of… quartz and tridymite”, and that “This was ultimately to prove rather a delusive approach, postulating a greater degree of order… in the liquid than actually exists there” (Bernal, 1964).

However, rather than return to the specific problem of water, he recognised that he first needed to understand the structures of simpler liquids. Theoretical approaches to the liquid state at the time treated liquids either as disordered (crystalline) solids (as Bernal had done in the 1933 water paper) or as dense gases. Though the disordered crystal approach was mathematically tractable and could yield correct densities, it assigned too much order to the liquid – the predicted entropy was too low. On the other hand, treating liquids as dense gases required unphysical mathematical approximations: though the entropy could come out OK, the densities that could be handled were too low to be representative of real condensed-phase liquids.

Bernal found both these approaches unsatisfactory. So instead he tried to find an approach that:

  • was a concrete picture of the structure (Bernal was a crystallographer and so naturally would want to visualise the atomic arrangement);
  • was consistent with Ockham’s razor (‘entities should not be multiplied beyond necessity’);
  • was homologous to that of the crystalline solid as well as radically different in kind;
  • had a general quality of homogeneity without the assumption of any special groups.

The most general hypothesis he came up with was to treat the liquid “as homogeneous, coherent and essentially irregular assemblages of molecules containing no crystalline regions” (Bernal, 1964). This concept he realised in the laboratory with assemblies of steel ball bearings, contrasting liquids as irregular heaps of molecules as against crystals as regular piles. Fig. 3 illustrates the differences!

 

[Figure7]Figure 3. Bernal’s concept of the simple liquid as an irregular heap of molecules (left) compared with the regular pile of the crystal (right).

This structural approach was indeed radically different from that of other workers on the liquid problem – and indeed Bernal apologised to “the modern theoretical physicist for introducing such a simple way of looking at things, but I believe on the whole that it is better to start with a model that has some resemblance to reality” (Bernal, 1959).

And indeed the model was successful for simple liquids such as those of the inert gases. It gave correct densities, explained density changes on melting, had the right degree of disorder and essentially predicted the observed X-ray scattering. In the late 1960s, it was also successful in explaining structures of amorphous metal alloys. The coordinates of a large laboratory model on which much of the later work was based continues to be requested and used for a variety of theoretical and practical purposes (Finney, 1970). And John Ziman, a key theoretician of liquids in the second half of the 20th century, commented that “This simple idea… is now seen to be the key to any qualitative or quantitative understanding of the physics of liquids” (Ziman, 1979). Similar comments were made in 1970 by John Rowlinson of Imperial College, one of the foremost theoretical chemists who has spent a lifetime working on liquids:

"It has therefore been hard to admit that the form or even the existence of the attractive forces has little direct effect on the structure of a liquid, as described, for example, by the pair distribution function g(r). The recent realization of this truth has followed the extensive studies… of the properties of assemblies of hard spheres without attractive forces” (Rowlinson, 1970).

Recent work is also suggesting that Bernal’s model can explain the behaviour of liquids above the critical point, where the liquid/vapour coexistence line that vanishes at the critical point continues into the supercritical region as a line of maximum heat capacity (Finney & Woodcock, 2014).

So how did Bernal move from this ‘irregular heap’ model to the more complex water problem? Simply by recognising that a disordered non-crystalline arrangement could also be built up of molecules interacting in the essentially tetrahedral fashion of Fig. 1 to produce a random network of molecules, as against the random packing of the spherical molecules of simple liquids. Fig. 4 shows a ball and stick visualisation of a random network compared to the ordered crystalline arrangement of hexagonal ice.

[Figure8]Figure 4. A ‘spaghetti model’ visualisation of (left) crystalline ice Ih, compared with (right) the ‘random network’ arrangement of liquid water.

So Bernal’s final view of water (Finney, 2007, 2015) was that:

  • Water is essentially a ‘random network’ of water molecules.

  • Each molecule interacts with its neighbours in an approximately tetrahedral geometry.

  • Local coordination is ideally fourfold, but with some variation.

And it compared well with experimental results. It explains the main properties of water such as expansion on freezing, the temperature of maximum density and other so-called anomalies, the mobility of hydrogen, and structural changes with temperature and pressure. It is consistent with current state-of-the-art experimental and computational work, which demonstrates that Bernal’s random network concept is essentially correct. And it has indeed helped us to understand water’s biological role – the reason that Bernal started working on the problem in the first place.

References

Bernal, J. D. (1959). Proc. Roy. Inst. 37, 355.

Bernal, J. D. (1964). Phil. Trans. Roy. Soc. A, 280, 299.

Bernal, J. D. & Fowler, R. H. (1933). J. Chem. Phys. 1, 515–548.

Finney, J. L. (1970). Phil. Trans. Roy. Soc. A, 319, 479. Data available at https://www.digitalrocksportal.org/projects/47

Finney, J. L. (2007). J. Phys. Conf. Ser. 57, 40–52.*

Finney, J. L. (2015). Water. A Very Short Introduction. Oxford University Press.**

Finney, J. L. & Woodcock, L. V. (2014). J. Phys. Condens. Matter, 26, 463102.

Rowlinson, J. S. (1970). Disc. Faraday. Soc. 49, 30.

Ziman, J. M. (1979). Models of disorder, p. 78. Cambridge University Press. 


*For a fuller account of the development of Bernal’s ideas on the structure of water.

**For an updated account of our understanding of water.

 

Bernal’s Irish connections and his enduring legacy at the Bernal Institute

Vincent Casey, University of Limerick, Ireland

John Desmond Bernal was born at the dawn of the 20th century (1901) and subsequently became one of the pioneering scientists associated with that century and the renaissance in science which it heralded. He addressed the big questions of his day. For instance: what is life and how did it originate? (Bernal, 1967). He was convinced that the answer lay within the structure of matter and the molecules where form and function would be closely entangled. Those he inspired were subsequently involved in the nascence of structural biology (see article by Christine Slingsby above) and were duly acknowledged for their pioneering work by the Nobel Committee. It is fair to assert that Bernal laid the groundwork that ultimately led to the extinction of the ‘vital force’ postulate in much the same way that Einstein’s relativity theories banished the luminiferous ether. Bernal was very much aware of the important role played by science in history, as is clear from his four-volume book set of that title (Bernal, 1969), and of its critical role in shaping society and so was active in pioneering the use of scientific methods to solve major social (Cross & Price, 1988) and political (Bernal, 1958) problems of his time. For a comprehensive account of his life and work, Andrew Brown’s biography is a most interesting and engaging read (Brown, 2005).

Bernal was born in Nenagh, Co. Tipperary, before Ireland won its independence. He was therefore a British citizen. Nevertheless, he was deeply ‘imprinted’ by his Irish childhood. He traced his roots to a mid-nineteenth century Sephardic Jewish migration. His grandfather, John Bernal, ran a successful auctioneering business in Limerick city and was also active in Limerick city politics. Around 1900, John Bernal’s son, Samuel George Bernal (J. D. Bernal’s father) bought a 147 acre country estate on the outskirts of Nenagh, complete with estate house, Brookwatson (National Inventory of Architectural Heritage, 2004). Considering those class-conscious times, this is likely to have placed the Bernals amongst the Anglo Irish landed gentry ruling class. The 1911 Irish census lists those staying at Brookwatson to include his parents, siblings, two relatives and four servants (Casey, 2021).

Bernal commemoration

Until recently, Bernal was largely unknown in Ireland although better established, if neglected, among our colleagues in the UK. In recent times, Bernal’s contributions to science and to society have been acknowledged and he has been commemorated in various ways both in the UK and in Ireland. On the occasion of the unveiling of a plaque (on 20 July 2005) in honour of J. D. Bernal by the National Committee for Science and Engineering Commemorative Plaques in his home town of Nenagh (see Fig. 1), Martin Bernal (J. D. Bernal's son) wrote: “Now, 35 years after his death, John Desmond Bernal has received this ultimate accolade”. In 2006, the Munster branch of the Institute of Physics in Ireland organised a conference entitled ‘John Desmond Bernal: Science and Society’ with keynote speakers who knew and worked with Bernal (Finney, 2007; Mackay, 2007). Earlier, in 2001, an English Heritage blue plaque was erected at 44 Albert Street, London, where Bernal lived. And in 2013, after some years of planning, the magnificent Bernal Institute was opened by the Taoiseach (Irish Prime Minister), Mr Enda Kenny, on the University of Limerick riverside campus.

[Figure9]Figure 1. Pictured (photograph by V. Casey) in front of the science and engineering commemorative plaque to John Desmond Bernal are (left to right) Professor Alan Mackay, Dr Martin Bernal, Professor John Finney, Professor Helena Sheahan and Dr Andrew Brown.

The Bernal Institute, University of Limerick

In October 2010, the University of Limerick, arising out of ongoing work with Atlantic Philanthropies, prepared an ambitious Science and Engineering development plan under the stewardship of Professor Kieran Hodnett. Coinciding with the publication of Andrew Brown’s book (Brown, 2005), the University of Limerick (UL) had an ideal opportunity to celebrate the life and achievements of a local lad (Nenagh lies just 35 km from the University of Limerick campus), who was one of the most influential scientists of the 20th century. This was the genesis of the Bernal Project, and preliminary planning for the Bernal Institute (BI) started in early 2011.

The Bernal Project ultimately resulted in a €100+ million investment in people and buildings to enable spatial integration of Science and Engineering disciplines at UL. The vision was to support synergies that result from close multidisciplinary collaborations and strong links with an Irish and international industrial base forged through UL’s ‘cooperative education’ programme, an industry–academia education partnership. The overall project objective is to address societal challenges that require disruptive new technologies enabled by materials science and engineering.

The preliminary proposal envisaged the recruitment of ten Bernal Professors to act as international leaders in their fields and to develop the resources, equipment and infrastructure needed for the successful pursuit of both fundamental and applied research. Bernal was an extraordinarily generous mentor to younger colleagues. In appointing Bernal Professors UL therefore sought out candidates who would exhibit this same generous spirit of mentorship. A preliminary schedule of accommodation for the new building envisioned ten specialised laboratory suites in a 6,000 m2 building, with associated office and write-up space, seminar rooms, lecture theatres and social space. The total cost of the project was projected to be €52 million. The BI project proposal was accepted for funding and an activity whirlwind of building design and recruitment followed with a three year timeline.

In September 2013, prior to the official launch of the Bernal Project, the President of the University of Limerick hosted a dinner for some family members and friends of Professor Bernal. The attendees included Gay-Caroline Bernal (Bernal’s granddaughter) who regaled the company with her childhood memories of visiting her grandfather in his offices in Birkbeck College, London, and playing with his modelling materials including, we suspect, those used in models to support his theory of liquids (see John Finney’s article above). Friends present included John Finney, UCL, a former external examiner to UL’s applied physics degree and a previous student of Bernal’s. Also present was R. J. Polle (Jack), just retired from active service as a vet having served the Brookwatson farm for over 70 years. He remembered meeting Bernal in 1950 when even at that stage, Bernal predicted how global warming caused by CO2 emissions would lead to climate change.

By the time the Bernal Project was officially launched in October 2013 by ‘An Taoiseach’, seven of the ten Bernal Chairs had been filled (Fig. 2) and the building aspect of the project was concluded in 2016 (Fig. 3). Three additional chairs have subsequently been filled in composite materials, process engineering and structured materials.

[Figure10]Figure 2. Official launch of the Bernal Institute: (left to right) Professor Edmond Magner, Professor Don Barry (President UL), Professor Bartek Glowacki (Bernal Chair in Energy), Professor Gavin Walker (Bernal Chair in Pharma Powder Engineering), Professor Ursel Bangert (Bernal Chair in Microscopy and Imaging), An Taoiseach Enda Kenny TD, Professor Jacques Huyghe (Bernal Chair), Jon O’Halloran (BI Operations Manager), Professor Michael Zaworotko (Bernal Chair in Crystal Engineering), Professor Harry Van den Akker (Bernal Chair in Fluid Mechanics), Mary Shire (Vice President Research, UL). Photograph courtesy of UL.

[Figure11]Figure 3. The sun about to rise over the Penrose tiling patterns that decorate ‘The Cube’, the large lecture hall in the Analog Devices Building of the Bernal Institute. Photograph courtesy of M. J. Zaworotko.

Bernal’s enduring science legacy – the Bernal Institute

Bernal had many and varied interests, making key scientific contributions in his own time. He remains highly influential in many scientific domains. His early work on graphite (Bernal, 1924), for instance, laid the foundation for the recent burgeoning research related to graphene (Sandhya et al., 2021). For a comprehensive bibliography of Bernal’s writings see Dorothy Hodgkin’s Royal Society Biographical Memoir (Hodgkin, 1980).

Some ongoing Bernal Institute projects

Under the umbrella of ‘structures matter’, the BI has developed five research clusters that span the full range of matter length scales and materials: (i) biomaterials, (ii) molecular and nanomaterials, (iii) 3D electron diffraction, (iv) composite materials, (v) process engineering. Each of these clusters engages in research projects targeted at societal challenges related to sustainability and/or human health. The clusters are supported by world-class imaging facilities and molecular modelling research groups. Some highlights of the research in these clusters, several of which involve the study of crystals including crystal growth, are summarised below.

(i) Biomaterials

The Biomaterials Research Cluster focuses on structured biological materials, and systems based on molecular and cellular building blocks that range from molecular ensembles to cells/cell aggregates, tissues and organs, and the interface with non-biological materials such as implants, drugs and their combination. Professor Tewfik Soulimane studies how diphenylalanine (FF) demonstrates a robust ability to self-assemble at the nanoscale forming a variety of structures ranging from nanospheres to nano- and microtubes resulting in outstanding functional properties including pyro- and piezoelectricity. FF nanotubes mimic the structure of β-amyloid fibrils characteristic of Alzheimer's disease and thus can serve as a model material in biology and medicine. Water confined in self-assembled FF peptides displays the properties of both bulk and nanoconfined water – confined water is critical to understanding the role of water in molecular biology where almost all water can be considered as confined water and/or mixed with ions and other molecules in aqueous solutions. Professors Tofail Syed and Damien Thompson study how piezoelectricity can be controlled through the self-assembly of amino acids. Piezoelectricity has attracted recent interest due to its manifestation in biological molecules such as synthetic polypeptides or amino acid crystals, including γ-glycine. It has also been demonstrated in bone, collagen, elastin and the synthetic bone mineral hydroxyapatite. Piezoelectric coefficients exhibited by these biological materials are generally low, limiting technological applications. Research guided by quantum mechanical calculations has changed this situation, with the demonstration that the amino acid crystal β-glycine possesses a piezoelectric coefficient similar in magnitude to materials such as barium titanate or lead zirconate titanate that are in commercial use.

(ii) Molecular and nanomaterials

The expansion of computational power, the development of better/faster characterization methods and the evolution of self-assembly and supramolecular chemistry have enabled the dream of ‘materials by design’ to approach fruition. This ‘materials design revolution’ is poised to profoundly influence society by impacting, amongst other matters, energy sustainability and drug development. Simply put, by finding the right chemistry, materials scientists and engineers can gain the level of power that architects have when they design new buildings. Crystalline materials by design – crystal engineering – is one of themes of this cluster.

[Figure12]Figure 4. ‘Skyscrapers’ – an image of crystals of coordination polymers taken by Bernal Institute post-graduate student Shi-Qiang Wang. This image was awarded a prize in the Crystal in Art Virtual Competition 2020 of the British Association of Crystal Growth (BACG). Photograph courtesy of M. J. Zaworotko.

Bernal Chair of Crystal Engineering Professor Michael Zaworotko leads the crystal engineering research group that he established upon joining UL in 2013. Crystal engineering is enabled by one of Bernal’s legacies: the Cambridge Structural Database, CSD. The CSD was proposed by Bernal (Bernal, 1960a,b) and constitutes perhaps the first scientific database. There are two main areas of study in the crystal engineering group: advanced porous materials and multi-component pharmaceutical materials. Recent highlights include articles in Science in 2016 and 2019 that dealt with improving the energy efficiency of ethylene purification, the largest volume product of the petrochemical industry. Dr Matteo Lusi leads a research group that studies mixed crystals – solid solutions of two or more molecular compounds that are characterized by structural disorder that enables variation of stoichiometry in continuum. Often such variation results in modulation of structural and physicochemical properties which, in turn, facilitates fine-tuning of bulk properties. Such behaviour is particularly important in pharmaceutical, agrichemical and optoelectronic materials. Professor Kevin Ryan leads a team that studies colloidal nanocrystals with particular emphasis on semiconductor nanorods and their device scale assembly by directed (electric fields) or non-directed approaches for scalable applications in photovoltaics. The team has pioneered routes whereby the nanorods can be assembled from solution such that each rod is vertically aligned and close-packed. A second work programme addresses low-cost solution synthesis of silicon and germanium nanowires by seeded and non-seeded strategies, targeted particularly towards generating wires in high yield. Control over nanowire length for the formation of nanorods was achieved by a modification of this synthesis protocol.

(iii) Timepix and 3D electron diffraction

Dr Andy Stewart leads a 3D Electron Diffraction group. Structure determination of nanocrystals of organic pharmaceutical compounds by 3D electron diffraction (3DED) at room temperature is possible using the Timepix direct electron detector with increased quantum detection efficiency (Genderen et al., 2016). A convolution of the electron density and the nuclear charge makes it possible to determine the position of hydrogen atoms in structures without the need to grow millimetre-sized crystals for neutron diffraction studies. It is hoped that the ability to investigate nano-sized crystals will answer the question of why so few crystal polymorphs are currently observed despite the many possible based on crystal structure predictions. Is it a question of kinetics – the crystals cannot be grown to sufficiently large size or in sufficient numbers to be used in X-ray studies? It is hoped that the fast developing field of 3DED will help reveal the deeper crystal physics behind this question.

Until recently, structure determination of organic compounds by transmission electron microscopy required data collection at liquid-nitrogen temperatures to reduce the effects of radiation damage. The novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, removing the need to freeze the specimens to obtain data good enough to enable ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e Å−2 s−1) collected at room temperature were of sufficient quality for structure determination using software developed for X-ray crystallography which includes the appropriate electron scattering factors.

The Stewart group showed that 3DED coupled with a sensitive Timepix detector allows fast and efficient three-dimensional crystal structure analysis of organic pharmaceutical compounds at room temperature. The technique will allow higher-throughput examination of nanometre-sized samples in a transmission electron microscope complementing standard single-crystal and powder X-ray diffraction. The recent advances in 3DED have led to an interesting new question for crystallography. Electron microscopes are sensitive enough to observe the transition from nucleation to particles and onto crystals during the growth process. This raises the question as to how many unit cells are sufficient to produce an observable crystal, the structure of which can be determined by 3DED methods. This question is particularly pertinent for crystal growth and phase-change materials. Currently, the International Union of Crystallography’s definition of a crystal does not provide a quantitative number to declare an object as a crystal. The Stewart group has been working on this question [a talk on this was given at the 2021 BCA-BACG Spring Meeting (Crystallography News, 2021)] and will be shortly publishing a paper suggesting a methodology to quantitatively define an object as crystalline.

(iv) Process engineering

Professor Gavin Walker leads the Process Engineering Cluster, which is aligned to UN Sustainable Development Goals in Health, Energy and the Environment/Sustainability. Improving population health and well-being is critically dependent on the development of new biopharma solutions which, in order to complete the drug approval process and have maximum impact, must be amenable to scalable processing and manufacture, this often demanding innovative processing. Ensuring access to affordable, reliable, sustainable and modern energy for all will require a substantial increase in the share of renewable energy in the global energy mix. Advanced energy storage solutions are sought and can help here through C-storage/conversion but so too can process synthesis and integration. Fostering and supporting responsible consumption and production ensuring sustainable consumption and production patterns can reduce waste generation through prevention, reduction, recycling and reuse. Reduced solvent waste can be achieved through solvent-free processing of advanced materials and through multiphase, bio- and hybrid processing.

(v) Composite materials

Professor Paul Weaver leads this cluster, a major aim of which is to help develop new industry in Ireland based on new intellectual property. To meet this aim the cluster focuses on two main application areas: renewable energy and sustainable aircraft transport. Research involves a combination of materials development, manufacturing technology and design methods where each will be pursued in balance and harmony with one other so that equi-fidelity contributions to technology are made. In terms of renewable energy, Dr Maurice Collins leads a research programme pursuing the development of new carbon fibre materials from sustainable resources (lignin). Once large-scale production of these materials is achieved, composite materials will be developed using thermoplastic matrices from natural, sustainable supplies. Research in manufacturing and design methods both contribute in a complementary manner to application areas such as renewable energy and sustainable transport. A research focus of the cluster is on the development of methods of manufacturing composites that will help reduce the cost of energy for wind turbine blades and lead to cheaper, better-performing aircraft (less fuel burn). Design methods will focus on advanced stress analysis development and subsequent tool development that exploits our new combination of materials and manufacturing technology.

Concluding remarks

The future focus of the Bernal Institute is likely to include, in addition to current themes, areas such as sustainability in food, energy and water, three areas of application where the Institute has growing momentum. It seems inevitable that the structure–function relationships of crystalline and non-crystalline materials that inspired Bernal will continue to guide its direction. We are now at the stage where crystal engineering can have major positive impact on our future. Engineered crystals that can efficiently separate mixed gases and abstract specific molecules from the atmosphere have been demonstrated. An application of this technology with obvious world-saving potential is one-step separation of CO2 from the air at ambient temperature and pressure to combat global warming. Another crystal engineering system currently under trial could help solve the developing world’s need for potable water by direct extraction from the atmosphere [these last two projects were described in Michael Zaworotko’s Plenary talk at the 2021 BCA-BACG Spring Meeting (Crystallography News, 2021)].

The field of crystallography has expanded enormously since the 1920s when Bernal commenced his pioneering research at Cambridge elucidating the structure of life’s molecules using XRD. A century later, it is clear that crystals and the science of crystallography will continue to expand the social function of science to create a more equitable and harmonious society. With what has already been achieved and the exciting future prospects, we may, with good reason, hope that crystals are going to play a major role in saving the world.

Acknowledgements

I would like to acknowledge contributions to this article by Professor Kieran Hodnett, Professor Edmond Magner, Professor Michael Zaworotko, Dr Matteo Lusi, Dr Tofail Syed, Professor Tewfik Soulimane and Dr Andrew Stewart, all of whom gave freely of their time and support. Jon O’Halloran, BI Operations Manager, has also been most supportive.

References

Bernal, J. D. (1924). Proc. R. Soc. A106, 749.

Bernal, J. D. (1958). World Without War. Routledge.

Bernal, J. D. (1960a). Acta Cryst. 12, 1097.

Bernal, J. D. (1960b). Aslib Proc. 12, 432–438.

Bernal, J. D. (1967). Origin of Life. Weidenfeld and Nicolson.

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The articles above have been reproduced with permission from Crystallography News, published by the British Crystallographic Association.

22 September 2021