Bernal structure

Fig. 1 Atomic structures of graphites, a) Bernal structure of perfect three-dimensional graphite, b) Warren structure of two-dimensional turbostatic graphite with no layer registration. (Reproduced by kind permission of Thermo-Hypersil-Keystone.)...

An even more general and correspondingly less detailed atomic model of amorphous oxide surfaces has been called the Bernal surface (BS)[3, 21]. It is based upon the fact that many oxides and halides can be regarded as close-packed arrays of large anions with much smaller cations occupying interstitial (usually tetrahedral or octahedral) positions (see., e.g. Ref. [4]). In line with this point of view, the BS is a surface of a collection of dense randomly packed hard spheres, a sphere representing an oxide anion. The cations in interstitial positions between hard spheres are excluded from the simulation since they do not attract adsorbed molecules due to their small polarizability. Thus only the atomic structure of the oxide ions is considered. This is called the Bernal structure and has been used for modelling simple liquids and amorphous metals [15]. 

Theoretically, protein structure can be described with the same structural parameters used for describing the constitution, configuration, local and overall conformation, and association as in the case of other types of macromolecules. However, partly for reasons of expediency, one speaks of primary, secondary, tertiary (Linderstr0m-Lang), and quarternary (Bernal) structure in protein chemistry. 

At this point we should also recall another application of the already mentioned Bernal model of amorphous surface. Namely, Cascarini de Torre and Bottani [106] have used it to generate a mesoporous amorphous carbonaceous surface, with the help of computer simulation and for further application to the computer simulation study of adsorption. They have added a new component to the usual Bernal model by introducing the possibility of the deletion of atoms, or rather groups of atoms, from the surface according to some rules. Depending on the particular choice of those rules, surfaces of different porosity and structure can be obtained. In particular, they have shown examples of mono- as well as pohdispersed porous surfaces... 

The theory of the structure of ice and water, proposed by Bernal and Fowler, has already been mentioned. They also discussed the solvation of atomic ions, comparing theoretical values of the heats of solvation with the observed values. As a result of these studies they came to the conclusion that at room temperature the situation of any alkali ion or any halide ion in water was very similar to that of a water molecule itself— namely, that the number of water molecules in contact with such an ion was usually four. At any rate the observed energies were consistent with this conclusion. This would mean that each atomic ion in solution occupies a position which, in pure water, would be occupied by a water moldfcule. In other words, each solute particle occupies a position normally occupied by a solvent particle as already mentioned, a solution of this kind is said to be formed by the process of one-for-one substitution (see also Sec. 39). 

More complicated and less known than the structure of pure water is the structure of aqueous solutions. In all cases, the structure of water is changed, more or less, by dissolved substances. A quantitative measure for the influence of solutes on the structure of water was given in 1933 by Bernal and Fowler 23), introducing the terminus structure temperature, Tsl . This is the temperature at which any property of pure water has the same value as the solution at 20 °C. If a solute increases Tst, the number of hydrogen bonded water molecules is decreased and therefore it is called a water structure breaker . Vice versa, a Tsl decreasing solute is called a water structure maker . Concomitantly the mobility of water molecules becomes higher or lower, respectively. 

In 1933, Bernal and Crowfoot [1] reported on the solid state polymorphism of p-azoxyanisole. They found two crystalline modifications of this compound, a stable yellow form and an unstable white polymorph. Krigbaum et al. [31 reexamined the crystal structure of the stable yellow form. The compound shows an imbricated structure which is the basic packing required for nematic behaviour according to Gray [132]. 

An important phenomenon when considering the differences between ice I and liquid water is that water achieves its maximum density not in the solid state, but at 4 °C, i.e. in the liquid state. The reasons for this were first discussed by Bernal Fowler (1933). They noted that the separation of molecules in ice I is about 0-28 nm, corresponding to an effective molecular radius of 014 nm. Close packing of molecules of such radius would yield a substance of density 1-84 g cm" . To account for the observed density of 10 g cm" , it was necessary to postulate that the arrangement of molecules was very open compared with the disordered, close-packed structures of simple liquids such as argon and neon. 

Del Nozal, M. J., Bernal, J. L., Gomez, L. A., Higes, M., and Meana, A. (2003b). Determination of oxalic acid and other organic acids in honey and in some anatomic structures of bees. Apidologie 34,181-188. 

Globular proteins were much more difficult to prepare in an ordered form. In 1934, Bernal and Crowfoot (Hodgkin) found, that crystals were better preserved if they were kept in contact with their mother liquor sealed in thin-walled glass capillaries. By the early 1940s crystal classes and unit cell dimensions had been determined for insulin, horse haemoglobin, RNAase, pepsin, and chymotrypsin. Complete resolution of the structures required identification of the crystal axes and some knowledge of the amino acid sequence of the protein—requirements which could not be met until the 1950s. 

Bell, P., and G. Nord (1974). Microscopic and Electron Diffraction Study of Fi-brolitic Sillimanite, pp. 443-446. Report of the Director, 1973-1974. Geophysical Laboratory, Yearbook No. 73, Carnegie Institute, Washington, DC. Bernal, J. D. (1924). The structure of graphite. Proc. Roy. Soc. London A 106 749-... 

Rossmann, M. G., Bernal, R. and Plemev, S. V. (2001). Combining electron microscopic with X-ray crystallographic structures. /. Struct. Biol. 136,190-200. 

Akaganeite (named after the Akagane mine in Japan) is isostructural with hollan-dite. Compounds with this structure have a tetragonal or monoclinic unit cell. Bernal et al. (1959) and Keller (1970) both concluded that the unit cell of akaganeite was tetragonal with a = 1.000 nm and c = 0.3023 nm. The structural refinement of a natural sample using XRD and Rietveld analysis indicated, however, that the unit cell is monoclinic with a = 1.060 nm, b = 0.3039 nm, c = 1.0513 nm and p = 90.24° (Post Buchwald, 1991). There are eight formula units per unit cell. 

This compound is isostructural with brucite (Mg(OH)2) and Cdl2. The unit cell is hexagonal with a = 0.3258 nm and c = 0.4605 nm. The structure consists of sheets of corner-sharing, trigonally distorted Fe(OH)6 octahedra stacked along the [001] direction. The Fe" ions occupy only half the available octahedral interstices and this results in a structure in which each filled layer of sites alternates with an empty layer of sites. The OH radical behaves as a single entity. Amakinite is a rare mineral of the composition (Fe,Mg,Mn)(OH)2, also with brucite structure. Fe(OH)2 is readily oxidized by air and even by water, upon which the colour changes from white to brownish. The structure can be maintained up to a replacement of one tenth Fe" by Fe " (Bernal et al., 1959). 

Bernal, J.D. Mackay, A.L. (1965) Topotaxy. Tschermaks mineralogische und petrogra-phische Mitteilungen 10 331-340 Bernal, J.D. Dasgupta, D.R. Mackay, A.L. (1959) The oxides and hydroxides of iron and their structural interrelationships. Clay Min. Bull. 4 15-29... 

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