Structural studies

Structural Studies. Structural characteristics of both natural and synthetic diamonds have been studied using electron microscopy and i.r. and optical absorption spectroscopy. — Greatest interest is associated with defect structures of electron-irradiated diamond.  

Molecular and large-scale structural parameters of vitreous carbon have been elucidated as a function of heat-treatment temperature, using X-ray diffraction and electron microscopic techniques. Short-range order in the carbon layers is characterized by an interatomic distance of 1.42 0.01 A (c/. graphite) but with a 

study has also been carried out to assess the influence of both heat-treatment and neutron irradiation on the structure of vitreous carbon. 

Although considerable research effort has been applied to the chemistry of carbon fibres, little is of relevance to the inorganic chemist. Even those structural investigations which have been carried out are primarily concerned with the morphology of the fibres rather than their detailed molecular structures.  

signals were not obtained after treatment with HCl, t-C4H9NH2, and CO. The effect of amine treatments on the reactivity of whetlerites, with respect to CNCl, has also been studied.  

The discussion of the structural aspects of the polysaccharide will be divided into two Sections. The first deals with the chemical elucidation of the structure the second, with the physical measurements made on dextran. A survey of the literature in this area has indicated that the fine structure of the dextran obtained is closely related to the particular strain that pro- 

Further studies have favored structures in which the side chain consists of only one D-glucose residue (x = 0). This structure will be discussed more thoroughly in the Section dealing with polymer studies (see p. 349). 

Jones and Wilkie, in a recent paper, describe a study of the structures of four dextrans currently being used as synthetic, blood-plasma expanders. These dextrans were shown to contain the (1 — 3)-linkage as the major branch point, with a small proportion of (1 — 4)-linkages present, in addition to the normal (1 — 6)-linkages. These conclusions may, however, be attributable to incomplete methyMion of the polysaccharides investigated. 

An improved way of utilizing the method of periodate oxidation for determining the nature of the linkages in polysaccharides was provided by Smith and coworkers. They realized that, if the periodate-oxidized polysaccharide were reduced to the corresponding alcohol, the resulting fragments, on hydrolysis, would be indicative of the types of linkage present in the parent polymer. This scheme is shown in Fig. 1. Such an approach was used in a study of the dextrans from 6 different strains of L. mesente- 

Neither of these methods, analysis of periodate consumption or isolation 

Physical Studies of Quadrivalent Silicon Germanium, and Tin Halides. (/) Structural studies. A -Ray diffraction studies of bis(chloromethyl)tin dichloride. (ClCH2)2SnCl2, show that the crystal is constructed of infinite 

Structural data for methyltrifluorosilane and trimethylbromo rmane have been obtained from microwave spectra. For MeSiFs, the following structural parameters were determined r(Si—C) = 1.812 0.014 A r(Si—F) = 1.574 0.007 A ZFSiC = 112° 20 1°6. The dipole moment of the molecule was determined to be 2.33 0.10 D. A barrier to internal rotation 

Understanding molecular mechanisms of enzymatic catalysis depends on a detailed knowledge of the structural framework within which substrate recognition and catalysis occur. Determination of the X-ray crystal structure of S. cerevisiae flavocytochrome 62 by Mathews and colleagues (23-25), coupled with the availability of the complete amino acid sequence (26, 27), has allowed detailed analysis of substrate recognition and catalysis in this enzyme. 

Flavocytochrome 62 is composed of a single polypeptide chain with a molecular weight, as estimated by SDS-polyacrylamide gel electrophoresis, of 57,500 in the case of the S. cerevisiae enzyme (28) and 58,000 for the enzyme from H. anomala (29). The native enzymes behave as oligomers with molecular weights around 230,000 (29-31), suggesting that each is a homotetramer. This has been confirmed for S. cerevisiae flavocytochrome 62 by X-ray crystallography, which shows the subunits to be related by a four-fold axis of symmetry (Fig. 3) (23-25). The tetrameric structure is important for activity because dissociation of the H. anomala enzyme at low ionic strength yields inactive monomers that can be reassociated with recovery of activity (32). 

The complete amino acid sequence of S. cerevisiae flavocytochrome 2 has been determined (26). The mature form of the enzyme is composed of 511 amino acids (Fig. 4). The DNA sequence has also been determined (27), revealing the presence of an 80-residue N-terminal presequence. This N-terminal extension directs the enzyme into the mitochondrion, where it is processed in two proteolytic steps that result in mature flavocytochrome 62, which is located in the intermembrane space (1, 33-36). 

LGPLVGEFEQ ir.EEE LSEEEIDRLE RIER.KPPLS QNINLHDFET lARQILPPPA LAYYCSAADD EVTLRENHNA 15Z 

ARIPGQQ.QH YQLYVNADRS ITEKAYRHAE ERGMKGLFIT VDAPSLGRRE KDHKMKF. EADS..DVO G..DDEDIDRI 300 

A number of novel methods, including those based on spectroscopy and chromatography, have facilitated the structural studies on oligo- and 

The Ring Size of Monosaccharide Units and the Position of Linkages 

Carbohydrates in nature are optically active and polarimetry is widely used in establishing their structure. Measurement of the specific rotation gives information about the linkage type (a or (3 form) and is also used to follow mutarotation. Nuclear magnetic resonance spectroscopy (NMR) can be used to differentiate between the anomeric protons in the a- or /3-pyranose and furanose anomers and their proportions can be measured from the respective peak areas. 

Enzymic methods are gaining wider applications. For example, maltase 

Ferrier, R. J., and Collins, P. M. (1972). Monosaccharide Chemistry. Clowes, London. Guthrie, R. D. (1974). Guthrie Honeyman s Introduction to Carbohydrate Chemistry, 4th ed. Oxford Univ. Press (Clarendon), London and New York. 

In principle, all the suprastructures shown in a still highly simplified manner in Fig. 11.13 are in equilibria that depend on many parameters such as pH (Section 11.3.1), concentration (Section 11.3.2), ionic strength (Section 11.3.1), nature of the bilayer (Sections 11.3.4 and 11.3.7), and so on. This dynamic supramolecular polymorphism restricts meaningful structural studies to conditions that are relevant for function but often incompatible with routine analytical methods (e.g. nanomolar to low micromolar concentrations in lipid bilayer membrane. The fact that the active conformers or supramolecules are often not the thermodynamically dominant ones [21] (Section 11.3.2) calls for additional caution as well as selective methods of detection). As a general rule, the complexity of the supramolecular polymorphism of synthetic ion channels and pores decreases with increasing complexity (size) of the monomer (in other words, synthetic efforts are often worthwhile [2] compare Fig. 11.2). 

Consideration of the supramolecular polymorphism of synthetic ion channels and pores reveals the relevant questions for structural studies Where do the monomers act (Fig. 11.13b-d), how many of them are needed (Fig. 11.13A-C), and where and how can they be regulated In the following, analytical methods available to address these questions will be briefly mentioned but not introduced in detail (compare, e.g. ref [4]). 

In the majority of cases where adsorbates form ordered structures, the unit cells of these structures are longer than that of the substrate they are referred to as superlattices. Two notations are used to describe the superlattice, the Wood notation and a matrix notation.18 Some examples of overlayer structures at an fcc(llO) surface are as follows  

The prefixes c and p mean centred and primitive , respectively, where centred refers to when an adsorbate is added in the centre of the primitive unit cell. 

Some conclusions that emerged in 1978 from the optical simulation study were as follows these could only be tested by (future) STM studies  

Weinberg and co-workers study in 198220 of the chemisorption of carbon monoxide on Ru(0001) by LEED exemplifies how lateral interactions determine 

Local surface structure and coordination numbers of neighbouring atoms can be extracted from the analysis of extended X-ray absorption fine structures (EXAFS). The essential feature of the method22 is the excitation of a core-hole by monoenergetic photons modulation of the absorption cross-section with energy above the excitation threshold provides information on the distances between neighbouring atoms. A more surface-sensitive version (SEXAFS) monitors the photoemitted or Auger electrons, where the electron escape depth is small ( 1 nm) and discriminates in favour of surface atoms over those within the bulk solid. Model compounds, where bond distances and atomic environments are known, are required as standards. 

The Series B of 12-heteropoly compounds is typified by the anion [CeMoi2042]-8, the structure of which has been determined in the salt 

These compounds are possible degradation products of 12-heteropolymolybdates. Their structure is unknown, but they may be dimeric. The 11-tungstoborate is not obtained by degradation of 12-tungstoborate, nor do the 11-molybdoborates or 12-molybdoborates exist. 

The publication, in 1995, of the crystal structure of recombinant pAPX (Patterson and Poulos, 1995) was arguably the single most important contribution to the area in recent years. The structure provided a dichotomy of 

Selected physical data for various cytosolic APXs 

Source M, Am ascorbate Am H2O/ Specinc activity Fe Fe Fe CN Fe CN pH optimum Relativity activity Reference 

Molecular weight given per monomer (kDa). Errors given where p Camellia sinensis. 

Km in pM. Errors given where published. acidic, the second is basic. 

Additional evidence has been provided by Russian workers30 that both synthetic carbyne and the natural mineral chaoite ( white carbon) consist of at least two modifications. Information has also been obtained recently regarding the conditions under which carbyne and chaoite are formed it is concluded that these modifications are not as uncommon as previously thought.30 

Those surface oxygen complexes on Spheron 6 which thermally desorb as CO2 are thought to be responsible for the acidity of the carbon.34 Two types of acidic oxide have been observed. An oxide which acts as a very weak monobasic acid is decomposed at ca. 250 °C whereas a second oxide, which is a stronger dibasic acid, is decomposed at ca. 600 °C these two structures are unlike those found on graphite, which decompose at ca. 400 °C and have different acidic properties. 

The kinetics of the C—C02 reaction have been analysed in a number of recent publications.48-50 In one of these, the oxidation of carbon in metallic melts (Fe-C and Ni-C) by exposure to a C02-N2 gas stream has been monitored.50 The reaction can best be rationalized by a combination of the two consecutive steps (2) and (3), in which the C02 is reduced at the metal surface to give CO and adsorbed oxygen, (0)m, which then reacts with soluble carbon, (C)m, to form CO.50 

An experimental study of the reaction (4) has demonstrated that the oxidation is linked to the nature of the carbon 51 it is not possible to accept the suggestion that the reaction depends solely on the transformation between the two crystal forms of silica. 

Serum albumins from goat, pig, horse, and human showed heterogeneity reflected in charge differences by chromatography on DEAE-cellulose. Each albumin was separated into three fractions using the stepwise elution system as that for BSA (Habeeb, 1978 ). All the albumins revealed the same elution pattern, showing three main components of which the first and third components eluted in a symmetrical peak while the second component trailed (Fig. 25). 

Serum albumins from goat, horse, and pig exhibited a neutral transition at pH 7.5-9.5 (at room temperature) characterized by increased activity of the disulfide bonds to reduction (Habeeb, 1978 ). Further increase in reactivity of the disulfide bonds was exhibited at 40 C. Albumins from goat, horse, and pig had a remarkable tendency to unfold (resulting in exposure of the disulfide bonds) thus a plateau of disulfide reducibility was reached at pH 8 and 40 C, whereas with BSA or HSA a higher pH was required to reach maximal exposure of the disulfide bonds to reduction (Fig. 26). 

Amino acid sequence studies of BSA (Brown, 1975) and HSA (Behrens et aL, 1975 Meloun et aL, 1975) revealed the albumin molecule to consist of three compact domains held by 17 disulfide bonds arranged in 

X-Ray analysis shows that bis-jr-benzene vanadium may exist in both cubic and monoclinic forms [64]. It has also been shown that the 

The X-ray studies also show that the Cr-0 distances in r-C6H6Cr(CO)3 are /) l A shorter than in Cr(C0)6 [66], This suggests that there is a 

Symmetry Metal orbitals Ligand orbitals Rotational symmetry 

Eoeiigy levd diagrain for bis-ir-benzeae chromiimi, after Schustorovkdi and Dyatkina riO] (and Cotton [720. 

Comptex Election assignment No. of unpaired electrons Calculated spin only value, B.M. Expected value B.M. Observed value B.M. 

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The field emission microscope (FEM), invented in 1936 by Muller [59, 60], has provided major advances in the structural study of surfaces. The subject is highly developed and has been reviewed by several groups [2, 61, 62], and only a selective, introductory presentation is given here. Some aspects related to chemisorption are discussed in Chapter XVII. 

Diehl R D and McGrath R 1996 Structural studies of alkali metal adsorption and coadsorption on metal surfaces Surf. Sc/. Rep. 23 43... 

An experimental teclmique that is usefiil for structure studies of biological macromolecules and other crystals with large unit cells uses neither the broad, white , spectrum characteristic of Lane methods nor a sharp, monocliromatic spectrum, but rather a spectral band with AX/X 20%. Because of its relation to the Lane method, this teclmique is called quasi-Laue. It was believed for many years diat the Lane method was not usefiil for structure studies because reflections of different orders would be superposed on the same point of a film or an image plate. It was realized recently, however, that, if there is a definite minimum wavelengdi in the spectral band, more than 80% of all reflections would contain only a single order. Quasi-Laue methods are now used with both neutrons and x-rays, particularly x-rays from synclirotron sources, which give an intense, white spectrum. 

Inelastic scattering processes are not used for structural studies in TEM and STEM. Instead, the signal from inelastic scattering is used to probe the electron-chemical environment by interpreting the specific excitation of core electrons or valence electrons. Therefore, inelastic excitation spectra are exploited for analytical EM. 

The unit cell area is measured relative to the unit cell area of the simple (1x1) structures studied in the early... 

Masson F and Rabalais J W 1991 Time-of-flight scattering and recoiling spectrometry (TOF-SARS) analysis of Pt 110. I. Quantitative structure study of the clean (1 x 2) surface Surf. Sc/. 253 245-57... 

Engel T and Rieder K H 1982 Structural studies of surfaces with atomic and molecular beam diffraction Structural Studies of Surfaces With Atomic and Molecular Beam Scattering (Springer Tracts in Modern Physics vol 91) (Berlin Springer) pp 55-180... 

Leadbetter A J 1979 Structural studies of nematic, smectic A and smectic C phases The Moiecuiar Physics of Liquid Crystais ed G R Luckhurst and G W Gray (London Academic)... 

Mortensen K 1996 Structural studies of PEO-PPO-PEO triblock copolymers, their micellar aggregates and mesophases a small-angle neutron scattering study J. Phys. Condens Matters A103-A104... 

Seddon K M, Flogan J L, Warrender N A and Pebay-Peyroula E 1990 Structural studies of phospholipid cubic phases Prog. Colloid Polym. Sol. 81 189-97... 

Peterson I R 1986 A structural study of the conducting defects in fatty acid Langmuir-Blodgett monolayers J. Mol. Electron. 2 95-9... 

Jones R, Tredgold R H, Hoorfar A, Allen R A and Hodge P 1985 Crystal-formation and growth in Langmuir-Blodgett multilayers of azobenzene derivatives—optical and structural studies Thin Solid Films 134 57-66... 

Palacin S, Lesieur P, Stefanelli I and Barraud A 1988 Structural studies of intermolecular interactions in pure and diluted films of a redox-active phthalocyanine Thin Soiid Fiims 159 83-90... 

Schneider J, Erdelen C, Ringsdorf H and Rabolt J F 1989 Structural studies of polymers with hydrophilic spacer groups. 2. Infrared-spectroscopy of Langmuir-Blodgett multilayers of polymers with fluorocarbon side-chains at ambient and elevated temperatures Macromolecules 22 3475-80... 

Wu S, Lipkowski J, Tyiiszczak T and Hitchcock A P 1997 Eariy stages of copper eiectrocrystaiiization eiectrochemicai and in situ x-ray absorption fine structure studies of coadsorption of copper and chioride at the Au(111) eiectrode surface J.Phys. Chem. B 101 10 310-22... 

These studies at the same time aroused my interest in the mechanistic aspects of the reaetions, including the complexes of RCOF and RF with BF3 (and eventually with other Lewis acid fluorides) as well as the complexes they formed with aromatics. 1 isolated for the first time at low temperatures arenium tetrafluoroborates (the elusive (T-complexes of aromatic substitutions), although I had no means to pursue their structural study. Thus my long fascination with the chemistry of car-bocationic complexes began. 

Nonclassical ions, a term first used by John Roberts (an outstanding Caltech chemist and pioneer in the field), were defined by Paul Bartlett of Harvard as containing too few electrons to allow a pair for each bond i.e., they must contain delocalized (T-electrons. This is where the question stood in the early 1960s. The structure of the intermediate 2-norbornyl ion could only be suggested indirectly from rate (kinetic) data and observation of stereochemistry no direct observation or structural study was possible at the time. 

The remarkable stability of the gold complexes is due to significant metal-metal bonding. However, their isolation and structural study are remarkable and greatly contributed to our knowledge of higher-coordinate carbocations. 

Structural studies show allene to be nonplanar As Figure 10 7 illustrates the plane of one HCH unit is perpendicular to the plane of the other Figure 10 7 also portrays the reason for the molecular geometry of allene The 2p orbital of each of the terminal car bons overlaps with a different 2p orbital of the central carbon Because the 2p orbitals of the central carbon are perpendicular to each other the perpendicular nature of the two HCH units follows naturally... 

The Protein Data Bank PDB ID 1A71 Colby T D Bahnson B J Chin J K Klinman J P Goldstein B M Active Site Modifications m a Double Mutant of Liver Alcohol Dehydrogenase Structural Studies of Two Enzyme Ligand Com plexes To be published... 

Siegbahn, K., Nordling, C., Fahlman, A., Nordberg, R., Hamerin, K., Hedman, J., Johansson, G., Bergmark, T., Karlsson, S.-E., Lindgren, I. and Lindberg, B. (1967) Electron Spectroscopy for Chemical Analysis Atomic, Molecular, and Solid State Structure Studies by Means of Electron Spectroscopy, Almqvist and Wiksells, Uppsala. 

A. W. Norman, R. Bouillon, M. Thomasset, eds.. Vitamin D. A Pluripotent Steroid Hormone Structural Studies, Molecular Endocrinology and Clinical Applications. Proceedings of the Ninth Workshop on Vitamin D, Orlando, Florida, May 1994, Walter de Gmyter, Berlin, 1994, p. 89. 

Theoretical methods ranging from the now obsolete HMO studies to ab initio calculations have been used extensively on pyrazoles. Although not emphasized in earlier reviews (66AHC(6)347,67HC(22)l), the most recent publications (B-76MI40402,79RCR289) contain several references to theoretical studies. Some publications related to structural studies are to be found in the following sections, especially in connection with NMR spectroscopy (Section 4.04.1.3.4), UV spectroscopy (Section 4.04.1.3.6), PE spectroscopy (Section 4.04.1.3.9) and tautomerism (Section 4.04.1.5). 

Theoretical and structural studies have been briefly reviewed as late as 1979 (79AHC(25)147) (discussed were the aromaticity, basicity, thermodynamic properties, molecular dimensions and tautomeric properties ) and also in the early 1960s (63ahC(2)365, 62hC(17)1, p. 117). Significant new data have not been added but refinements in the data have been recorded. Tables on electron density, density, refractive indexes, molar refractivity, surface data and dissociation constants of isoxazole and its derivatives have been compiled (62HC(17)l,p. 177). Short reviews on all aspects of the physical properties as applied to isoxazoles have appeared in the series Physical Methods in Heterocyclic Chemistry (1963-1976, vols. 1-6). 

The role of IR spectroscopy in the early penicillin structure studies has been described (B-49MI51103) and the results of more recent work have been summarized (B-72MI51101). The most noteworthy aspect of a penicillin IR spectrum is the stretching frequency of the /3-lactam carbonyl, which comes at approximately 1780 cm" This is in contrast to a linear tertiary amide which absorbs at approximately 1650 cm and a /3-lactam which is not fused to another ring (e.g. benzyldethiopenicillin), which absorbs at approximately 1740 cm (the exact absorption frequency will, of course, depend upon the specific compound and technique of spectrum determination). The /3-lactam carbonyl absorptions of penicillin sulfoxides and sulfones occur at approximately 1805 and 1810 cm respectively. The high absorption frequency of the penicillin /3-lactam carbonyl is interpreted in terms of the increased double bond character of that bond as a consequence of decreased amide resonance, as discussed in the X-ray crystallographic section. Other aspects of the penicillin IR spectrum, e.g. the side chain amide absorptions at approximately 1680 and 1510 cm and the carboxylate absorption at approximately 1610 cm are as expected. 

As a class the penicillins do not have a characteristic UV absorption spectrum. UV spectra did, however, play an important role in the structure elucidation of some of the penicillin degradation products during the early structure studies (B-49MI51104). 

Although experimental studies of DNA and RNA structure have revealed the significant structural diversity of oligonucleotides, there are limitations to these approaches. X-ray crystallographic structures are limited to relatively small DNA duplexes, and the crystal lattice can impact the three-dimensional conformation [4]. NMR-based structural studies allow for the determination of structures in solution however, the limited amount of nuclear overhauser effect (NOE) data between nonadjacent stacked basepairs makes the determination of the overall structure of DNA difficult [5]. In addition, nanotechnology-based experiments, such as the use of optical tweezers and atomic force microscopy [6], have revealed that the forces required to distort DNA are relatively small, consistent with the structural heterogeneity observed in both DNA and RNA. 

X-ray structural studies have played a major role in transforming chemistry from a descriptive science at the beginning of the twentieth century to one in which the properties of novel compounds can be predicted on theoretical grounds. When W.L. Bragg solved the very first crystal structure, that of rock salt, NaCl, the results completely changed prevalent concepts of bonding forces in ionic compounds. 

The presence of this common helix-turn-helix motif poised for DNA binding in lambda Cro and repressor provided considerable stimulus for further genetic and structural studies of these and other procaryotic DNA-binding proteins. All the results essentially supported the proposed mode of binding between these regulator proteins and DNA. 

Structural studies of a repressor-DNA complex have shown that helices 4 and 5 form a helix-turn-helix motif and that side chains from the recognition helix 5 form water-mediated interactions with bases in the major groove. 

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