Polymorphism structures

Chasman, D. and R.M. Adams, "Predicting the Functional Consequences of Non-Synonymous Single Nucleotide Polymorphisms Structure-Based Assessment of Amino Acid Variation," /. Mol. Biol., 307, 683-706 (2001). 

Fig. 3. Solubility of silk proteins in solution as a function of time. Low solubility corresponds to protein aggregation. The fast and slow aggregations are observed in vitro (Dicko et al., 2004a), whereas the stable helical conformation (storage structure) is observed in vivo (Dicko et al., 2004b,d). This illustrates the inherent instability of silk protein in solution and shows the /(-sheet polymorph structure as the most stable form. In other words, the spiders actively control and modulate the unavoidable silk protein aggregation prior to fiber formation.

Unfortunately, the description of amyloid fibrils given above is simplistic since in vitro self-assembly of amyloid peptides and proteins yields polymorphic structures, as has been commonly observed in the past for other protein assemblies such as actin filaments (Millonig et al, 1988) and intermediate filaments (Herrmann and Aebi, 1999). On the one hand, assembly polymorphism complicates the characterization of fibril structure. On the other hand, it offers some insight into fibril formation. For this reason a more rational understanding of amyloid fibril formation at the molecular level is a key issue in the field of amyloidosis. 

Most polymers do not form crystals suitable for single crystal X-ray diffraction, so powder or film methods are usually employed. X-ray and LJV data recorded at various temperatures provide the detailed information required to correlate conformational and electronic properties, since the former is sensitive to the inter- and intrachain packing, and the latter is sensitive to the conformation. DSC provides further evidence for any phase transitions. Detailed studies have been performed by Winokur and West,260 261 who reported a comparison of the polymorphism, structure, and chromism in poly(di- -octylsilylene), (Si- -Oct2), 89, and poly(di- -dccylsilylcnc)(Si- -Dcc2) , 90. These investigations will be described in detail for the useful insights into polysilane structures that they afford. 

Bicyclopropylidene (1) with its melting point of -10.4°C undergoes a solid state phase transition at -40.2°C with AH = 0.038 kcal/mol, and the two polymorphous structures possess different structural parameters (Table 2) [85,86]. A similar behavior was also observed for me50-bis(bicyclopropylidenyl) meso-87 [56]. The structure of meso-S represents essentially a combination of the two bicyclopropylidene units the central bond length h (1.494 A, Table 2) which is practically the same as that in bicyclopropyl (1.492 A) indicates the absence of any strong electronic interaction between the two bicyclopropylidene units in meso-S which should thus react independently of each other. 

In other studies, changes in the structural arrangement of the trinudear units was not only due to the change in substituents. In fact, another unusual structural finding, that also led to a difference in the optical properties of the complex [Au3(CH3N=COCH3)3], appeared as a consequence of the discovery of polymorphic structures in the crystallization process [45]. 

Tarahovsky, R., Khusainova, A., Gorelov, K., Dawson, A.K., Ivanitsky, G. (1996). DNA initiates polymorphic structural transition in lectin. FEBS Lett., 390, 133-137. 

Simpson, A.J., Dame, J.B., Lewis, F.A. and McCutchan, T.F. (1984) The arrangement of ribosomal RNA genes in Schistosoma mansoni identification of polymorphic structural variants. European Journal of Biochemistry 139, 41 15. 

There are two polymorphic structures of ZnS, zinc blende (or sphalerite) (3 2PT) and wurtzite (2 2PT). In zinc blende there is a ccp arrangement of S atoms with Zn atoms filling one of the two T layers as shown in Figure 6.1. The diamond has the same structure, with the sites of P and one T layer filled by C atoms (Section 4.3.3). The structure of zinc blende has six (3 2) layers in the repeating unit. This structure is encountered for many binary compounds with significant covalent character as shown in Table 6.1. The space group for zinc blende is T%, F43m, and a0 = 5.4093 A, for the cubic unit cell. ... 

The formula for silica is very simple—SiC>2. The silica structures (and those of metal silicates) have only SiC>4 tetrahedra, and the 1 2 ratio of SiC>2 requires that each oxygen atom is shared by two tetrahedra in silica. Even though the basis of the structures is very simple, there are three polymorphic structures of silica, and each of these has a low temperature form (a) and a high temperature form ((S). The three polymorphic structures and their temperature ranges are shown below. 

The inclusion crystals of CA with m-xylene or /j-xylcnc has a unique bilayer structure, while those of CA with o-xylene show the two polymorphic structures described above. The lattice parameters, the type of host framework, the host-guest molar ratios and PC cavity are shown in Table 7 [34],... 

Daniel Chasman R, Adams M. Predicting the functional consequences of non-synonymous single nucleotide polymorphisms structure-based assessment of amino acid variation. J Mol Biol 1996 307 683-706. 

Alpha silver iodide (a-Agl), a fast ion conductor, is one of the different polymorphic structures of Agl showing a cubic structure [51], where I occupies anionic positions, that is, the Cl- sites in the CsCl-type structure (see Figure 2.19). On the other hand, the low temperature phase, that is, p-Agl, exhibits a hexagonal wurtzite-type structure. 

The majority of unipolar ionic conductors identified to date are polymorphic compounds with several phase transitions, where the phases have different ionic conductivities owing to modifications in the substructure of the mobile ions [28], One of the first studied cationic conductors was a-Agl [21]. Silver iodide exhibits different polymorphic structures. Agl has a low-temperature phase, that is, [3-Agl, which crystallizes in the hexagonal wurtzite structure type, and a high-temperature cubic phase, a-Agl, which shows a cubic CsCl structure type [20,22] (see Section 2.4.5). 

SPS takes two different conformations in its crystal, TT and TTGG conformations, depending on the crystallization conditions, and exhibits a very complex polymorphic structure [6-14]. One is the TT conformation which appears when SPS crystallizes from the melt. Two different transcrystals are reported when SPS takes the TT conformation in the crystal, a-form [15-19] and 3-form. The identity period is 5.06 A (Figure 18.3) in both crystal forms. The 3-form is more thermally stable than the a-form. Figure 18.4 shows the detailed structure of the 3-form [6,10]. 

With the growing awareness among chemists of the phenomenon of polymorphism its actual occurrence in any particular system may not be as great a surprise as a generation or two ago. The predicted existence of any particular polymorphic structure for a single compound, the conditions and methods required to obtain it, and the properties it will exhibit are still problems that will challenge researchers for many years to come. ... 

Similarly the chain-like structure of polymers also results in a proliferation of polymorphic structures (e.g. Keller and Cheng 1998 Lotz 2000 Rastogi and Kurelec 2000). The differences in structure lead to a variety of properties (e.g. Calleja et al. 1993 Chunwachirasiri et al. 2000), which of course is one of the driving forces for the development of new polymeric materials. Although not referenced specifically, many of the principles and examples presented in subsequent chapters apply equally well to many of the polymorphic molecular systems. 

Polymorphic structures of molecular crystals are different phases of a particular molecular entity. To understand the formation of those phases and relationships between them we make use of the classic tools of the Phase Rule, and of thermodynamics and kinetics. In this chapter we will review the thermodynamics in the context of its relevance to polymorphism and explore a number of areas in which it has proved useful in understanding the relationship between polymorphs and polymorphic behaviour. This will be followed by a summary of the role of kinetic factors in detecting the growth of polymorphic forms. We will then provide some guidelines for presenting and comparing the structural aspects of different polymorphic structures, with particular emphasis on those that are dominated by hydrogen bonds. 

From this analysis it is clear that the trade-off between kinetics and thermodynamics is not at all obvious. Consider a monotropic, dimorphic system (for simplicity) whose solubility diagram is shown schematically in Fig. 2.10. It is quite clear that for the occurrence domain given by solution compositions and temperatures that lie between the form II and I solubility curves only polymorph I can crystallize. However, the outcome of an isothermal crystallization that follows the crystallization pathway indicated by the vector in Fig. 2.10 is not so obvious since the initial solution is now supersaturated with respect to both polymorphic structures, with thermodynamics favouring form I and kinetics (i.e. supersaturation) form II. 

Structure is the fundamental property of polymorphs. In this section we will deal with the definition of that structure, how it may be best viewed and understood, and how polymorphic structures may be compared. The determination of crystal structure, by... 

A solution or melt can contain a variety of clusters Ai,..., A , in a system of competing equilbria. Each cluster in turn is a potential critical cluster for the nucleus of one or more polymorphic crystal modifications. In the context of polymorphic structures, in particular those which crystallize under similar conditions, there must be a number of processes of this type, all involved in competing equilibria. This... 

Some experimental evidence for the presence of different aggregates in solution leading to polymorphic structures has been presented recently by Nather et al. (1996a,b), and there have been attempts to relate nucleation rates with proposed structures in solution based on molecular modelling (Petit et al. 1994). The number of studies of this nature is sure to increase with increasing sensitivity and sophistication of both experimental and computational tools those are the kinds of investigations that can provide answers to Powers challenge. 

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