Three-dimensional structure series

These requirements have been formulated on the basis of a systematical study of linear structure series. The requirements i) and ii) apply to the linear homogeneous structure series. In the description of the inhomogeneous series the requirements iii) and iv) have to be added. It may be possible, that in two- and three-dimensional structure series the segments must conform to additional requirements. 

However, from our point of view, there remains a lack of sufficiently precise and reliable methods to compute thermodynamic water solubility. The majority of methods work only for congeneric series of compounds, and many have not been developed to function in areas of pharmaceutical research using drug-like molecules. Most of the methods do not use the three-dimensional structure of the compounds, while some depend on previous knowledge of certain experimental properties of the compounds of interest. Moreover, all of the methods are dependent upon the quality of solubility values in the training set used to develop the model indeed, this latter point is a critical limitation that has a major influence on solubility estimations. 

Chemical identity may appear to present a trivial problem, but most chemicals have several names, and subtle differences between isomers (e.g., cis and trans) may be ignored. The most commonly accepted identifiers are the IUPAC name and the Chemical Abstracts System (CAS) number. More recently, methods have been sought of expressing the structure in line notation form so that computer entry of a series of symbols can be used to define a three-dimensional structure. For environmental purposes the SMILES (Simplified Molecular Identification and Line Entry System, Anderson et al. 1987) is favored, but the Wismesser Line Notation is also quite widely used. 

X-ray diffraction analysis reveals the three-dimensional structure of both IL-l molecules to be quite similar. Both are globular proteins, composed of six strands of antiparallel P pleated sheet forming a barrel that is closed at one end by a further series of P sheets. 

Mineral series are composed of species whose basic chemistry and three-dimensional structure are so similar that they differ in a well-documented, predictable manner, based on the substitution of comparable chemical elements. Such a series is usually defined by the end members, that is, the compounds that contain only one of the substituting cations. End members... 

Monensin belongs to the family of polyether ionophores. These compounds consist of a series of tetrahydrofuran and tetrahydro-pyran rings and have a carboxyl group that forms neutral salts with alkali metal cations. Their three-dimensional structure presents a lipophilic hydrocarbon exterior with the cation encircled in the oxygen-rich interior. They probably act by transporting cations through the lipid bi-layer of cell membranes, thereby preventing the concentration of potassium by the cells. Evidence for this is... 

The three-dimensional periodic electron-density distribution in a single crystal can be represented by a three-dimensional Fourier series with the so-called structure factors Fhkl as Fourier coefficients ... 

An x-ray analysis will measure the diffraction pattern (positions and intensities) and the phases of the waves that formed each spot in the pattern. These parameters combined result in a three-dimensional image of the electron clouds of the molecule, known as an electron density map. A molecular model of the sequence of amino acids, which must be previously identified, is fitted to the electron density map and a series of refinements are performed. A complication arises if disorder or thermal motion exist in areas of the protein crystal this makes it difficult or impossible to discern the three-dimensional structure (Perczel et al. 2003). 

In the late 1980s when we began the pursuit of bradykinin receptor antagonists, information of relevance to medicinal chemists was scarce. For example, not one nonpeptide antagonist of this receptor was known, nor were any series upon which to base a structure-activity relationship. Moreover, all publications described bradykinin as being highly flexible in an aqueous environment, such that no structural mimetics could be rationalized. Of course the receptors had not been cloned at that time so nothing was known about the primary sequence of the receptor or the three-dimensional structure. 

Although neither the function nor the origin of this enigmatic organelle is yet known, the three-dimensional structure of the CB visualized by tomographic reconstruction suggested that the closely packed vesicles observed by might actually be a series of interconnected channels (see Fig. 20, Keithly et al. 

Generally, LEED experiments are conducted on specified faces of single crystals. When this is done, the diffraction pattern produced consists of a series of spots with a location, shape, and intensity that can be interpreted in terms of the surface structure. We focus attention on what can be learned from the location and shape of the spots since the study of intensity is beyond the scope of this book. It is generally assumed that the surface examined by LEED is an extension of an already-known bulk crystal structure. The correctness of this assumption can be tested, and results are often expressed in terms of modifications of the three-dimensional structure at the surface. Before we turn to the LEED patterns below, we must first figure out how they are read. 

Superficially, except for the sign change (in the exponential term) that accompanies the transform operation, this equation appears identical to Eq. (5.9), a general three-dimensional Fourier series. But here, each Fhkl is not just one of many simple numerical amplitudes for a standard set of component waves in a Fourier series. Instead, each Fhkl is a structure factor, itself a Fourier series, describing a specific reflection in the diffraction pattern. ("Curiouser and curiouser," said Alice.)... 

---