Molecular fragments chirality

In this chapter, we will discuss the present status of CHIRBASE and describe the various ways in which two (2D) or three-dimensional (3D) chemical structure queries can be built and submitted to the searching system. In particular, the ability of this information system to locate and display neighboring compounds in which specified molecular fragments or partial structures are attached is one of the most important features because this is precisely the type of query that chemists are inclined to express and interpret the answers. Another aspect of the project has been concerned with the interdisciplinary use of CHIRBASE. We have attempted to produce a series of interactive tools that are designed to help the specialists or novices from different fields who have no particular expertise in chiral chromatography or in searching a chemical database. 

In 2007, Moda et al. [60] developed a set of Hologram QSAR models for a much smaller data set of 250 molecules in comparison to the above-discussed models. They found that using all atoms, bonds, connections, and chirality to define molecular fragments led to a set of encouraging models and the best one was achieved when the fragment size was from 4 to 7, which had q2 of 0.7 and r2 of 0.93. This model was too good to be true since the standard error was only 7.60, much smaller than the average experimental error, which is 14.5 based on 367 experimental data [55]. 

Among the many chemical processes in which chirality/achirality relationships may be important is the fragmentation of some molecules and the reverse process of the association of molecular fragments. Such fragmentation and association can be considered generally and not just for molecules. The usual cases are those in which an achiral object is bisected into achiral or heterochiral halves. On the... 

Molecules whose mirror images caimot be superimposed on each other are identified as being chiral, and a very important branch of separation science has developed around the resolution of compoimds having pharmaceutical interest. At one time, scientists associated the phenomenon of optical rotation with the presence of carbon atoms boimd to four different molecular fragments, and these asymmetrically substituted carbon atoms became knovm as "asymmetric carbons." Continued work showed that compounds incapable of rotating the plane of polarized light, but which... 

Analysis of the nature of Cn axes suggests that one can create high-symmetry chiral figures by proper arrangement of n AS units with the same chirality around appropriate axes. A simple example of this procedure can be found in the planar diketopiperazine (3) (Figure 3) of C2 symmetry, which is constructed by combining two AS units of the same chirality, that is, two molecular fragments of (+)-(S)-alanine. 

Due to the important role of chirality in liquid crystals, a large number and variety of chiral chemical compounds have been developed. This chapter describes the most important molecular fragments and classes of chemical structures (Section 4.2) which provide both chirality and mesogenic properties. The form of chiral phases depends on the principles of the mesophase formation (Section 4.3). Some relations between the molecular chirality and the appearance of mesophase chirality are discussed and chiral dopants are classified (Section 4.4). With respect to the mesophase behavior and to optical and electro-optical applications, it is important to know how the mesogenic chirality can be modified, e.g., chemically by photoisomerization, or by changes of temperature or composition for certain suitable compounds (Section 4.5). Finally, chiral liquid crystals provide not only optical and electro-optical applications but also applications in Chemistry, e.g., as chiral solvents for synthesis, chiral stationary phases in chromatography, or chemical sensors (Section 4.6). 

Besides compounds with double bonds, which were described in the preceding paragraph one should also mention compounds that contain such bonds and, in addition, possess chiral quaternary carbon atoms. In such cases, the molecular fragment containing a double bond acts as a substituent at the chiral carbon atom or another heteroatom. 

The fragmentation/cyclization ratio is determined by the relative orientation of the respective molecular orbitals, and thus by the conformation of diradical species 2. The quantum yield with respect to formation of the above products is generally low the photochemically initiated 1,5-hydrogen shift from the y-carbon to the carbonyl oxygen is a reversible process, and may as well proceed back to the starting material. This has been shown to be the case with optically active ketones 7, containing a chiral y-carbon center an optically active ketone 7 racemizes upon irradiation to a mixture of 7 and 9 ... 

An approach, similar to that employed in the analysis of tartrate mixtures, has been used for the chiral discrimination of amino acid (M/j/s) mixtures, using an amino acid of defined configuration as reference (S). The proton-bound trimers [S2-M H]+ form [S M H]+ and [S2H]+ fragments upon CID or MIKE decay (equations (9)-(12)). With two independent measurements of the fragmentation ratio [S-M-H] /[S2H] from either [S2-M -H] and [52-M5-H]" , the differences in binding energies can be determined. The relative gas phase basicities (GB) of the molecular pairs [S-M] and [S2] can be derived from equations (13) and (14). 

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