Atom stereochemistry

A chiral Ru hydride 23 is formed and it is assumed that the hydrogen transfer occurs via metal-ligand bifunctional catalysis. The N-H linkage may stabilize a transition state 24 by formation of a hydrogen bond to the nitrogen atom. Stereochemistry is determined by formal discrimination of the enantiofaces at the sp2 nitrogen atom of the cyclic imine. 

Jacques, J., Gros, C. and Bourcier, S. (1977) in H.B. Kagan (Ed.), Absolute Configurations of 6000 Selected Compounds with One Asymmetric Carbon Atom, Stereochemistry—Fundamentals and Methods, Vol. 4, Georg Thieme, Stuttgart. 

Isomer and Tautomer Search. A search types where bond order, hydrogen counts, certain atom valences, and bond or atom stereochemistry may be allowed to vary from those specified in the query. Such searching allows re-... 

The second effect is manifested by the formation of the m/z 193 ion which is also sensitive to C-14 stereochemistry, but which nonetheless is not produced by the migration of the hydrogen on this atom. Stereochemistry participates directly on the carbon ring, thus facilitating the formation of this m/z 193 ion (Fig. 54) via a similar McLafferty rearrangement. 

Stereochemistry is the study of the three-dimensional structures of compounds. In this chapter, we will discuss the various concepts in stereochemistry starting with some simple terms such as isomers. What are isomers Isomers are compounds with the same molecular formula, but with different arrangements of atoms. Stereochemistry takes us further into the intricacies of isomerism in terms of three-dimensional perspectives. Furthermore, stereochemistry helps us imderstand the differences in activities of molecules that are stmcturally rather close. In many compounds, the slightest changes in the three-dimensional form of molecules make them active or inactive. This concept is especially important in many biologically significant molecules. Stereochemistry has taken us deep into the secrets of many naturally occurring molecules in our body. 

The rate of complex formation depends on various factors, such as the nature of the bond, the constitution of the electronic shells of the central metal atom, stereochemistry of the complex, and so on [29]. It has been suggested [30] that the rate constant for ligand penetration is characteristic of the metal ion alone. However, the exceptions are possible for chelation reactions in which steric effects,... 

Besides specifications on atoms, bonds, branches, and ring closure, SLN additionally provides information on attributes of atoms and bonds, such as charge or stereochemistry. These are also indicated in square [ ] or angle < > brackets behind the entity e.g., trans-butane CH3CH=[s=t]CHCH3). Furthermore, macro atoms allow the shorthand specification of groups of atoms such as amino adds, e.g., Ala, Protein2, etc. A detailed description of these specifications and also specifications for 2D substructure queries or combinatorial libraries can be found in the literature [26]. 

Central the molecular graph is completely coded (each atom and bond is represented) matrix algebra can be used the niimber of entries in the matrix grows with the square of the number of atoms in ) no stereochemistry included... 

Stereochemistry can also be expressed in the SMILES notation [113]. Depending on the clockwise or anti-clockwise ordering of the atoms, the stereocenter is specified in the SMILES code with or respectively Figure 2-78). The atoms around this stereocenter are then assigned by the sequence of the atom symbols following the identifier or (g). This means that, reading the SMILES code from the left, the three atoms behind the identifiers ( ) or ( )( )) describe the stereochemistry of the stereocenter. The sequence of these three atoms is dependent only on the order of writing, and independent of the priorities of the atoms. 

Clearly, the next step is the handling of a molecule as a real object with a spatial extension in 3D space. Quite often this is also a mandatory step, because in most cases the 3D structure of a molecule is closely related to a large variety of physical, chemical, and biological properties. In addition, the fundamental importance of an unambiguous definition of stereochemistry becomes obvious, if the 3D structure of a molecule needs to be derived from its chemical graph. The moleofles of stereoisomeric compounds differ in their spatial features and often exhibit quite different properties. Therefore, stereochemical information should always be taken into ac-count if chiral atom centers are present in a chemical structure. 

Figure 3-22 shows a nucleophilic aliphatic substitution with cyanide ion as a nucleophile, i his reaction is assumed to proceed according to the S f2 mechanism with an inversion in the stereochemistry at the carbon atom of the reaction center. We have to assign a stereochemical mechanistic factor to this reaction, and, clearly, it is desirable to assign a mechanistic factor of (-i-1) to a reaction with retention of configuration and (-1) to a reaction with inversion of configuration. Thus, we want to calculate the parity of the product, of 3 reaction from the parity of the... 

The stereochemistry of reactions can also be treated by permutation group theory for reactions that involve the transformation of an sp carbon atom center into an sp carbon atom center, as in additions to C=C bonds, in elimination reactions, or in eIcctrocycHc reactions such as the one shown in Figure 3-21. Details have been published 3l]. 

Fig. 9.76 The stereochemistry about tetrahedral atoms can be maintained with an appnrpriate chiral constraint.

A second option is to displace all atoms in Cartesian coordinates and then run an optimization. This second option works well for ring systems, but is not so efficient for long chains. This may also result in changing the stereochemistry of the molecule. 

A useful catalyst for asymmetric aldol additions is prepared in situ from mono-0> 2,6-diisopropoxybenzoyl)tartaric acid and BH3 -THF complex in propionitrile solution at 0 C. Aldol reactions of ketone enol silyl ethers with aldehydes were promoted by 20 mol % of this catalyst solution. The relative stereochemistry of the major adducts was assigned as Fischer- /ir o, and predominant /i -face attack of enol ethers at the aldehyde carbonyl carbon atom was found with the (/ ,/ ) nantiomer of the tartaric acid catalyst (K. Furuta, 1991). 

The term syn addition describes the stereochemistry of reactions such as this m which two atoms or groups add to the same face of a double bond When atoms or groups add to opposite faces of the double bond the process is called anti addition... 

Stereochemistry refers to chemistry in three dimensions Its foundations were laid by Jacobus van t Hoff and Joseph Achille Le Bel m 1874 Van t Hoff and Le Bel mde pendently proposed that the four bonds to carbon were directed toward the corners of a tetrahedron One consequence of a tetrahedral arrangement of bonds to carbon is that two compounds may be different because the arrangement of their atoms m space IS different Isomers that have the same constitution but differ m the spatial arrangement of their atoms are called stereoisomers We have already had considerable experience with certain types of stereoisomers—those involving cis and trans substitution patterns m alkenes and m cycloalkanes... 

Cholesterol was isolated m the eighteenth century but its structure is so complex that Its correct constitution was not determined until 1932 and its stereochemistry not verified until 1955 Steroids are characterized by the tetracyclic ring system shown m Figure 26 9a As shown m Figure 26 9b cholesterol contains this tetracyclic skeleton modified to include an alcohol function at C 3 a double bond at C 5 methyl groups at C 10 and C 13 and a C Hn side chain at C 17 Isoprene units may be discerned m var lous portions of the cholesterol molecule but the overall correspondence with the iso prene rule is far from perfect Indeed cholesterol has only 27 carbon atoms three too few for It to be classed as a tnterpene... 

A novel technique for dating archaeological samples called ammo acid racemiza tion (AAR) IS based on the stereochemistry of ammo acids Over time the configuration at the a carbon atom of a protein s ammo acids is lost m a reaction that follows first order kinetics When the a carbon is the only chirality center this process corresponds to racemization For an ammo acid with two chirality centers changing the configuration of the a carbon from L to D gives a diastereomer In the case of isoleucme for example the diastereomer is an ammo acid not normally present m proteins called alloisoleucme... 

Expand your answer to Problem 27 10 by showing the struc tural formula for each dipeptide m a manner that reveals the stereochemistry at the a carbon atom... 

Stereochemistry (Chapter 7) Chemistry in three dimensions the relationship of physical and chemical properties to the spatial arrangement of the atoms in a molecule Stereoelectron ic effect (Section 5 16) An electronic effect that depends on the spatial arrangement between the or bitals of the electron donor and acceptor Stereoisomers (Section 3 11) Isomers with the same constitu tion but that differ in respect to the arrangement of their atoms in space Stereoisomers may be either enantiomers or diastereomers... 

Example You could explore the possible geometries of two molecules interacting in solution and guess at initial transition structures. For example, if molecule Aundergoes nucleophilic attack on molecule B, you could impose a distance restraint between the two atoms that would form a bond, allowing the rest of the system to relax. Simulations such as these can help to explain stereochemistry or reaction kinetics and can serve as starting points for quantum mechanics calculations and optimizations. 

You can interpret the stereochemistry and rates of many reactions involving soft electrophiles and nucleophiles—in particular pericyclic reactions—in terms of the properties of Frontier orbitals. This applies in particular to pericyclic reactions. Overlap between the HOMO and the LUMO is a governing factor in many reactions. HyperChem can show the forms of orbitals such as HOMO and LUMO in two ways a plot at a slice through the molecule and as values in a log file of the orbital coefficients for each atom. 

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