Rotamer, defined

More recent developments in the mechanistic aspects of the alkene metathesis reaction include the observation that the alkene coordinates to the metal carbene complex prior to the formation of the metallacyclobutane complex. Thns a 2 - - 2 addition reaction of the alkene to the carbene is very unlikely, and a vacant coordination site appears to be necessary for catalytic activity. It has also been shown that the metal carbene complex can exist in different rotameric forms (equation 11) and that the two rotamers can have different reactivities toward alkenes. " The latter observation may explain why similar ROMP catalysts can produce polymers that have very different stereochemistries. Finally, the synthesis of a well-defined Ru carbene complex (equation 12) that is a good initiator for ROMP reactions suggests that carbenes are probably the active species in catalysts derived from the later transition elements. ... 

The calculated harmonic force field given in cartesian coordinates was transformed into a force field defined by symmetry coordinates. A normal coordinate analysis was performed using the geometry and the symmetry force constants from ab initio calculations, resulting in a description of the normal modes by their potential energy distribution (FED). Table 3 presents the potential energy distribution for v SiSi and v, SiCb for both rotamers, and Table 4 summarizes the SiSi, SiCl, and SiC stretching force constants. 

Scheme 3 Definition of hydroxyl rotamers about the C3-03 bond. The 0 torsion angle is defined by the corresponding H-Ci-O—Hi angle.

The mean-field approach is now described. The side chain degrees of freedom are defined by a conformational matrix, CM, where each rotamer, k, has a probability of CM( i, k), where the sum of the probabilities for a given residue, i, must be equal to 1. The potential of mean force, E(i,k), on the k-th rotamer of residue, i, is given by ... 

Alternatively, one tries to extrapolate the correct rotamer from examples of residues in a similar environment in the database of known structures. The main problem here is how to define similar environments. In practice, similar environments for residues have most often been defined as having the same secondary structure (a-helix, P-strand, or loop). Until recently, side chains were normally placed using standard rotamer libraries [28-30]. A variety of procedures have been used to get rid of van der Waals clashes. These range from manual... 

Our studies have revealed that the structures of aromatic amine-DNA adducts are determined primarily by their size and coplanarity, as well as the nature of the adduct linkage (C8, N2, etc). It has been shown that aromatic amine lesions exist primarily in three well-defined conformational categories (S, B, W) and their population balance is strongly influenced by the sequences surrounding the lesion site. It is believed that the S/B/W ratios of aromatic amine adducts, not the subtle structural differences at the lesion site (e.g., rotamers, C8 versus N2 linkage, etc), determine the nature of the conformation-specific repair and mutational outcomes. As such, the available data points towards a new paradigm lesion bypass (either error-free or error-prone) depends on various factors, including the thermodynamic and conformational characteristics of the lesion at the replication fork,... 

Method E is similar to method D in that it relies upon the nucleophilic cleavage of epoxides to generate stereochemically defined betaines. A two-step procedure is employed, starting with the reaction of a lithium phosphide with the cis or trans epoxides (36 or 37). The resulting alkoxy phosphines 34 or 35 are converted into betaines by direct alkylation with methyl iodide (19). This contrasts with method A where the betaine is generated by the deprotonation of a -hydroxyphosphonium salt, and method E may therefore produce a different population of betaine rotamers than does method A. This subtle difference may explain why method E proceeds with higher stereospecificity than does method A in the Trippett-Jones experiment (Table 7 entry 16,... 

---