Amino acid quantum-mechanical calculations

Classical electrostatic modeling based on the Coulomb equation demonstrated that the model system chosen could account for as much as 85% of the effect of the protein electric field on the reactants. Several preliminary computations were, moreover, required to establish the correct H-bond pattern of the catalytic water molecule (WAT in Fig. 2.6). Actually, in the crystal structure of Cdc42-GAP complex [60] the resolution of 2.10 A did not enable determination of the positions of the hydrogen atoms. Thus, in principle, the catalytic water molecule could establish several different H-bond patterns with the amino acids of the protein-active site. Both classical and quantum mechanical calculations showed that WAT, in its minimum-energy conformation,... 

The presence of the cation protonated on N-1 cannot account for the fluorescence of aqueous acidic adenine solutions (pH = 2), since the 1-methyl derivative does not fluoresce under the same conditions (Borresen, 1967). It has therefore been suggested that other tautomeric forms of the cation are also present, the fluorescent tautomer probably being protonated on the amino-group with another proton on N-7. Quantum mechanical calculations (Veillard and Pullman, 1963) indicate similar proton affinity for N-1 and N-3, and a lesser one for N-7. There are numerous calculations in the literature on the electronic structure of adenine (see Boyd, 1972, and references quoted therein) and a recent one on N-7-H and N-9-H tautomers protonated on N-1 (Jordan and Sostman, 1972). The N-9-H form is preferred according to hoth MINDO and CNDO/2 calculations. 

Dwyer DS. Electronic properties of amino acid side chains quantum mechanics calculations of substituent effects. BMC Chem. Biol. 2005 5 2. 

Quantum mechanical calculations on the conformational properties of norepinephrine have also been reported. Interconversion of ephedrine and pseudo-ephedrine to a slight extent under y-irradiation has been observed. Absorption of carbon dioxide by cupric ephedrinates can be accounted for by carbamate formation rather than formation of metal-carbon dioxide bonds. -Acylation of /3-phenethylamines by protected amino-acids, e.g. N-CBZ-leucine, has been reported. ... 

Most of the mechanistic studies have focussed on NiFe-hydrogenases. A common approach has been to develop mechanisms using theoretical quantum mechanical calculations. Much attention has been paid to attempting to assign structures to the EPR spectroscopically-characterised states using these theoretical models. To date this approach has paid little or no attention to the role of the surrounding polypeptide, and potential roles for conserved amino acid residues such as His-371. 

Three distinct types of study have been carried out in connection with the electronic structure of proteins and their constituents. In the first place, quantum-mechanical calculations have been performed on the electronic distribution in all the twenty a-amino acids which enter into the constitution of proteins " . These calculations have been carried out for the neutral, cationic, anionic and dipolar forms of the amino acids and they represent the... 

The large number of research programs aimed at the syntheses of steroids produced a phenomenal wealth of reaction methods for organic synthesis. The development of the asymmetric proline-catalyzed Robinson annulation reaction for the preparation of the Wieland-Miescher ketone (36, Equation 3) in the early 1970s [41] is noteworthy and marks an important milestone for catalysis by small organic molecules. Asymmetric amine-catalyzed aldol reactions represent an additional variant of the stereoselective aldol addition reaction. The mechanism of the proline-catalyzed aldol addition reaction has been the subject of extensive debate, but the general consensus, based on recent mechanistic studies and quantum mechanical calculations, supports the notion of the involvement of a single amino acid molecule in the transition state structure (39, Scheme 4.4) [42]. 

---