Amino 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. 

Quantum mechanical calculations on C-protonated cations of aromatic amines satisfactorily predict cases of C-protonation and the electronic transitions of these ions (Yamaoka, 1970). Amino-groups in the 1-, 3-, and 5-positions greatly stabilize the benzenium ion [163], the effect of amino-groups in other positions being much smaller. 

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

In spite of the various difficulties and limitations, quantum-mechanical calculations may provide valuable information concerning the tautomeric equilibria of many molecules with similar structure, e.g., influence of substituents on tautomeric equilibria. It can be assumed that the errors in estimating the relative stabilities for a series of molecules with similar structures are of the same order. The results obtained for the amino and imino tautomers of cytosine (8a/8b) and 7V(4)-hydroxy cytosine (9a/9b) fall in this category. 

Both the C and N chemical shifts of a number of quinoxalines substituted at position 2 with the n-electron excess 2 -benzo[ ]furanyl substituent, which has at position 3 a hydroxy or amino group, could be satisfactorily calculated by the GIAO method on the basis of HF and DFT ab initio structures. Quantum mechanical calculations using the 3-21 G(d) basis-set were performed on some p-substituted diaryl tellurides and aryl Me tellurides, and the corresponding cationic radicals of these compounds. Calculated relative radical stabilization energies were shown to correlate with experimental data, and the peak oxidation potentials and Te chemical shifts were... 

The isomeric equilibria of 2-acyl-2-nitroenamines with primary or secondary amino group are strongly solvent-dependent, as already seen for other enamines. An increase in the polarity of the solvent increases the population of the isomer(s) with Z-configuration, as deduced from the H-NMR spectra . In 3-amino-2-nitroacry-lic esters (567-574), the IR spectra show that an increase of solvent polarity increases the population of the ZE isomer , which has the highest calculated dipole moment. The effect of solvent polarity on the isomeric equilibria of some model 2-acyl-2-nitroenamines (554, R = H, Me R = Me, OMe R = R = H) has been qualitatively predicted by quantum-mechanical calculations using the self-consistent reaction field approach . 

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. 

The first example of the use of L-proline amino alcohol amides was reported by Gong and coworkers. The reaction between various substituted aldehydes and acetone is mediated by catalyst 30, which was previously prepared from L-proline and (l5,2S)-diphenyl-2-aminoethanol, and gave the desired hydro g ketones in excellent enantioselectivity and moderate to good yields (Scheme 13.20a). Additionally, quantum mechanical calculations of the transition structures of the model reaction revealed that hydrogen bonding between the peptide, mediated by amide N-H and the terminal... 

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... 

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