Protonation of thymine,cytosine, adenine,and guanine DNA nucleic acid bases: Theoretical investigation into the framework of density functional theory

Gradient-corrected density functional computations with triple-zeta-type basis sets were performed to determine the preferred protonation site and the absolute gas-phase proton affinities of the most stable tautomer of the DNA bases thymine (T), cytosine (C), adenine (A), and guanine (G). Charge distribution, bond orders, and molecular electrostatic potentials were considered to rationalize the obtained results. The vibrational frequencies and the contribution of the zero-point energies were also computed. Significant geometrical changes in bond lengths and angles near the protonation sites were found. At 298 K, proton affinities values of 208.8 (T), 229.1 (C), 225.8 (A), and 230.3 (G) kcal/mol were obtained in agreement with experimental results. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 989–1000, 1998     

A Practical Route to Chiral Phenylalanine via the Condensation of Keto Acids with Amides and Asymmetric Hydrogenation

The condensation of β-phenylpyruvic acid with amides gave olefinic intermediates in good yields (75-80%). The asymmetric catalytic hydrogenation of α-acetamidocinnamic acid with high enantioselectivity is described.     

Ab initio quantum chemical study on the mechanism of exceptional behavior of lysine for ion yields in MALDI--role of vibrational entropic contribution in thermally averaged proton affinities

To elucidate the mechanism of the exceptional behavior of lysine for the ionization (protonation) yields in matrix-assisted laser desorption/ionization (MALDI) observed by Nishikaze and Takayama [Rapid Commun. Mass Spectrom. 2006, 20, 376], the temperature dependences of proton affinity (PA) and gas phase basicity for 20 amino acids are theoretically analyzed with correlated ab initio molecular orbital method under ideal gas condition. We have found that two different conformations, the linear structure with elongation of the side chain and the folded one having intramolecular hydrogen bonding, play important roles for the exceptional behavior of lysine. At low temperatures of around 298 K, the most stable conformation of the protonated lysine is the folded structure due to the formation of intramolecular hydrogen bonding. Meanwhile, at high temperatures, the Gibbs free energy of linear structure of protonated lysine becomes lower than that of the folded one because of the increment of vibrational entropic contribution. To explicitly take account of the contribution of the free energies, we have proposed the effective PA values thermally averaged using the ratio of Boltzmann distributions for two conformations. Since the effective PA value for lysine drastically decreases as the temperature increases above 1000 K, the linear correlation is clearly obtained between our effective PA values at high temperature and the ion yields in MALDI.     

Ab initio calculations on Pro-Ala and Pro-Gly dipeptides

The geometries of the dipeptides -Pro- -Ala, -Pro- -Ala and -Pro-Gly were investigated by a grid scan ab initio calculation. The 6-31G basis set was used to estimate the effect of the alanyl side-chain on the conformation of the peptide backbone and to provide a computational basis for the interpretation of known physical-chemical properties of larger peptides that contain these dipeptides. These calculations furnish a direct quantum mechanical assessment of the energetic consequences of a methyl side-chain in the i + 2 position of a turn. The results of the calculation support the current view that the presence of a -Ala residue in the i + 2 position favors a type II β-turn over a type I β-turn conformation, while -Ala has the opposite effect. Total and relative energies for all the optimized conformations identified by the grid search are given and geometric parameters (bond lengths, bond angles and dihedral angles) and net atomic charges have been calculated.     

Ab initio assessment of the electronic structure of 5α-reduced progestins

Progesterone (P) yields to 5α-reduced progestins, namely 5α-pregnanedione (DHP), tetrahydroprogesterone (THP), and allopregnanolone (ALLO-P). The geometries and electronic structure of these steroids were assessed by ab initio calculations using the 6-31G* basis set. The parameters measured were bond distances, valence angles, and dihedral angles. Likewise, the following were calculated: total energy; frontier orbitals, i.e., highest occupied molecular orbital (HOMO); lowest unoccupied molecular orbital (LUMO); dipole moment; atomic charges; and electrostatic potentials. The frontier orbitals of P were located at the π-double bond. However, the HOMO of the 5α-progestins was extended into the molecule, while the LUMO was confined at the C20 carbonyl group. The atomic charges, electronic density surfaces and electrostatic potentials showed patterns according to the stereochemical arrangement of the C3 and C20 carbonyl and hydroxyl functional groups. Interestingly, P and THP showed the larger dipole moment and high electronic density at the A-ring because the double bond and the 3α-hydroxy group, respectively. The present results might explain to some extent the metabolism of the studied progestins. Similarly, some physicochemical properties, such as dipole moments and electrostatic potentials, seem related with important biological actions such as uterine contractility and control of gonadotropin secretion. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 67: 329–338, 1998     

The Hydrophobic and Metal-Ion Coordinating Properties of α-Lipoic Acid—An Example of Intramolecular Equilibria in Metal-Ion Complexes

Hydrophobic interactions as structure determining factors for macromolecules are well-known in biochemistry. Considerably less recognized is the fact that these law-energy interactions may also determine the structure of low-molecular species. The same applies for weak ligand-metal ion interactions. That both these factors may lead to intramolecular, contraction-independent equilibria between isomeric metal-ion complexes is demostrated with α-lipoic acid as ligand. This cofactor affers metal ions two different binding sites: the carboxylate group and the disulfide linkage. The carboxylate group dominates the coordinating properties of this ligand towards the biologically important metal ions, but a disulfide-metal ion interaction is still possible and under sterically favourable conditions may becomevery important; this could also be true under enzymic conditions here the carboxyl group is no longer free but amide-liked to the protein. Furthermore, due to the valeric acid side chain, the lipoyl moiety is ideally suited to undergo hydrophobic ligand-ligand interactions in mixed-ligand complexes. Such hydrophobic interactions seem to be ideal to allwe migration, e.g., of the 14 Å long lipoyllysyl moiety, and also to caciliutate the correct ‘fixation’ at the surface of the enzyme.     

1,2-二硒方酸气相酸性和芳香性的理论研究

在RHF/6-311G^*^*水平优化得到1,2-二硒方酸(3,4-二羟基-3-环丁烯-1,2-二硒酮)三种平面构象异构体的平衡几何构型。进一步用MP2(full)/6-311G^*//RHF/6-311G^*^*方法计算三种异构体的单点能量,发现ZZ型异构体是能量最低构象,且ZZ和ZE型能量非常接近。用优化的最稳定构象ZZ型异构体在RHF/6-311G^*^*//RHF/6-311G^*^*,RHF/6-311+G^*^*//RHF/6-311+G^*^*,MP2(full)/6-311+G^*^*//RHF/6-311+G^*^*和B3LYP/6-311+G^*^*//B3LYP/6-311+G^*^*水平计算其气相酸性[ΔGⅲ~(~2~9~8~K~)]和同键反应芳香性稳定化能(HASE)。用基团加和法(groupincrementapproach)在RHF/6-311+G^*^*//RHF/6-311+G^*^*和B3LYP/6-311+G^*^*//B3LYP/6-311+G^*^*水平计算其磁化率增量(Λ)。计算结果指出标题化合物的键长发生了平均化,同键反应芳香性稳定化能和磁化率增量均为负值,表明它具有芳香性,实现了标题化合物芳香性的几何、能量和磁性的判定。     

Unprecedented Chain‐Length‐Dependent Conformational Conversion Between 11/9 and 18/16 Helix in α/β‐Hybrid Peptides

α,β‐Hybrid oligomers of varying lengths with alternating proteogenic α‐amino acid and the rigid β^2,3,3‐trisubstituted bicyclic amino acid ABOC residues were studied using both X‐ray crystal and NMR solution structures. While only an 11/9 helix was obtained in the solid state regardless of the length of the oligomers, conformational polymorphism as a chain‐length‐dependent phenomenon was observed in solution. Consistent with DFT calculations, we established that short oligomers adopted an 11/9 helix, whereas an 18/16 helix was favored for longer oligomers in solution. A rapid interconversion between the 11/9 helix and the 18/16 helix occurred for oligomers of intermediate length.