Ab initio studies on the tri- and diphosphate fragments of adenosine triphosphate

Complex interplay of interatomic bonding in a multi-component pyrophosphate crystal: K2Mg (H2P2O7)2·2H2O

The electronic structure and interatomic bonding of pyrophosphate crystal K₂Mg (H₂P₂O₇)₂·2H₂O are investigated for the first time showing complex interplay of different types of bindings. The existing structure from single-crystal X-ray diffraction is not sufficiently refined, resulting in unrealistic short O─H bonds which is rectified by high-precision density functional theory (DFT) calculation. K₂Mg (H₂P₂O₇)₂·2H₂O has a direct gap of 5.22 eV and a small electron effective mass of 0.14 m_e. Detailed bond analysis between every pair of atoms reveals the complexity of various covalent, ionic, hydrogen bonding and bridging bonding and their sensitive dependence on structural differences. The K--O bonds are much weaker than Mg--O bonds and contributions from the hydrogen bonds are non-negligible. Quantitative analysis of internal cohesion in terms of total bond order density and partial bond order density divulges the relative importance of different types of bonding. The calculated optical absorptions show multiple peaks and a sharp Plasmon peak at 23 eV and a refractive index of 1.44. The elastic and mechanical properties show features unique to this low-symmetry crystal. Phonon calculation gives vibrational frequencies in agreement with reported Raman spectrum. These results provide new insights indicating that acidic pyrophosphates could have a variety of unrealized applications in advanced technology.

Hydration properties of adenosine phosphate series as studied by microwave dielectric spectroscopy

Hydration properties of adenine nucleotides and orthophosphate (Pi) in aqueous solutions adjusted to pH=8 with NaOH were studied by high-resolution microwave dielectric relaxation (DR) spectroscopy at 20 °C. The dielectric spectra were analyzed using a mixture theory combined with a least-squares Debye decomposition method. Solutions of Pi and adenine nucleotides showed qualitatively similar dielectric properties described by two Debye components. One component was characterized by a relaxation frequency (f(c)=18.8-19.7 GHz) significantly higher than that of bulk water (17 GHz) and the other by a much lower f(c) (6.4-7.6 GHz), which are referred to here as hyper-mobile water and constrained water, respectively. By contrast, a hydration shell of only the latter type was found for adenosine (f(c)~6.7 GHz). The present results indicate that phosphoryl groups are mostly responsible for affecting the structure of the water surrounding the adenine nucleotides by forming one constrained water layer and an additional three or four layers of hyper-mobile water.

Hydrolysis of aspartic acid phosphoramidate nucleotides: a comparative quantum chemical study

L-Aspartic acid has recently been found to be a good leaving group during HIV reverse transcriptase catalyzed incorporation of deoxyadenosine monophosphate (dAMP) in DNA. This showed that L-Asp is a good mimic for the pyrophosphate moiety of deoxyadenosine triphosphate. The present work explores the thermochemistry and mechanism for hydrolysis of several models for L-aspartic-dAMP using B3LYP/DGDZVP, MP2/6-311++G** and G3MP2 level of theory. The effect of the new compound is gradually investigated: starting from a simple methyl amine leaving group up to the aspartic acid leaving group. The enzymatic environment was mimicked by involving two Mg(2+) ions and some important active site residues in the reaction. All reactions are compared to the corresponding O-coupled leaving group, which is methanol for methyl amine and malic acid for aspartic acid. With methyl amine as a leaving group a tautomeric associative or tautomeric dissociative mechanism is preferred and the barrier is lower than the comparable mechanism with methanol as a leaving group. The calculations on the aspartic acid in the enzymatic environment show that qualitatively the mechanism is the same as for triphosphate but the barrier for hydrolysis by the associative mechanism is higher for L-aspartic-dAMP than for L-malic-dAMP and pyrophosphate.