Electronic structure and mechanism for the uptake of nitric oxide by the Ru(iii) antitumor complex NAMI-A.

Nitric oxide (NO) has well known vasodilation effects in living organisms and its participation in the metastasis of cancer cells through the angiogenesis process has been demonstrated experimentally. Therefore, the uptake of NO has become one focus of investigation to produce anti-metastatic drugs. In this article we have investigated the uptake of NO by the ruthenium based metallodrug trans-tetrachloride(dimethylsulfoxide)imidazole ruthenate(iii) [Im]trans-[RuCl4(Im)(DMSO)], known as New Anti-tumor Metastasis Inhibitor-A (NAMI-A). Electronic structure calculations using Density Functional Theory, DFT, and State-Averaged Complete Active Space Self Consistent Field, SA-CASSCF, with second order perturbation theory corrections, NEVPT2 were carried out to investigate the mechanism involved in the uptake of NO by the Ru-based anticancer metallodrug NAMI-A. The calculations revealed that the reaction takes place at the triplet potential energy surface, with the singlet surface being ∼15 kcal mol-1 shifted to higher energies, and there is a surface crossing to form the most stable singlet product after the reaction takes place at the triplet surface. The spin pairing and electron transfer from the nitric oxide to the metallic fragment takes place at the region of the minimum energy crossing point between the two surfaces. The Ru-NO bond in the {Ru-NO}6 product has ∼10% of the RuIII-NO0 character. The SA-CASSCF/NEVPT2 calculations revealed that the uptake of NO by NAMI-A has a small energy barrier of ∼8 kcal mol-1 and, therefore a rate constant of 11.3 × 106 s-1 at 300 K. In addition, the reaction is thermodynamically favorable, with a Gibbs free energy of ∼30 kcal mol-1. These results show that the uptake of nitric oxide by the NAMI-A complex is kinetically and thermodynamically feasible in biological medium and, therefore, gives support to the anti-angiogenesis theory associated to the mode of action of NAMI-A and other related compounds.

Theoretical investigation of the neutral hydrolysis of diethyl 4-nitrophenyl phosphate (paraoxon) in aqueous solution.

In this work the neutral or spontaneous hydrolysis of paraoxon, one of the most popular organophosphate pesticides, in aqueous solution was investigated at the DFT and MP2 levels of theory, using a combination of local solvation of the phosphoryl group with explicit water molecules, and treating the long range solvent effects using continuum solvation model. In contrast to the alkaline hydrolysis, the neutral hydrolysis takes place in two steps, through an AN + DN mechanism, with formation of a pentacoordinate phosphorane intermediate. The reaction has activation free energies of 31.8 and 1.9 kcal mol-1 for the first and second steps, respectively, and has an overall reaction free energy of -9.3 kcal mol-1, computed at the MP2/6-311++G(2d,2p)//B3LYP/6-31+G(d) level of theory. The reaction proceeds through a sequence of proton transfer processes from the attacking water molecule and ends with the protonation of the nitrophenolate leaving group. Explicit description of the local solvating water molecules is essential to describe the proton transfer processes along the reaction coordinate and to stabilize the pentacoordinate intermediate formed. The neutral hydrolysis is very slow and has an overall rate constant of 3.05 × 10-11 s-1, computed at the MP2/6-311++G(2d,2p)//B3LYP/6-31+G(d) level of theory. This result, in conjunction with the sensitivity of the rate constant to the experimental conditions, indicates that the hydrolysis of paraoxon in aqueous solution can be even slower than predicted experimentally.

Base Mechanism to the Hydrolysis of Phosphate Triester Promoted by the Cd2+/Cd2+ Active site of Phosphotriesterase: A Computational Study.

In the present work, density functional theory (DFT) calculations at the B3LYP/6-31+G(d) and including dispersion effects were used to investigate the hydrolysis of paraoxon, using a cluster model of the active site of Cd2+/Cd2+-phosphotriesterase (PTE) from Pseudomonas diminuta. The mechanism proposed here consist of (i) Exchange of the coordinated water molecule and coordination of the substrate to the more solvent exposed Cdß center in monodentate fashion, (ii) protonation of the µ-hydroxo bridge by the uncoordinated water molecule and in situ formation of the nucleophile, (iii) formation of a pentacoordinate intermediate with significant bond breaking to the leaving group and bond formation to the nucleophile, and (iv) protonation of the Asp301 residue and restoration of the active site through the coordination of another water molecule of the medium. The water molecules initially coordinated to the active site play a crucial role in stabilizing the transition states and the pentacoordinate intermediate. The reaction takes place in a two-step (AN + DN) mechanism, with energy barriers of 12.9 and 1.9 kcal/mol for the first and second steps, respectively, computed at the B3LYP-D3/6-311++G(2d,2p) level of theory, in excellent agreement with the experimental findings. Dispersion effects alone contribute to diminish the energy barriers as much as 26%. The base mechanism for the Cd2+/Cd2+-PTE proposed here, in conjunction with the agreement found with the experimental energetic value for the energy barrier, makes it a consistent and kinetically viable mechanistic proposal for the hydrolysis of phosphate triesters promoted by the Cd2+ substituted PTE enzyme.

Phosphorane lifetime and stereo-electronic effects along the alkaline hydrolysis of phosphate esters.

Hybrid quantum mechanical/effective fragment potential (QM/EFP) calculations, in conjunction with the quantum theory of atoms in molecules (QTAIM) and energy decomposition analysis (EDA), were employed to investigate the reaction mechanism and stereo-electronic effects along the alkaline hydrolysis of the monoethyl phosphate dianion (MEP) and the diethylphosphate monoanion (DEP). Reactions proceed through a synchronous bimolecular ANDN mechanism for MEP and a stepwise (AN + DN) mechanism for DEP, with the formation of a phosphorane intermediate, having an overall reaction free energy and barrier of 11.5 and 43.0 kcal mol(-1), respectively. In addition, ab initio molecular dynamics simulations were performed to investigate the stability of the phosphorane pentacoordinate intermediate observed in the reaction of the phosphate diester. The phosphorane intermediate has a lifetime of ∼1 ps after which it decomposes into the corresponding alcohol and phosphate monoester dianion. Electrostatics governs the interaction between the nucleophile and the phosphate ester. However, some degree of covalence in the interaction starts to appear at distances shorter than 2.45 Šfor MEP and 2.63 Šfor DEP. For the monoester, the electrostatic repulsive terms are the dominant contributions for the formation of the transition state. On the other hand, for the phosphate diester, the formation of the P-OH bond is dominated by associative terms of electrostatic nature.