Determination of Amino Acids' pKa: Importance of Cavity Scaling within Implicit Solvation Models and Choice of DFT Functionals

Protonation states of molecules significantly influence the thermodynamics and kinetics of chemical reactions. This is especially important in biochemical processes, where appropriate protonation states of amino acids control the exo/endoergicity of practically all biochemical cycles. This paper is focused on appraisal of the impact of DFT functionals and PCM solvation models on the accuracy of pKa evaluations for all proteinogenic amino acids. Eight functionals (B3LYP, PBE0, revPBE0, M06-2X, M11, M11-L, TPSSh, and ωB97X-D) and four basis sets are considered, together with four kinds of implicit solvation models when additional attention is paid to a cavity construction. An influence of nonelectrostatic contributions and Wertz's corrections on Gibbs free energy is investigated together with accuracy of provided proton solvation energy. The best model is based on the M06-2X/6-311++G**/D-PCM/UAKS computational level. The fitting procedure is utilized to improve the accuracy of the evaluated models. All of these results are also compared with values obtained from the COSMOtherm program and CCSD(T) calculations. Results for cysteine and histidine are discussed individually, as they can be found in different protonation states at neutral pH.

Mechanism of Nitrogen-Carbon Bond Formation from Iron(IV) Disilylhydrazido Intermediates during N2 Reduction

We recently reported a reaction sequence that activates C-H bonds in simple arenes as well as the N-N triple bond in N₂, delivering the aryl group to N₂ to form a new N-C bond (Nature 2020, 584, 221). This enables the transformation of abundant feedstocks (arenes and N₂) into N-containing organic compounds. The key N-C bond forming step occurs upon partial silylation of N₂. However, the pathway through which reduction, silylation, and migration occurred was unknown. Here, we describe synthetic, structural, magnetic, spectroscopic, kinetic, and computational studies that elucidate the steps of this transformation. N₂ must be silylated twice at the distal N atom before aryl migration can occur, and sequential silyl radical and silyl cation addition is a kinetically competent pathway to a formally iron(IV)-NN(SiMe₃)₂ intermediate that can be isolated at low temperature. Kinetic studies show its first-order conversion to the migrated product, and DFT calculations indicate a concerted transition state for migration. The electronic structure of the formally iron(IV) intermediate is examined using DFT and CASSCF calculations, which reveal contributions from iron(II) and iron(III) resonance forms with oxidized NNSi₂ ligands. The depletion of electron density from the Fe-coordinated N atom makes it electrophilic enough to accept the incoming aryl group. This new pathway for the N-C bond formation offers a method for functionalizing N₂ using organometallic chemistry.

QM and QM/MM umbrella sampling MD study of the formation of Hg(II)-thymine bond: Model for evaluation of the reaction energy profiles in solutions with constant pH

The formation of the Hg-N3(T) bond between the 1-methylthymine (T) molecule and the hydrated Hg²⁺ cation was explored with the combined quantum mechanics/molecular mechanics (QM/MM) method including Free Energy Perturbation corrections. The thermodynamic properties were determined in the whole pH range, when these systems were explicitly investigated and considered as the QM part: (1) T + [Hg(H₂ O)₆ ]²⁺ , (2) T + [Hg(H₂ O)₅ (OH)]⁺ , (3) T + Hg(H₂ O)₄ (OH)₂ , and (4) N3-deprotonated T + Hg(H₂ O)₄ (OH)₂ . The MM part contained only solvent molecules and counterions. As a result, the dependence of Gibbs-Alberty reaction free energy on pH was obtained along the reaction coordinate. We found that an endoergic reaction in acidic condition up to pH < 4-5 becomes exoergic for a higher pH corresponding to neutral and basic solutions. The migration of the Hg²⁺ cation between N3 and O4/2 positions in dependence on pH is discussed as well. For the verification, DFT calculations of stationary points were performed confirming the qualitative trends of QM/MM MD simulations and NMR parameters were determined for them.

Side Reactions with an Equilibrium Constraint: Detailed Mechanism of the Substitution Reaction of Tetraplatin with dGMP as a Starting Step of the Platinum(IV) Reduction Process

Two possible pathways of the substitution reaction within the reduction process of the Pt^IV(DACH)Cl₄ by dGMP are compared: associative reaction course and autocatalytic Basolo-Pearson mechanisms. Since two forms: single-protonated and fully deprotonated phosphate group of dGMP are present in equilibrium at neutral and mildly acidic solutions, consideration of a side reactions scheme with acido-basic equilibrium-constraint is a very important model for obtaining reliable results. The examined complexes are optimized at the B3LYP-GD3BJ/6-31G(d) level with the COSMO implicit solvation model and Klamt's radii used for cavity construction. Energy characteristics and thermodynamics for all reaction branches are determined using the B3LYP-GD3BJ/6-311++G(2df,2pd)/IEF-PCM/scaled-UAKS level with Wertz's entropy corrections. Rate constants are estimated for each individual branch according to Eyring's transition state theory (TST), averaged according to equilibrium constraint and compared with available experimental data. The determined reaction barriers of the autocatalytic pathway fairly correspond with experimental values. Furthermore, autocatalytic reaction of tetraplatin and its two analogues complexes [Pt^IV(en)Cl₄ and Pt^IV(NH₃)₂Cl₄] are explored and compared with measured data in order to examined general reaction descriptors.

Investigation of the Inertness to Hydrolysis of Platinum(IV) Prodrugs

Platinum(IV) complexes are an important class of compounds that can act as prodrugs, and due to their inertness, if correctly designed, they could have low toxicity outside the cancer cell and improve the pharmacological properties of the platinum(II) anticancer agents that are currently used in the clinic. Because of the efforts that are concentrated on the use of axial ligands able to control the reduction potentials, lipophilicity, charge, selectivity, targeting, and cell uptake of the Pt(IV) complexes, we considered to be of interest to probe the inertness of such complexes that is assumed to be a fulfilled prerequisite. To this aim, a density functional theory computational analysis of the hydrolysis mechanism and the corresponding energy profiles for a series of Pt(IV) derivatives of cisplatin, carboplatin, and oxaliplatin with acetato, haloacetato, and chlorido ligands was performed to probe their stability in biological fluids. The heights of the barriers calculated along the hydrolysis pathways for the associative displacement of ligands both in axial and equatorial positions confirm that Pt(IV) complexes are, in general, more inert than the corresponding Pt(II) drugs even if inertness is lower than expected. Some exceptions exist, such as derivatives of oxaliplatin for the hydrolysis in equatorial position. The nature of the axial ligands influences the course of the hydrolysis reaction even if a decisive role is played by the ligands in equatorial positions. The mechanism of the aquation in axial position of cisplatin Pt(IV) derivative with two chlorido axial ligands assisted by Pt(II) cisplatin was elucidated, and the calculated activation energy confirms the catalytic role played by the Pt(II) complex.

DFT Investigation of the Mechanism of Action of Organoiridium(III) Complexes As Anticancer Agents

The potential use of synthetic metal complexes able to catalyze chemical transformations in living organisms is currently attracting a great deal of attention. Recently, organometallic ruthenium and iridium complexes have revealed an unexpected ability to modulate the redox status of cancer cells. In particular, half-sandwich organoiridium(III) cyclopentadienyl complexes of general formula [(η(5)-Cp(x))Ir(III)(X(∧)Y)Z](0/+), where Cp(x) = Cp*, Cp(xph) (tetramethyl-(phenyl)cyclopentadienyl) or Cp(xbiph) (tetramethyl(biphenyl)-cyclopentadienyl), X(∧)Y = bidentate ligand with nitrogen, oxygen, and/or carbon donor atoms, and Z = Cl, H2O, or pyridine (py) have shown promising antiproliferative activity toward cancer cells, higher potency than cisplatin, and a different mechanism of action due to the increase of the oxidative stress in cells. As such, complexes can belong to the class of DNA interacting compounds and attack on DNA can represent a secondary mechanism of action. We have explored here by means of density functional calculations (M06-L) and with the support of experimental observations for both [(η(5)-Cp(xbiph))Ir-(phpy) (Cl)], 1-Cl, and [(η(5)-Cp(xbiph))Ir-(phpy) (py)], 1-py, complexes the mechanistic aspects of the hydrolysis reaction, H2O2 ROS production by assisted hydride transfer from NADH to molecular oxygen, interaction with purine nucleobases adenine and guanine as well as gluthatione, that is highly abundant in cells, alongside the reaction mechanism for the oxidation of the formed sulfur-coordinated thiolate to the corresponding sulfenato complex. The comparison between kinetic and thermodynamic parameters calculated for all the involved processes shows that, according to the hypothesis based on experimental findings, the interaction with the tripeptide glutathione causes deactivation of 1-Cl, whereas 1-py, in both its aquated and nonaquated form, can induce cell apoptosis in a dual manner: DNA damage and H2O2 ROS production to increase oxidative stress.