Reaction mechanism of Ru(II) piano‐stool complexes: Umbrella sampling QM/MM MD study

Biologically relevant interactions of piano‐stool ruthenium(II) complexes with ds‐DNA are studied in this article by hybrid quantum mechanics—molecular mechanics (QM/MM) computational technique. The whole reaction mechanism is divided into three phases: (i) hydration of the [Ru^II(η⁶‐benzene)(en)Cl]⁺ complex, (ii) monoadduct formation between the resulting aqua‐Ru(II) complex and N7 position of one of the guanines in the ds‐DNA oligomer, and (iii) formation of the intrastrand Ru(II) bridge (cross‐link) between two adjacent guanines. Free energy profiles of all the reactions are explored by QM/MM MD umbrella sampling approach where the Ru(II) complex and two guanines represent a quantum core, which is described by density functional theory methods. The combined QM/MM scheme is realized by our own software, which was developed to couple several quantum chemical programs (in this study Gaussian 09) and Amber 11 package. Calculated free energy barriers of the both ruthenium hydration and Ru(II)‐N7(G) DNA binding process are in good agreement with experimentally measured rate constants. Then, this method was used to study the possibility of cross‐link formation. One feasible pathway leading to Ru(II) guanine‐guanine cross‐link with synchronous releasing of the benzene ligand is predicted. The cross‐linking is an exergonic process with the energy barrier lower than for the monoadduct reaction of Ru(II) complex with ds‐DNA. © 2014 Wiley Periodicals, Inc.     

Interactions of the “piano‐stool” [ruthenium(II)(η6‐arene)(quinolone)Cl]+ complexes with water; DFT computational study

Full optimizations of stationary points along the reaction coordinate for the hydration of several quinolone Ru(II) half‐sandwich complexes were performed in water environment using the B3PW91/6‐31+G(d)/PCM/UAKS method. The role of diffuse functions (especially on oxygen) was found crucial for correct geometries along the reaction coordinate. Single‐point (SP) calculations were performed at the B3LYP/6‐311++G(2df,2pd)/DPCM/saled‐UAKS level. In the first part, two possible reaction mechanisms—associative and dissociative were compared. It was found that the dissociative mechanism of the hydration process is kinetically slightly preferred. Another important conclusion concerns the reaction channels. It was found that substitution of chloride ligand (abbreviated in the text as dechlorination reaction) represents energetically and kinetically the most feasible pathway. In the second part the same hydration reaction was explored for reactivity comparison of the Ru(II)‐complexes with several derivatives of nalidixic acid: cinoxacin, ofloxacin, and (thio)nalidixic acid. The hydration process is about four orders of magnitude faster in a basic solution compared to neutral/acidic environment with cinoxacin and nalidixic acid as the most reactive complexes in the former and latter environments, respectively. The explored hydration reaction is in all cases endergonic; nevertheless the endergonicity is substantially lower (by ～6 kcal/mol) in basic environment. © 2016 Wiley Periodicals, Inc.     

Hydrolysis of chemically distinct sites of human serum albumin by polyoxometalate: A hybrid QM/MM (ONIOM) study

In this study, mechanisms of hydrolysis of all four chemically diverse cleavage sites of human serum albumin (HSA) by [Zr(OH)(PW₁₁O₃₉)]⁴⁻ (ZrK) have been investigated using the hybrid two-layer QM/MM (ONIOM) method. These reactions have been proposed to occur through the following two mechanisms: internal attack (IA) and water assisted (WA). In both mechanisms, the cleavage of the peptide bond in the Cys392-Glu393 site of HSA is predicted to occur in the rate-limiting step of the mechanism. With the barrier of 27.5 kcal/mol for the hydrolysis of this site, the IA mechanism is found to be energetically more favorable than the WA mechanism (barrier = 31.6 kcal/mol). The energetics for the IA mechanism are in line with the experimentally measured values for the cleavage of a wide range of dipeptides. These calculations also suggest an energetic preference (Cys392-Glu393, Ala257-Asp258, Lys313-Asp314, and Arg114-Leu115) for the hydrolysis of all four sites of HSA. © 2018 Wiley Periodicals, Inc.     

Piano‐stool Ru (II) arene complexes that contain ethylenediamine and application in alpha‐alkylation reaction of ketones with alcohols

A series of piano‐stool Ru (II) complexes ( Ru _1–7 ) bearing ethylenediamine with aryl and aliphatic groups were prepared and fully characterized by ¹H, ¹³C, ¹⁹F and ³¹P NMR spectroscopy, FT‐IR and elemental analysis. The crystal structures of Ru _2–4 and Ru ₇ were determined by X‐ray crystallography. They were successfully applied to the alpha(α)‐alkylation of aliphatic and aromatic ketones with alcohols via the borrowing hydrogen strategy in mild reaction conditions within a short time. The catalytic system has a broad substrate scope, which allows the synthesis of alpha alkylated ketones with excellent yields. The electronic and steric effects of complexes on catalytic activity were analysed. The influence of the carbon chain length of the ligand on the alpha‐alkylation reaction of ketones was also investigated. The catalytic cycle was also examined by ¹H‐NMR spectroscopy in d₈‐toluene.     

Interactions of the “piano‐stool” [ruthenium(II) (η6‐arene)(en)CL]+ complexes with water and nucleobases; ab initio and DFT study

Piano stool ruthenium complexes of the composition [Ru(II)(η⁶‐arene)(en)Cl]^+/2+ (en = ethylenediamine) represent an emerging class of cisplatin‐analogue anticancer drug candidates. In this study, we use computational quantum chemistry to characterize the structure, stability and reactivity of these compounds. All these structures were optimized at DFT(B3LYP)/6‐31G(d) level and their single point properties were determined by the MP2/6‐31++G(2df,2pd) method. Thermodynamic parameters and rate constants were determined for the aquation process, as a replacement of the initial chloro ligand by water and subsequent exchange reaction of aqua ligand by nucleobases. The computations were carried out at several levels of DFT and ab initio theories (B3LYP, MP2 and CCSD) utilizing a range of bases sets (from 6‐31G(d) to aug‐cc‐pVQZ). Excellent agreement with experimental results for aquation process was obtained at the CCSD level and reasonable match was achieved also with the B3LYP/6‐31++G(2df,2pd) method. This level was used also for nucleobase‐water exchange reaction where a smaller rate constant for guanine exchange was found in comparison with adenine. Although adenine follows a simple replacement mechanism, guanine complex passes by a two‐step mechanism. At first, Ru‐O6(G) adduct is formed, which is transformed through a chelate TS2 to the Ru‐N7(G) final complex. In case of guanine, the exchange reaction is more favorable thermodynamically (releasing in total by about 8 kcal/mol) but according to our results, the rate constant for guanine substitution is slightly smaller than the analogous constant in adenine case when reaction course from local minimum is considered. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009     

Role of structural water molecule in HIV protease-inhibitor complexes: a QM/MM study

Structural water molecule 301 found at the interface of HIV protease-inhibitor complexes function as a hydrogen bond (H-bond) donor to carbonyl groups of the inhibitor as well as H-bond acceptor to amide/amine groups of the flap region of the protease. In this study, six systems of HIV protease-inhibitor complexes were analyzed, which have the presence of this "conserved" structural water molecule using a two-layer QM/MM ONIOM method. The combination of QM/MM and QM method enabled the calculation of strain energies of the bound ligands as well as the determination of their binding energies in the ligand-water and ligand-water-protease complexes. Although the ligand experiences considerable strain in the protein bound structure, the H-bond interactions through the structural water overcomes this strain effect to give a net stability in the range of 16-24 kcal/mol. For instance, in 1HIV system, the strain energy of the ligand was 12.2 kcal/mol, whereas the binding energy associated with the structural water molecule was 20.8 kcal/mol. In most of the cases, the calculated binding energy of structural water molecule showed the same trend as that of the experimental binding free energy values. Further, the classical MD simulations carried out on 1HVL system with and without structural water 301 showed that this conserved water molecule enhances the H-bond dynamics occurring at the Asp-bound active site region of the protease-inhibitor system, and therefore it will have a direct influence on the mechanism of drug action.     

Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach

The extent to which accuracy of electric charges plays a role in protein-ligand docking is investigated through development of a docking algorithm, which incorporates quantum mechanical/molecular mechanical (QM/MM) calculations. In this algorithm, fixed charges of ligands obtained from force field parameterization are replaced by QM/MM calculations in the protein environment, treating only the ligands as the quantum region. The algorithm is tested on a set of 40 cocrystallized structures taken from the Protein Data Bank (PDB) and provides strong evidence that use of nonfixed charges is important. An algorithm, dubbed "Survival of the Fittest" (SOF) algorithm, is implemented to incorporate QM/MM charge calculations without any prior knowledge of native structures of the complexes. Using an iterative protocol, this algorithm is able in many cases to converge to a nativelike structure in systems where redocking of the ligand using a standard fixed charge force field exhibits nontrivial errors. The results demonstrate that polarization effects can play a significant role in determining the structures of protein-ligand complexes, and provide a promising start towards the development of more accurate docking methods for lead optimization applications.     

An embedded QM/MM study for different SiO2/Al2O3 ratios of the HZSM‐5 zeolite and for their interaction with n‐heptane

We carried out a theoretical study of the HZSM‐5 zeolite, for different SiO₂/Al₂O₃ ratios, that interacts with the n‐heptane molecule. The study was performed using a QM/MM (quantum mechanics/molecular mechanics) methodology. For the QM part, we have chosen a hybrid Hartree‐Fock density functional theory (DFT). The hybrid ACM/DZP approach, as implemented in Turbomole, was used for the treatment of the QM cluster containing 84 atoms that represents a ring structure model of the zeolite‐n‐heptane interacting system. The MM part was represented by means of an electrostatic forcefield (ESFF), which assesses the electronic embedding. The chosen QM/MM silicalite base model contains 3862 atoms. The studied SiO₂/Al₂O₃ ratios were 2300, 573.5, 287.7, and 189.83, containing 1, 4, 8, and 12 Al atoms, respectively. For the first ratio, the site for the substitution of Al for Si was that of minimum QM total energy value, because this replacement was done in the QM region. For the other SiO₂/Al₂O₃ ratios, the Al atoms were randomly spread through the MM region in accordance with the Lowenstein substitution rule. These results show the importance of the environment on the electronic properties in the QM region, where the active site lies, and their effects on the earlier steps on the activation experienced by the n‐heptane moiety. A minimal content of 12 Al atoms produces significant effects of the environment on the electronic structure of the QM region. Moreover, the carbocationic character of n‐heptane increases with the aluminum content. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Theoretical modeling of the heme group with a hybrid QM/MM method

The quality of the results obtained in calculations with the hybrid QM/MM method IMOMM on systems where the heme group is partitioned in QM and MM regions is evaluated through the performance of calculations on the 4‐coordinate [Fe(P)] (P = porphyrin), the 5‐coordinate [Fe(P)(1−(Me)Im)] (Im = imidazole) and the 6‐coordinate [Fe(P)(1−(Me)Im)(O₂)] systems. The results are compared with those obtained from much more expensive pure quantum mechanics calculations on model systems. Three different properties are analyzed—namely, the optimized geometries, the binding energies of the axial ligands to the heme group, and the energy cost of the biochemically relevant out‐of‐plane displacement of the iron atom. Agreement is especially good in the case of optimized geometries and energy cost of out‐of‐plane displacements, with larger discrepancies in the case of binding energies. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 282–294, 2000     

Pseudobond ab initio QM/MM approach and its applications to enzyme reactions

This perspective article mainly focuses on the development and applications of a pseudobond ab initio QM/MM approach to study enzyme reactions. The following aspects of methodology development are discussed: the approaches for the QM/MM covalent boundary problem, an efficient iterative optimization procedure, the methods to determine enzyme reaction paths, and the approaches to calculate free energy change in enzyme reactions. Several applications are described to illustrate the capability of the methods. Finally, future directions are discussed.     

Contributions of pauli repulsions to the energetics and physical properties computed in QM/MM methods

Conventional combined quantum mechanical/molecular mechanical (QM/MM) methods lack explicit treatment of Pauli repulsions between the quantum‐mechanical and molecular‐mechanical subsystems. Instead, classical Lennard‐Jones (LJ) potentials between QM and MM nuclei are used to model electronic Pauli repulsion and long‐range London dispersion, despite the fact that the latter two are inherently of quantum nature. Use of the simple LJ potential in QM/MM methods can reproduce minimal geometries and energies of many molecular clusters reasonably well, as compared to full QM calculations. However, we show here that the LJ potential cannot correctly describe subtle details of the electron density of the QM subsystem because of the neglect of Pauli repulsions between the QM and MM subsystems. The inaccurate electron density subsequently affects the calculation of electronic and magnetic properties of the QM subsystem. To explicitly consider Pauli interactions with QM/MM methods, we propose a method to use empirical effective potentials on the MM atoms. The test case of the binding energy and magnetic properties of a water dimer shows promising results for the general application of effective potentials to mimic Pauli repulsions in QM/MM calculations. © 2013 Wiley Periodicals, Inc.     

Comparative study on the photophysical properties between carbene-based Fe (II) and Ru (II) complexes

The comparative study on the photophysical properties between cheap metal Fe (II) complexes and noble metal Ru (II) complexes with identical ligand coordination is performed by the combination of density functional theory (DFT) and time-dependent density functional theory (TDDFT) to evaluate the potential alternative applications of Fe (II) complexes. RuBIP (BIP = 2,6-bis (imidazol-2- ylidene)pyridine) is theoretically established that the radiative lifetime of the second lowest triplet state is more consistence with experimental value. However, FeBIP retains nonluminous because of low-lying ³MC originated from weak d orbital splitting. FeBIPC (FeBIP with carboxylic acid groups) has twice longer lifetime than its parent complex FeBIP due to the great decrease of the energy gap between ³MLCT and ³MC. What's more, the lifetimes of Fe (II) complexes detected in the experiments are more accessible to nonradiative decay lifetimes of ³MC. The carboxylic acid groups are beneficial for the improvement of luminescent possibility and controllability of Fe (II) complexes, while there is still a huge challenge for effective material replacement comparing with Ru (II) complexes.     

Methodological aspects of QM/MM calculations: A case study on matrix metalloproteinase‐2

We address methodological issues in quantum mechanics/molecular mechanics (QM/MM) calculations on a zinc‐dependent enzyme. We focus on the first stage of peptide bond cleavage by matrix metalloproteinase‐2 (MMP‐2), that is, the nucleophilic attack of the zinc‐coordinating water molecule on the carbonyl carbon atom of the scissile fragment of the substrate. This step is accompanied by significant charge redistribution around the zinc cation, bond cleavage, and bond formation. We vary the size and initial geometry of the model system as well as the computational protocol to demonstrate the influence of these choices on the results obtained. We present QM/MM potential energy profiles for a set of snapshots randomly selected from QM/MM‐based molecular dynamics simulations and analyze the differences in the computed profiles in structural terms. Since the substrate in MMP‐2 is located on the protein surface, we investigate the influence of the thickness of the water layer around the enzyme on the QM/MM energy profile. Thin water layers (0–2 Å) give unrealistic results because of structural reorganizations in the active‐site region at the protein surface. A 12 Å water layer appears to be sufficient to capture the effect of the solvent; the corresponding QM/MM energy profile is very close to that obtained from QM/MM/SMBP calculations using the solvent macromolecular boundary potential (SMBP). We apply the optimized computational protocol to explain the origin of the different catalytic activity of the Glu116Asp mutant: the energy barrier for the first step is higher, which is rationalized on structural grounds. © 2016 Wiley Periodicals, Inc.     

Structure-breaking effects of solvated Rb(I) in dilute aqueous solution--an ab initio QM/MM MD approach

Structural properties of the hydrated Rb(I) ion have been investigated by ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations at the double-zeta HF quantum mechanical level. The first shell coordination number was found to be 7.1, and several other structural parameters such as angular distribution functions, radial distribution functions and tilt- and theta-angle distributions allowed the full characterization of the hydration structure of the Rb(I) ion in dilute aqueous solution. Velocity autocorrelation functions were used to calculate librational and vibrational motions, ion-ligand motions, as well as reorientation times. Different dynamical parameters such as water reorientation, mean ligand residence time, the number of ligand exchange processes, and rate constants were also analyzed. The mean ligand residence time for the first shell was determined as tau = 2.0 ps.     

Application of QM simulations and multivariate analysis in the study of alkene reactivity in the zeolite H‐ZSM5

Reported herein are the results of an investigation into the effect of the extended framework of the zeolite ZSM‐5 on the reaction energetics and structures of (a) the physisorbed complex formed between the zeolite and six alkenes, (b) the corresponding chemisorbed alkoxide intermediate and (c) the transition states (TS) connecting the two. For this, quantum mechanical (QM) simulations of ZSM‐5 in the presence and absence of the zeolite framework have been employed. A 46T density functional theory (DFT) cluster model and a 3T:46T DFT:UFF ONIOM model are used to represent the former scenario and a simple 3T DFT cluster model for the latter. The structural implications of neglecting the zeolite framework have been rigorously compared using the multivariate statistical method principal components analysis (PCA). This method allows one to assess the correlated nature of the changes in structure along the reaction coordinate, for multiple different alkenes, in a facile, reliable way. Copyright © 2008 John Wiley & Sons, Ltd.     

Ruthenium(II) complexes containing 4‐methoxybenzhydrazone ligands: synthesis,characterization, DNA binding,DNA cleavage,radical scavenging and in vitro cytotoxic activity

Three ruthenium(II) hydrazone complexes of composition [RuCl(CO)(PPh₃)₂L] were synthesized from the reactions of [RuHCl(CO)(PPh₃)₃] with hydrazones derived from 4‐methoxybenzhydrazide and 4‐formylbenzoic acid (HL¹), 4‐methylbenzaldehyde (HL²) and 2‐bromobenzaldehyde (HL³). The synthesized hydrazone ligands and their metal complexes were characterized using elemental analysis and infrared, UV–visible, NMR (¹H, ¹³C and ³¹P) and mass spectral techniques. The hydrazone ligands act as bidentate ones, with O and N as the donor sites, and are predominantly found in the enol form in all the complexes studied. The molecular structures of the ligands HL¹, HL² and HL³ were determined using single‐crystal X‐ray diffraction. The interactions of the ligands and the complexes with calf thymus DNA were studied using absorption spectroscopy and cyclic voltammetry which revealed that the compounds could interact with calf thymus DNA through intercalation. The DNA cleavage activity of the complexes was evaluated using a gel electrophoresis assay which revealed that the complexes act as good DNA cleavage agents. In addition, all the complexes were subjected to antioxidant assay, which showed that they all possess significant scavenging activity against 2,2‐diphenyl‐2‐picrylhydrazyl, OH and NO radicals. The in vitro cytotoxic effect of the complexes examined on cancerous cell lines (HeLa and MCF‐7) showed that the complexes exhibit substantial anticancer activity. Copyright © 2016 John Wiley & Sons, Ltd.     

Introducing Mutations to Modify the C13/C9 Ratio in Linoleic Acid Oxygenations Catalyzed by Rabbit 15‐Lipoxygenase: A QM/MM and MD Study

Lipoxygenases (LOs) are a family of nonheme iron‐containing enzymes that catalyze the hydroperoxidation of several polyunsaturated fatty acids with a huge regio‐ and stereospecificity. Mammalian 15‐LO‐1 yields almost exclusively oxygenation at the C13 position of the linoleic acid (LA), its preferred substrate. This is very important because metabolites derived from oxidation in distinct positions produce opposite physiological effects. We have combined here quantum mechanics/molecular mechanics calculations with molecular dynamics simulations to show how a suitable mutation of the rabbit 15‐LO‐1 enzyme can produce a significant amount of products derived from oxygenation at the C9 position of LA. In effect, the Leu597Val or Leu597Ala mutants are predicted to lead to a diminution of the oxygenation C13/C9 ratio in LA as huge as five orders of magnitude. This shows that the conserved residue Leu597 actually drives the regiospecific hydroperoxidation of LA catalyzed by 15‐LO‐1 enzyme.     

Synthesis of 2‐aminomethylpiperidine ruthenium(II) phosphine complexes and their applications in transfer hydrogenation of aryl ketones

The complex trans,cis‐[RuCl₂(PPh₃)₂(ampi)] (2) was prepared by reaction of RuCl₂(PPh₃)₃ with 2‐aminomethylpiperidine(ampi) (1). [RuCl₂(PPh₂(CH₂)_nPPh₂)(ampi) (n = 3, 4, 5)] (3–5) were synthesized by displacement of two PPh₃ with chelating phosphine ligands. All complexes (2–5) were characterized by ¹ H, ¹³C, ³¹P NMR, IR and UV‐visible spectroscopy and elemental analysis. They were found to be efficient catalysts for transfer hydrogen reactions. Copyright © 2012 John Wiley & Sons, Ltd.     

A QM/MM study on the aqueous solvation of the tetrahydroxouranylate [UO2(OH)4]2- complex ion

We report a QM augmented QM/MM study on the coordination of the tetrahydroxouranylate ion in aqueous solution. QM/MM geometry optimizations followed by full QM single-point calculations on the optimized structures show that a hexa-coordinated structure is more stable than the hepta-coordinated structure by 43 kJ/mol. Charge transfer of the tetrahydroxouranylate to the solvating water molecules is relatively modest, and can be modeled by including a solvation layer consisting of 12 explicit water molecules.