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Described are multiple approaches using density functional theory to probe the acid catalyzed aquation of the hexaammineruthenium(II) cation (Ru(NH₃)₆²⁺ + H₃O⁺ → Ru(NH₃)₅(H₂O)²⁺ + NH₄⁺) reported initially by Taube and co-workers. These computations support the proposal that the initial step is protonation of the Ru(II) center and/or the metal-NH₃ bond, thereby activating the latter toward dissociation. DFT analysis was also carried out for the hypothetical acid-mediated aquation of the isoelectronic hexaamminerhodium(III) complex, Rh(NH₃)₆³⁺. The computations suggest a key mechanistic difference for the latter pathway, namely that protonation of the NH₃ occurs late in a reaction coordinate involving dissociation of the Rh-NH₃ with no direct interaction of H⁺ with the metal center. Furthermore, while the calculated activation energy is considerably higher in the latter case, the calculations suggest that protonation could play an important role in such ligand substitution reactions. Show less

In the frame of our research aiming to develop efficient triplet-emitting materials, we are exploring the role of the second coordination sphere in enhancing the rigidity of structures and its controlling aspect over the extents of excited state distortions. We thus synthesised three N^C^N cyclometalated complexes [M(LBn)Cl] (M = Pt, Pd, and Ni), where the two ortho-positions of the pyridyl moieties in 1,3-di(2-pyridyl)-benzene are benzyl substituted (Bn) forming a tight binding pocket for the metal and the Cl− ancillary ligand. The molecular structures from single-crystal X-ray diffraction show a markedly distorted square planar M(II) coordination with τ4 values of around 0.4. UV-vis absorption spectra show long-wavelength bands in the range 350 to 5400 nm with the energies increasing along the series Ni < Pt < Pd. The Pt(II) complex emits in solution at 298 K (λmax = 544 nm) and displays aggregated emission within poly(methyl methacrylate) (PMMA) films at various concentrations at 298 K. The Pd(II) derivative exhibits a broad emission band at 77 K in a frozen glassy 2-MeTHF matrix, peaking at 530 nm. Very different from the Pt(II) and Pd(II) spectra, the Ni(II) sample showed a broad emission with λmax = 699 nm at 77 K, with a quantum yield of 20% and ms lifetime. TD-DFT calculated decomposition of the assumed emissive T1 state showed similar 3MLCT character of about 30% for all three complexes, but marked differences in LC character of about 38% for Pd and Pt and only 5% for Ni. In turn, for Ni the by far the highest MC character (42%) was calculated which strongly speaks against triplet photoluminescence from the Ni(II) complex. Show less

Copper(II), manganese(II), and mercury(II) complexes of 4-amino-5-(2-(1-pyridine-2-yl)ethylidene)hydrazinyl)-4H-1,2,4-triazole-3-thiol (H2TAP) were synthesized and characterized using CHN analysis, FT-IR, 1H-NMR, 13C-NMR, UV–Vis, ESR, MS, PXRD, magnetic moment measurements, molar conductance, and TG/DTA. DFT calculations indicate octahedral geometries and the neutral bidentate or tridentate chelating behavior of the ligand. Cyclic voltammetry revealed the complexes’ redox properties, and Job’s method elucidated stoichiometric compositions in solution. Biochemical assays demonstrated antimicrobial activity against Escherichia coli, Staphylococcus aureus, and Candida albicans. The MnII complex exhibited potent antitumor activity against HepG-2 cells. Antioxidant and DNA binding studies showed promising results, with docking investigations indicating strong interactions between the ligand/complexes and target proteins (PDB: 1YWN) and DNA (PDB: 8EC1), suggesting therapeutic potential. Show less

Abstract The crystal structure of the Cu(II) binuclear complex with 5-phenyltetrazole and 4,4'-dimethyl-2,2'-bipyridine (dmbipy), [Cu2(dmbipy)2L4], has been determined. The complex crystallizes in a monoclinic space group P21/c. The distorted square-pyramidal environment of Cu(II) atoms is formed by five nitrogen atoms belonging to three 5-phenyltetrazolate anions and one dmbipy molecule. Due to the presence of the intermolecular interactions π···π and C–H···π, the binuclear molecules combine into a supramolecular layered structure. The bonding energy has been calculated in terms of the density functional theory for two models of the [Cu2(dmbipy)2L4] complex with various coordination modes of the bridging 5-phenyltetrazole. Show less

The stable complex [bis(toluene-3,4-dithiolato)copper(III)][NEt3H] has been synthesised and characterised as a square-planar Cu(III) complex by X-ray photoelectron spectroscopy, cyclic voltammetry and DFT calculations. Intriguingly, when fragmented in FTICR-MS, an unusual [(toluene-3,4-dithiolate)Cu(III)(peroxide)]− complex is formed by reaction with oxygen. Natural 1,2-dithiolenes known to bind molybdenum might stabilise Cu(III) in vivo. Show less

Two new coordination complexes of Cu(II) and Mn(II), viz., [Cu(bpy)(H2O)4]SO4·2H2O (1) and [Mn(4-CNpy)2(H2O)3SO4]·H2O (2) (bpy = 2,2′-bipyridine, 4-CNpy = 4-cyanopyridine), have been synthesized and characterized by using single crystal X-ray diffraction, elemental analysis, FT-IR spectroscopy, electronic spectroscopic techniques and TGA. The crystal structure of 1 uncovers the formation of sulfate–water assemblies involving lattice and coordinated water molecules, while complex 2 reveals the presence of unconventional weak T-shaped CN⋯CN contacts in the layered architecture. We have analysed the unconventional interesting interactions using DFT calculations, molecular electrostatic potential (MEP), the NCI plot and QTAIM computational tools. The interaction energies of the two H-bonded dimers in 1 are very large because of the coulombic attraction between the dicationic H-bonded donor and the dianionic acceptor. It is interesting to observe that despite the energy of the H-bonds being very small compared to the total dimerization energy, the final geometry of the assembly in 1 is due to the charge assisted directional H-bonds instead of the non-directional ion-pair interactions. The DFT study reveals that the T-shaped CN⋯CN interaction in 2 is very weak, in good agreement with the small MEP energy at the nitrile carbon atom. Anticancer studies of the compounds have been carried out using Dalton's lymphoma cell line using MTT and apoptosis assay. The results of compound 1 and 2 mediated cell cytotoxicity on the DL cancer cell line showed a significant concentration-dependent reduction in cell viability, while negligible cytotoxicity was observed in normal (PBMC) cells. The docking simulation results also confirm the interaction of the complexes with the active sites of amino acids of the target proteins. Furthermore, pharmacophore models (2D and 3D) for the compounds were mapped to the H-bond donor, positive ionisable area and hydrophobic features that are important for establishing biological activities. No hematotoxicity was recorded for the compounds after treatment in normal mice. Show less

The results of theoretical simulations of reaction paths for oxaliplatin from pro-drug into its active form responsible for cytostatic effect are presented. The studies based on the quantum-chemical density functional theory approach were performed considering environmental influence resulting from the aquation or electron donation. The hybrid mechanisms: hydrolytic mixed with electron driven were found to be the energetically favourable. Show less

AbstractIn the effort to overcome issues of toxicity and resistance inherent to treatment by the approved platinum anticancer agents, a large number of cisplatin variants continues today to be prepared and tested. One of the applied strategies is to use monofunctional platinum complexes that, unlike traditional bifunctional compounds, are able to form only a single covalent bond with nuclear DNA. Chirality, aquation reaction, interaction with guanine and N‐acetyl methionine as well as, intercalation into, binding to and distortion of DNA have been investigated by using both quantum mechanical DFT and molecular dynamics computations aiming at contributing to the elucidation of the molecular mechanism underlying the significantly enhanced spectrum of activity of the monofunctional PtII drug phenanthriplatin. Analogous calculations have been performed in parallel for other two less potent monofunctional PtII drugs, pyriplatin and enpyriplatin, which show very different cytotoxic effects. Show less

The CH3NH3PbI3 (methylammonium lead triiodide) perovskite semiconductor system has been viewed as a blockbuster research material during the last five years. Because of its complicated architecture, several of its technological, physical and geometrical issues have been examined many times. Yet this has not assisted in overcoming a number of problems in the field nor in enabling the material to be marketed. For instance, these studies have not clarified the nature and type of hydrogen bonding and other noncovalent interactions involved; the origin of hysteresis; the actual role of the methylammonium cation; the nature of polarity associated with the tetragonal geometry; the unusual origin of various frontier orbital contributions to the conduction band minimum; the underlying phenomena of spin-orbit coupling that causes significant bandgap reduction; and the nature of direct-to-indirect bandgap transition features. Arising from many recent reports, it is now a common belief that the I···H–N interaction formed between the inorganic framework and the ammonium group of CH3NH3+ is the only hydrogen bonded interaction responsible for all temperature-dependent geometrical polymorphs of the system, including the most stable one that persists at low-temperatures, and the significance of all other noncovalent interactions has been overlooked. This study focussed only on the low temperature orthorhombic polymorph of CH3NH3PbI3 and CD3ND3PbI3, where D refers deuterium. Together with QTAIM, DORI and RDG based charge density analyses, the results of density functional theory calculations with PBE with and without van der Waals corrections demonstrate that the prevailing view of hydrogen bonding in CH3NH3PbI3 is misleading as it does not alone determine the a−b+a− tilting pattern of the PbI64− octahedra. This study suggests that it is not only the I···H/D–N, but also the I···H/D–C hydrogen/deuterium bonding and other noncovalent interactions (viz. tetrel-, pnictogen- and lump-hole bonding interactions) that are ubiquitous in the orthorhombic CH3NH3PbI3/CD3ND3PbI3 perovskite geometry. Their interplay determines the overall geometry of the polymorph, and are therefore responsible in part for the emergence of the functional optical properties of this material. This study also suggests that these interactions should not be regarded as the sole determinants of octahedral tilting since lattice dynamics is known to play a critical role as well, a common feature in many inorganic perovskites both in the presence and the absence of the encaged cation, as in CsPbI3/WO3 perovskites, for example. Show less

Abstract The coordination compound of the antihypertensive ligand irbesartan (irb) with copper(II) (CuIrb) was synthesized and characterized by FTIR, FT-Raman, UV–visible, reflectance and EPR spectroscopies. Experimental evidence allowed the implementation of structural and vibrational studies by theoretical calculations made in the light of the density functional theory (DFT). This compound was designed to induce structural modifications on the ligand. No antioxidant effects were displayed by both compounds, though CuIrb behaved as a weak 1,1-diphenyl-2-picrylhydrazyl radical (DPPH·) scavenger (IC50 = 425 μM). The measurements of the contractile capacity on human mesangial cell lines showed that CuIrb improved the antihypertensive effects of the parent medication. In vitro cell growth inhibition against prostate cancer cell lines (LNCaP and DU 145) was measured for CuIrb, irbesartan and copper(II). These cell lines have been selected since the angiotensin II type 1 (AT1) receptor (that was blocked by the angiotensin receptor blockers, ARB) has been identified in them. The complex exerted anticancer behavior (at 100 μM) improving the activity of the ligand. Flow cytometry determinations were used to determine late apoptotic mechanisms of cell death. Graphical Abstract Experimental and DFT characterization of an irbesartan copper(II) complex has been performed. The complex exhibits low scavenging activity against DPPH· and significant growth inhibition of LNCaP and DU 145 prostate cancer cell lines. Flow cytometry determinations were used to determine late apoptotic mechanisms of cell death. This compound improved the antihypertensive effect of irbesartan. This effect was observed earlier for the mononuclear Cu–candesartan complex, but not in structurally modified sartans forming dinuclear or octanuclear Cu–sartan compounds. Show less

Two new mononuclear water soluble copper(II) complexes, [Cu{(5-pyrazinyl)tetrazolate}2(1,10-phenanthroline)] 1 and [Cu{(5-pyrazinyl)tetrazolate}(1,10-phenanthroline)2](NO3)0.5(N3)0.52, have been synthesized using the metal mediated [2 + 3] cycloaddition reaction between copper bound azide and pyrazinecarbonitrile. The interactions of these copper tetrazolate complexes 1 and 2 with biomolecules like DNA and bovine serum albumin (BSA) are studied and the catecholase like catalytic activity of compound 2 is also explored. Structural determination reveals that both compounds 1 and 2 are octahedral in nature. Screening tests were conducted to quantify the binding ability of complexes (1 and 2) towards DNA and it was revealed that complex 2 has a stronger affinity to bind to CT-DNA. DFT studies indicated that a lower HOMO–LUMO energy gap between the DNA fragment and metal complexes might be the reason for this type of stronger interaction. DNA cleavage activity was explored by gel-electrophoresis and moderate to strong DNA cleavage properties were observed in the presence and absence of co-reagents. Inhibition of cleavage in the presence of sodium azide indicates the propagation of the activity through the production of singlet molecular oxygen. Furthermore enzyme kinetic studies reflect that complex 2 is also effective in mimicking catecholase like activities. An ESI-MS spectral study indicates the probable involvement of dimeric species [(phen)2Cu-(OH)2-Cu(phen)2]2+ in the catalytic cycle. Show less

Readily synthesised and functionalised di-1,2,3-triazole “click” ligands are shown to self-assemble into coordinatively saturated, quadruply stranded helical [Pd2L4](BF4)4 cages with Pd(II) ions. The cages have been fully characterised by elemental analysis, HR-ESMS, IR, 1H, 13C and DOSY NMR, DFT calculations, and in one case by X-ray crystallography. By exploiting the CuAAC “click” reaction we were able to rapidly generate a small family of di-1,2,3-triazole ligands with different core spacer units and peripheral substituents and examine how these structural modifications affected the formation of the [Pd2L4](BF4)4 cages. The use of both flexible (1,3-propyl) and rigid (1,3-phenyl) core spacer units led to the formation of discrete [Pd2L4](BF4)4 cage complexes. However, when the spacer unit of the di-1,2,3-triazole ligand was a 1,4-substituted-phenyl group steric interactions led to the formation of an oligomeric/polymeric species. By keeping the 1,3-phenyl core spacer constant the effect of altering the “click” ligands’ peripheral substituents was also examined. It was shown that ligands with alkyl, phenyl, electron-rich and electron-poor benzyl substituents all quantitatively formed [Pd2L4](BF4)4 cage complexes. The results suggest that a wide range of functionalised palladium(II) “click” cages could be rapidly generated. These novel molecules may potentially find uses in catalysis, molecular recognition and drug delivery. Show less

Cardiolipin is a key lipid component in many biological membranes. Proton conduction and proton-lipid interactions on the membrane surface are thought to be central to mitochondrial energy production. However, details on the cardiolipin headgroup structure are lacking and the protonation state of this lipid at physiological pH is not fully established. Here we present ab initio DFT calculations of the cardiolipin (CL) headgroup and its 2'-deoxy derivative (dCL), with the aim of establishing a connection between structure and acid-base equilibrium in CL. Furthermore, we investigate the effects of solvation on the molecular conformations. In our model, both CL and dCL showed a significant gap between the two pK(a) values, with pK(a2) above the physiological range, and intramolecular hydrogen bonds were found to play a central role in the conformations of both molecules. This behavior was also observed experimentally in CL. Structures derived from the DFT calculations were compared with those obtained experimentally, collected for CL in the Protein Data Bank, and conformations from previous as well as new molecular dynamics simulations of cardiolipin bilayers. Transition states for proton transfer in CL were investigated, and we estimate that protons can exchange between phosphate groups with an approximate 4-5 kcal/mol barrier. Computed NMR and IR spectral properties were found to be in reasonable agreement with experimental results available in the literature. Show less

The hydrolysis of oxaliplatin, a third generation anticancer drug, is expected to play an important role in the activation of this compound before it reaches DNA. The first and second hydrolysis corresponding to the addition of the first water molecule concomitant with the ring-opening, followed by addition of a second water and loss of the monodentate oxalato ligand, respectively, were studied combining density functional theory (DFT) with the conductor-like dielectric continuum model (CPCM) approach. The reaction was studied in neutral and acidic conditions, and all stationary points have been identified. The computed potential energy surfaces show that, for the neutral hydrolysis, the ring-opening reaction is the rate-limiting process, with an activation barrier of about 28 kcal/mol. For the acid degradation in water, according to experimental data, the reaction is expected to proceed in a faster biphasic process, and the rate-limiting process is the ligand detachment that occurs with a barriers of about 22 kcal/mol. According to the calculated results, we expect that the reaction is favored in acidic conditions and that the monoaquated complex should be the species reacting with DNA. Show less

Three potential anticancer agents {trans-[PtCl(2)(NH(3))(thiazole)], cis-[PtCl(2)(NH(3))(piperidine)], and PtCl(2)(NH(3))(cyclohexylamine) (JM118)} were explored and compared with cisplatin and the inactive [PtCl(dien)](+) complex. Basic electronic properties, bonding and stabilization energies were determined, and thermodynamic and kinetic parameters for the aquation reaction were estimated at the B3LYP/6-311++G(2df,2pd) level of theory. Since the aquation process represents activation of these agents, the obtained rate constants were compared with the experimental IC(50) values for several tumor cells. Despite the fact that the processes in which these drugs are involved and the way in which they affect cells are very complex, some correlations can be deduced. Show less

Theoretical bioinorganic and biomimetic chemistry involves the careful description of the electronic structure: for example, 'valence bond reading' of broken-symmetry density functional theory computations gives insight into the structure and bonding of metal-radical systems with complex electronic structures. Exploring the reactivities of such systems leads to the design of novel compounds with better reactivities. Combined quantum-mechanics/molecular-mechanics (QM/MM), where the QM part is a sophisticated ab initio method, aids in understanding nature's most complicated reaction mechanisms in atomic detail. First principles molecular dynamics simulations (Car-Parrinello simulations) open up exciting new avenues for studying transition metal centers and enable several questions to be addressed that cannot be resolved with either standard quantum chemical or traditional force-field methods. Show less

AbstractQM/MM calculations were employed to investigate the role of hydrogen bonding and π stacking in several single‐ and double‐stranded cisplatin–DNA structures. Computed geometrical parameters reproduce experimental structures of cisplatin and its complex with guanine–phosphate–guanine. Following QM/MM optimisation, single‐point DFT calculations allowed estimation of intermolecular forces through atoms in molecules (AIM) analysis. Binding energies of platinated single‐strand DNA qualitatively agree with myriad experimental and theoretical studies showing that complexes of guanine are stronger than those of adenine. The topology of all studied complexes confirms that platination strongly affects the stability of both single‐ and double‐stranded DNAs: PtNH⋅⋅⋅X (X = N or O) interactions are ubiquitous in these complexes and account for over 70 % of all H‐bonding interactions. The π stacking is greatly reduced by both mono‐ and bifunctional complexation: the former causes a loss of about 3–4 kcal mol−1, whereas the latter leads to more drastic disruption. The effect of platination on Watson–Crick GC is similar to that found in previous studies: major redistribution of energy occurs, but the overall stability is barely affected. The BH&H/AMBER/AIM approach was also used to study platination of a double‐stranded DNA octamer d(CCTG*G*TCC)⋅d(GGACCAGG), for which an experimental structure is available. Comparison between theory and experiment is satisfactory, and also reproduces previous DFT‐based studies of analogous structures. The effect of platination is similar to that seen in model systems, although the effect on GC pairing was more pronounced. These calculations also reveal weaker, secondary interactions of the form Pt⋅⋅⋅O and Pt⋅⋅⋅N, detected in several single‐ and double‐stranded DNA. Show less