Synergistic Effects of Metals in a Promising RuII−PtII Assembly for a Combined Anticancer Approach: Theoretical Exploration of the Photophysical Properties

Ru^II?Pt^II complexes are a class of bioactive molecules of interest as anticancer agents that combine a light‐absorbing chromophore with a cisplatin‐like unit. The results of a DFT and TDDFT investigation of a Ru^II complex and its conjugate with a cis‐PtCl₂ moiety reveal that a synergistic effect of the metals makes the assembly a promising multitarget anticancer drug. Inspection of type I and type II photoreactions and spin–orbit coupling computations reveals that the cis‐PtCl₂ moiety improves the photophysical properties of the Ru^II chromophore, ensuring efficient singlet oxygen generation and making the assembly suitable for photodynamic therapy. At the same time, the Ru^II chromophore promotes a new alternative activation mechanism of the Pt^II ligand via a triplet metal‐to‐ligand charge transfer (³M LCT) state, before reaching the biological target. The importance of the supramolecular architecture is accurately derived, opening interesting new perspectives on the use of bimetallic Ru^II?Pt^II assemblies in a combined anticancer approach.     

Reducing the Cost and Preserving the Reactivity in Noble‐Metal‐Based Catalysts: Oxidation of CO by Pt and Al–Pt Alloy Clusters Supported on Graphene

The oxidation mechanisms of CO to CO₂ on graphene‐supported Pt and Pt‐Al alloy clusters are elucidated by reactive dynamical simulations. The general mechanism evidenced is a Langmuir–Hinshelwood (LH) pathway in which O₂ is adsorbed on the cluster prior to the CO oxidation. The adsorbed O₂ dissociates into two atomic oxygen atoms thus promoting the CO oxidation. Auxiliary simulations on alloy clusters in which other metals (Al, Co, Cr, Cu, Fe, Ni) replace a Pt atom have pointed to the aluminum doped cluster as a special case. In the nanoalloy, the reaction mechanism for CO oxidation is still a LH pathway with an activation barrier sufficiently low to be overcome at room temperature, thus preserving the catalyst efficiency. This provides a generalizable strategy for the design of efficient, yet sustainable, Pt‐based catalysts at reduced cost.     

Computational approaches to activity in rhodium-catalysed hydroformylation

In this theoretical study on rhodium-catalysed hydroformylation we examine an unmodified hydridorhodium(I) carbonyl system a together with three variants modified by the model phosphane ligands PF3 (system b), PH3 (system c) and PMe3 (system d), which show increasing basicity on the Tolman chi parameter scale. The olefinic substrate for all systems is ethene. Based on the dissociative hydroformylation mechanism, static and dynamic quantum-mechanical approaches are made for preequilibria and the whole catalytic cycle. Agreement with experimental results was achieved with regard to the predominance of phosphane monocoordination in systems b-d, different sensitivity of unmodified and modified systems towards hydrogen pressure and the early location of the rate-determining step. Neither the catalytic cycle as a whole nor olefin insertion as an important selectivity-determining step gives a clear picture of activity differences among a-d. However, the crucial first catalytic step, association of ethene to the active species [HRhL3] (L=CO, PR3), may play the key role in the experimentally observed higher activity of a and systems with less basic phosphane ligands modelled by b.     

Rationalization of the Color Properties of Fluorescein in the Solid State: A Combined Computational and Experimental Study

Fluorescein is known to exist in three tautomeric forms defined as quinoid, zwitterionic, and lactoid. In the solid state, the quinoid and zwitterionic forms give rise to red and yellow materials, respectively. The lactoid form has not been crystallized pure, although its cocrystal and solvate forms exhibit colors ranging from yellow to green. An explanation for the observed colors of the crystals is found using a combination of UV/Vis spectroscopy and plane‐wave DFT calculations. The role of cocrystal coformers in modifying crystal color is also established. Several new crystal structures are determined using a combination of X‐ray and electron diffraction, solid‐state NMR spectroscopy, and crystal structure prediction (CSP). The protocol presented herein may be used to predict color properties of materials prior to their synthesis.     

Exploration of the Ca2+ interaction modes of the nifedipine calcium channel antagonist.

A comprehensive study is carried out using quantum chemical computation and molecular dynamics (MD) simulations to gain insight into the interaction between Ca(2+) ions and the most important class of calcium channel antagonists--nifedipine. First, the chelating structures and energetic characters of nifedipine-Ca(2+) in the gas phase are explored, and 25 isomers are found. The most favorable chelating mode is a tridentate one, that is, Ca(2+) binds to two carbonyl O atoms and one nitryl O atom, where Ca(2+) is above the plane of the three O atoms to form a pyramidal structure. Accurate geometric structures, relative stabilities, vertical and adiabatic binding energies, and charge distributions are discussed. The differences in the geometries and energies among these isomers are analyzed from the contributions of chelating sites, electrostatics and polarizations, steric repulsions, and charge distributions. The interconversions among isomers with similar geometries and energies are also investigated because of the importance of the geometric transformation in the biological system. Furthermore, certain numbers of water molecules are added to the nifedipine-Ca(2+) system to probe the effect of water. A detailed study is performed on the hydrated geometries on the basis of the most stable isomer 1. Stepwise hydration can weaken the nifedipine-Ca(2+) interaction, and the chelating sites of nifedipine are gradually replaced by the added water molecules. Hexacoordination is found to be the most favorable geometry no matter how many water molecules were added, which can be verified by the MD simulations. The transfer of water molecules from the inner shell to the outer shell is also supported by MD simulations of the hexahydrated complexes.     

Reduction Process of Tetraplatin in the Presence of Deoxyguanosine Monophosphate (dGMP): A Computational DFT Study

The reduction mechanism of [Pt^IV(dach)Cl₄] (dach=diaminocyclohexyl) in the presence of dGMP was studied. The first step is substitution of a chloro ligand by dGMP, followed by nucleophilic attack of a phosphate or sugar oxygen atom to the C8‐position of guanine. Subsequent reduction forms the [Pt^II(dach)Cl₂] complex. The whole process is completed by a hydrolysis. Two different pathways for the substitution reaction were examined: a direct associative and a Basolo–Pearson autocatalytic mechanism. All the explored structures were optimized at the B3LYP‐D3/6‐31G(d) level and by using the COSMO solvation model with Klamt's radii. Single‐point energetics was determined at the B3LYP‐GD3BJ/6‐311++G(2df,2pd)/PCM/scaled‐UAKS level. Activation barriers were used for an estimation of the rate constants and these were compared with experimental values. It was found that the rate‐determining step is the nucleophilic attack with a slightly faster performance in the 3′‐dGMP branch than in the case of 5′‐dGMP with activation barriers of 21.1 and 20.4 kcal mol^?1 (experimental: 23.8 and 23.2 kcal mol^?1). The reduction reaction is connected with an electron flow from guanine. The product of the reduction reaction is a chelate structure, which dissociates within the last reaction step, that is, a hydrolysis reaction. The whole redox process (substitution, reduction, and hydrolysis) is exergonic by 34 and 28 kcal mol^?1 for 5′‐dGMP and 3′‐dGMP, respectively.     

The Catalytic Mechanism of Fluoroacetate Dehalogenase: A Computational Exploration of Biological Dehalogenation

The biological dehalogenation of fluoroacetate carried out by fluoroacetate dehalogenase is discussed by using quantum mechanical/molecular mechanical (QM/MM) calculations for a whole‐enzyme model of 10 800 atoms. Substrate fluoroacetate is anchored by a hydrogen‐bonding network with water molecules and the surrounding amino acid residues of Arg105, Arg108, His149, Trp150, and Tyr212 in the active site in a similar way to haloalkane dehalogenase. Asp104 is likely to act as a nucleophile to attack the α‐carbon of fluoroacetate, resulting in the formation of an ester intermediate, which is subsequently hydrolyzed by the nucleophilic attack of a water molecule to the carbonyl carbon atom. The cleavage of the strong C? F bond is greatly facilitated by the hydrogen‐bonding interactions between the leaving fluorine atom and the three amino acid residues of His149, Trp150, and Tyr212. The hydrolysis of the ester intermediate is initiated by a proton transfer from the water molecule to His271 and by the simultaneous nucleophilic attack of the water molecule. The transition state and produced tetrahedral intermediate are stabilized by Asp128 and the oxyanion hole composed of Phe34 and Arg105.     

Computational study of the phosphoryl transfer catalyzed by a cyclin-dependent kinase

A cyclin-dependent kinase, Cdk2, catalyzes the transfer of the gamma-phosphate from ATP to a threonine or serine residue of its polypeptide substrates. Here, we investigate aspects of the reaction mechanism of Cdk2 by gas-phase density functional calculations, classical molecular dynamics, and Car-Parrinello QM/MM simulations. We focus on the role of the conserved Asp127 and on the nature of the phosphoryl transfer reaction mechanism catalyzed by Cdk2. Our findings suggest that Asp127 is active in its deprotonated form by assisting the formation of the near-attack orientation of the substrate serine or threonine. Therefore, the residue does not act as a general base during the catalysis. The mechanism for the phosphoryl transfer is a single SN2-like concerted step, which shows a phosphorane-like transition state geometry. Although the resulting reaction mechanism is in agreement with a previous density functional study of the same catalytic reaction mechanism (Cavalli et al., Chem. Comm. 2003, 1308-1309), the reaction barrier is considerably lower when QM/MM calculations are performed, as in this study ( approximately 42 kcal mol(-1) QM vs. approximately 24 kcal mol(-1) QM/MM); this indicates that important roles for the catalysis are played by the protein environment and solvent waters. Because of the high amino acid sequence conservation among the whole family of cyclin-dependent kinases (CDKs), these results could be general for the CDK family.     

Structural and Dynamic Properties of Monoclonal Antibodies Immobilized on CNTs: A Computational Study

Due to the widespread application of carbon nanotube (CNT)‐based materials in nanomedicine, it is nowadays of paramount importance to unravel at the atomistic level of detail the structural properties of such bioconjugates in order to rationalize and predict the effect exerted by the graphitic framework on the bio‐active counterpart. In this paper, we report for the first time all‐atom explicit solvent molecular dynamics (MD) simulations investigating the structural and dynamic properties of a noncovalent bioconjugate in which the monoclonal Cetuximab antibody (Ctx) is adsorbed on a CNT surface. Upon selection of the three most representative adsorption modes as obtained by docking studies, force‐field MD and DFT simulations unambiguously showed that hydrophobic interactions mainly govern the adsorption of the protein on the graphitic surface. Two main adsorption poses have been predicted: a pose‐fab (p‐fab) and pose‐fc (p‐fc) (fab = fragment antigen binding region; fc = fragment crystallizable region), the former being favored with small‐diameter tubes (≤40 Å). In all the predicted poses, the secondary structure of Ctx is largely unaffected by the presence of the graphitic surface and, consistently with previous literature studies, our simulations reveal that positively charged amino acidic residues, such as Lys and Arg, predominantly contribute to the stabilization of the CNT?Ctx complex acting like surfactants. The predicted structural models are consistent with the experimental data, for which the immobilization of the antibody on CNTs does not disrupt the structural and recognition properties of the Ctx, consequently supporting the reliability of the used bioconjugation strategy for engineering stable and responsive hybrid nanomaterials for therapeutic applications. Moreover, a remarkable structural similarity of Ctx with antibodies of different isotypes suggests that in principle the CNT framework can interact in the same manner with all antibodies currently used in clinical applications.     

Elucidating the Glucokinase Activating Potentials of Naturally Occurring Prenylated Flavonoids: An Explicit Computational Approach

Glucokinase activators are considered as new therapeutic arsenals that bind to the allosteric activator sites of glucokinase enzymes, thereby maximizing its catalytic rate and increasing its affinity to glucose. This study was designed to identify potent glucokinase activators from prenylated flavonoids isolated from medicinal plants using molecular docking, molecular dynamics simulation, density functional theory, and ADMET analysis. Virtual screening was carried out on glucokinase enzymes using 221 naturally occurring prenylated flavonoids, followed by molecular dynamics simulation (100 ns), density functional theory (B3LYP model), and ADMET (admeSar 2 online server) studies. The result obtained from the virtual screening with the glucokinase revealed arcommunol B (−10.1 kcal/mol), kuwanon S (−9.6 kcal/mol), manuifolin H (−9.5 kcal/mol), and kuwanon F (−9.4 kcal/mol) as the top-ranked molecules. Additionally, the molecular dynamics simulation and MM/GBSA calculations showed that the hit molecules were stable at the active site of the glucokinase enzyme. Furthermore, the DFT and ADMET studies revealed the hit molecules as potential glucokinase activators and drug-like candidates. Our findings suggested further evaluation of the top-ranked prenylated flavonoids for their in vitro and in vivo glucokinase activating potentials.     

Solution Structure of Mannobioses Unravelled by Means of Raman Optical Activity

Structural analysis of carbohydrates is a complicated endeavour, due to the complexity and diversity of the samples at hand. Herein, we apply a combined computational and experimental approach, employing molecular dynamics (MD) and density functional theory (DFT) calculations together with NMR and Raman optical activity (ROA) measurements, in the structural study of three mannobiose disaccharides, consisting of two mannoses with varying glycosidic linkages. The disaccharide structures make up the scaffold of high mannose glycans and are therefore important targets for structural analysis. Based on the MD population analysis and NMR, the major conformers of each mannobiose were identified and used as input for DFT analysis. By systematically varying the solvent models used to describe water interacting with the molecules and applying overlap integral analysis to the resulting calculational ROA spectra, we found that a full quantum mechanical/molecular mechanical approach is required for an optimal calculation of the ROA parameters. Subsequent normal mode analysis of the predicted vibrational modes was attempted in order to identify possible marker bands for glycosidic linkages. However, the normal mode vibrations of the mannobioses are completely delocalised, presumably due to conformational flexibility in these compounds, rendering the identification of isolated marker bands unfeasible.     

Exploring Excited‐State Tunability in Luminescent Tris‐cyclometalated Platinum(IV) Complexes: Synthesis of Heteroleptic Derivatives and Computational Calculations

The synthesis, structure, electrochemistry, and photophysical properties of a series of heteroleptic tris‐ cyclometalated Pt^IV complexes are reported. The complexes mer‐[Pt(C^N)₂(C′^N′)]OTf, with C^N=C‐deprotonated 2‐(2,4‐difluorophenyl)pyridine (dfppy) or 2‐phenylpyridine (ppy), and C′^N′=C‐deprotonated 2‐(2‐thienyl)pyridine (thpy) or 1‐phenylisoquinoline (piq), were obtained by reacting bis‐ cyclometalated precursors [Pt(C^N)₂Cl₂] with AgOTf (2 equiv) and an excess of the N′^C′H pro‐ligand. The complex mer‐[Pt(dfppy)₂(ppy)]OTf was obtained analogously and photoisomerized to its fac counterpart. The new complexes display long‐lived luminescence at room temperature in the blue to orange color range. The emitting states involve electronic transitions almost exclusively localized on the ligand with the lowest π–π* energy gap and have very little metal character. DFT and time‐dependent DFT (TD‐DFT) calculations on mer‐[Pt(ppy)₂(C′^N′)]⁺ (C′^N′=thpy, piq) and mer/fac‐[Pt(ppy)₃]⁺ support this assignment and provide a basis for the understanding of the luminescence of tris‐cyclometalated Pt^IV complexes. Excited states of LMCT character may become thermally accessible from the emitting state in the mer isomers containing dfppy or ppy as chromophoric ligands, leading to strong nonradiative deactivation. This effect does not operate in the fac isomers or the mer complexes containing thpy or piq, for which nonradiative deactivation originates mainly from vibrational coupling to the ground state.     

Inelastic Neutron Scattering Study of PtII Complexes Displaying Anticancer Properties

The well‐known platinum(II) chemotherapeutic drugs cisplatin [cis‐(NH₃)₂PtCl₂] and carboplatin [Pt(NH₃)₂C₆O₄H₆], as well as the analogous transplatin [trans‐(NH₃)₂PtCl₂], were studied by inelastic neutron scattering (INS) spectroscopy, coupled to quantum mechanical methods, and some ancillary work with X‐ray diffraction on powders. An assignment of the experimental spectra was carried out based on the calculated INS transition frequencies and intensities (at the DFT level), thereby achieving a good correspondence between the calculated and observed data. Unusually good‐quality INS spectra were obtained from about 250 mg, which is the smallest sample of a hydrogenous compound for which a successful INS interpretation has been reported. The knowledge of the local configuration of this kind of complexes is essential for an accurate understanding of their activity, which will pave the way for the rational design of novel third‐generation drugs comprising cisplatin‐ and carboplatin‐like moieties.     

Exploration on regulating factors for proton transfer along hydrogen-bonded water chains.

Proton transfer along a single-file hydrogen-bonded water chain is elucidated with a special emphasis on the investigation of chain length, side water, and solvent effects, as well as the temperature and pressure dependences. The number of water molecules in the chain varies from one to nine. The proton can be transported to the acceptor fragment through the single-file hydrogen-bonded water wire which contains at most five water molecules. If the number of water molecule is more than five, the proton is trapped by the chain in the hydroxyl-centered H(7)O(3) (+) state. The farthest water molecule involved in the formation of H(7)O(3) (+) is the fifth one away from the donor fragment. These phenomena reappear in the molecular dynamics simulations. The energy of the system is reduced along with the proton conduction. The proton transfer mechanism can be altered by excess proton. The augmentation of the solvent dielectric constant weakens the stability of the system, but favors the proton transfer. NMR spin-spin coupling constants can be used as a criterion in judging whether the proton is transferred or not. The enhancement of temperature increases the thermal motion of the molecule, augments the internal energy of the system, and favors the proton transfer. The lengthening of the water wire increases the entropy of the system, concomitantly, the temperature dependence of the Gibbs free energy increases. The most favorable condition for the proton transfer along the H-bonded water wire is the four-water contained chain with side water attached near to the acceptor fragment in polar solvent under higher temperature.