Comments on the nature of the bonding in oxygenated dinuclear copper enzyme models

Insights Into the Explication of Potent Tyrosinase Inhibitors with Reference to Computational Studies

Background:

Pigment melanin has primarily a photo defensive role in human skin, its unnecessary production and irregular distribution can cause uneven skin tone ultimately results in hyper pigmentation. Melanin biosynthesis is initiated by tyrosine oxidation through tyrosinase, the key enzyme for melanogenesis. Not only in humans, tyrosinase is also widely distributed in plants and liable for browning of vegetables and fruits. Search for the inhibitors of tyrosinase have been an important target to facilitate development of therapies for the prevention of hyperpigmentary disorders and an undesired browning of vegetables and fruits.

Methods:

Different natural and synthetic chemical compounds have been tested as potential tyrosinase inhibitors, but the mechanism of inhibition is not known, and the quest for information regarding interaction between tyrosinase and its inhibitors is one of the recent areas of research. Computer based methods hence are useful to overcome such issues. Successful utilization of in silico tools like molecular docking simulations make it possible to interpret the tyrosinase and its inhibitor’s intermolecular interactions and helps in identification and development of new and potent tyrosinase inhibitors.

Results:

The present review has pointed out the prominent role of computer aided approaches for the explication of promising tyrosinase inhibitors with a focus on molecular docking approach. Highlighting certain examples of natural compounds whose antityrosinase effects has been evaluated using computational simulations.

Conclusion:

The investigation of new and potent inhibitors of tyrosinase using computational chemistry and bioinformatics will ultimately help millions of peoples to get rid of hyperpigmentary disorders as well as browning of fruits and vegetables.

Study of the docking of competitive inhibitors at a model of tyrosinase active site: insights from joint broken-symmetry/Spin-Flip DFT computations and ELF topological analysis

Following our previous study (Piquemal et al., New J. Chem., 2003, 27, 909), we present here a DFT study of the inhibition of the Tyrosinase enzyme. Broken-symmetry DFT computations are supplemented with Spin-Flip TD-DFT calculations, which, for the first time, are applied to such a dicopper enzyme. The chosen biomimetic model encompasses a dioxygen molecule, two Cu(II) cations, and six imidazole rings. The docking energy of a natural substrate, namely phenolate, together with those of several inhibitor and non-inhibitor compounds, are reported and show the ability of the model to rank the most potent inhibitors in agreement with experimental data. With respect to broken-symmetry calculations, the Spin-Flip TD-DFT approach reinforces the possibility for theory to point out potent inhibitors: the need for the deprotonation of the substrates, natural or inhibitors, is now clearly established. Moreover, Electron Localization Function (ELF) topological analysis computations are used to deeply track the particular electronic distribution of the Cu-O-Cu three-center bonds involved in the enzymatic Cu(2)O(2) metallic core (Piquemal and Pilmé, J. Mol. Struct.: Theochem, 2006, 77, 764). It is shown that such bonds exhibit very resilient out-of-plane density expansions that play a key role in docking interactions: their 3D-orientation could be the topological electronic signature of oxygen activation within such systems.

Separation of geometric isomers of a dicopper complex by using a (19)F-labeled ligand: dynamics, structures, and DFT calculations

Introducing a fluorine group on two pyridines of the HL(CH(3)) ligand (2,6-bis[(bis(2-pyridylmethyl)amino)methyl]-4-methylphenol) allows the separation of two geometric isomers after complexation by two copper(II) ions. Methods for isolating the isomers (1(meso) and 1(rac)) as a mu-phenoxo,mu-hydroxo dicopper(II) complex as a crystalline product have been developed. Both isomers (1(meso) and 1(rac)) have been characterized by X-ray crystallography and (19)F NMR. The isomerism is determined by the disposition of the fluorine atoms with respect to the plane containing the Cu(2)O(2) core. Density functional theory calculations using different functionals were performed to provide additional support for the existence of these two forms. Dissolution of 1(meso) in acetone or acetonitrile causes its spontaneous isomerization into the 1(rac) form at room temperature. Combined experimental studies (UV-vis, (19)F NMR) and theoretical calculations support this process. Paramagnetic (19)F NMR appears as a unique and powerful probe for distinguishing the two isomers and supplying direct evidence of this isomerization process in solution.

An integrated experimental and theoretical investigation on Cu(hfa)2. TMEDA: structure, bonding and reactivity

The physico-chemical properties of the beta-diketonate diamine Cu(ii) compound with hfa (1,1,1,5,5,5-hexafluoro-2-4-pentanedionate) and TMEDA (N,N,N',N' tetramethylethylenediamine), Cu(hfa)(2).TMEDA, have been thoroughly investigated via an integrated multi-technique experimental-computational approach. In the newly found orthorhombic polymorph, as revealed by low temperature single-crystal X-ray studies, the complex is present as a monomer with a distorted octahedral geometry at the Cu(ii) centre. The compound sublimates, without premature side decompositions, at 343 K and 10(-3) Torr. The structural, vibrational, electronic and thermal behavior of the neutral Cu(hfa)(2).TMEDA complex has been investigated along with its fragmentation pathways, initiated by the release of an anionic hfa ligand with formation of a positive Cu(hfa).TMEDA(+) ion. Joint experimental and theoretical analyses led to the rationalization of the first fragmentation steps in terms of the Cu(ii)-ligands bonding properties and Jahn-Teller distortion. The present study suggests applications of Cu(hfa)(2).TMEDA as a precursor for copper and copper oxide materials by Chemical Vapor Deposition.

Advancing beyond charge analysis using the electronic localization function: Chemically intuitive distribution of electrostatic moments

We propose here an evaluation of chemically intuitive distributed electrostatic moments using the topological analysis of the electron localization function (ELF). As this partition of the total charge density provides an accurate representation of the molecular dipole, the distributed electrostatic moments based on the ELF partition (DEMEP) allows computing of local moments located at non atomic centers such as lone pairs, sigma bonds and pi systems. As the local dipole contribution can be decomposed in polarization and charge transfer components, our results indicate that local dipolar polarization of the lone pairs and chemical reactivity are closely related whereas the charge transfer contribution is the key factor driving the local bond dipole. Results on relevant molecules show that local dipole contributions can be used to rationalize inductive polarization effects in alcohols derivatives and typical hydrogen bond interactions. Moreover, bond quadrupole polarization moments being related to a pi character enable to discuss bond multiplicities, and to sort families of molecules according to their bond order. That way, the nature of the C-O bond has been revisited for several typical systems by means of the DEMEP analysis which appears also helpful to discuss aromaticity. Special attention has been given to the carbon monoxide molecule, to the CuCO complex and to a weak intramolecular N|-CO interaction involved in several biological systems. In this latter case, it is confirmed that the bond formation is mainly linked to the CO bond polarization. Transferability tests show that the approach is suitable for the design of advanced force fields.

Singlet-triplet gaps in large multireference systems: Spin-flip-driven alternatives for bioinorganic modeling

The proper description of low-spin states of open-shell systems, which are commonly encountered in the field of bioinorganic chemistry, rigorously requires using multireference ab initio methodologies. Such approaches are unfortunately very CPU-time consuming as dynamic correlation effects also have to be taken into account. The broken-symmetry unrestricted (spin-polarized) density functional theory (DFT) technique has been widely employed up to now to bypass that drawback, but despite a number of relative successes in the determination of singlet-triplet gaps, this framework cannot be considered as entirely satisfactory. In this contribution, we investigate some alternative ways relying on the spin-flip time-dependent DFT approach [Y. Shao et al. J. Chem. Phys. 118, 4807 (2003)]. Taking a few well-documented copper-dioxygen adducts as examples, we show that spin-flip (SF)-DFT computed singlet-triplet gaps compare very favorably to either experimental results or large-scale CASMP2 computations. Moreover, it is shown that this approach can be used to optimize geometries at a DFT level including some multireference effects. Finally, a clear-cut added value of the SF-DFT computations is drawn: if pure ab initio data are required, then the electronic excitations revealed by SF-DFT can be considered in designing dramatically reduced zeroth-order variational spaces to be used in subsequent multireference configuration interaction or multireference perturbation treatments.

Towards understanding performance differences between approximate density functionals for spin states of iron complexes

Density functional theory has been widely used to investigate the structural and electronic properties of heme-containing proteins such as cytochrome P450. Nevertheless, recent studies have shown that approximate exchange-correlation energy density functionals can incorrectly predict the stability order of spin states in, for instance, iron-containing pyridine and imidazole systems. This raises questions about the validity of earlier theoretical studies. In this work, we systematically investigate a few typical inorganic and organic iron-containing complexes and try to understand the performance difference of various density functionals. Two oxidation states of iron, Fe(II) and Fe(III), with different spin states and both adiabatic and vertical structures are considered. A different description of the outmost molecular orbital is found to play the crucial role. Local density and generalized gradient based functionals bias the lower spin state and produce a more localized frontier orbital that is higher in energy than the hybrid functionals. Energy component analysis has been performed, together with comparison of numerous structural and electronic properties. Implications of the present work to the theoretical study of heme-containing biological molecules and other spin-related systems are discussed.

Theoretical modelling of tripodal CuN3 and CuN4 cuprous complexes interacting with O2, CO or CH3CN

Dioxygen binding at copper enzymatic sites is a fundamental aspect of the catalytic activity observed in many biological systems such as the monooxygenases, especially peptidylglycine alpha-hydroxylating monooxygenase (PHM), in which two mononuclear Cu(I) sites are involved. Biomimetic models have been developed: dipods, tripods, and, more recently, functionalized calixarenes. The modelling of calixarene systems, although not unreachable for theory yet, requires, however, a number of preliminary investigations to ensure proper calibrations if relevant description of the metal-ligand interaction at the hybrid quantum mechanical/molecular mechanics levels of theory is the aim. In this paper, we report quantum chemistry investigations on a coherent series of representative cuprous tripodal species characterized by (1) monodentate ligands [Cu(ImH)3]+ (where ImH is imidazole), [Cu(MeNH2)3]+ and [Cu(MeNH2)4]+ , (2) neutral tripodal ligands [CuCH(ImH)3]+, [Cu(tren)]+ [where tren is tris(2-aminoethyl)amine], and [Cu(trenMe3)]+ [where trenMe3 is tris(2-methylaminoethyl)amine] and (3) a hydrido-tris(pyrazolyl)borate [CuBH(Pyra)3]. The structures of these complexes, the coordination mode (eta(2) side-on or eta(1) end-on) of O2 to Cu(I) and the charge transfer from the metal to dioxygen have been computed. For some systems, the coordination by CH3CN and CO is also reported. Beyond results relative to structural properties, an interesting feature is that it is possible to build from computational results only a set of abacuses linking the nu(16O-16O) vibrational frequency of the coordinated O2 molecule to the O-O bond length or to the net charge of the O2 moiety. Such abacuses may help experimentalists in distinguishing between the four possible ways of binding O2 to CuN3 and CuN4 cuprous centres, namely (1) end-on triplet states, (2) side-on triplet states, (3) end-on singlet states and (4) side-on singlet states. These abacuses are extended to three tripods obtained by the substitution of one nitrogen atom by either a phosphorus or a sulphur atom. Moreover, it is shown that any factor favouring pyramidalization at copper favours charge transfer and thus coordination of the incoming O2 moiety. All these allow insight into the coordination mode of O2 and into the charge transfer from Cu(I) in site Cu(M) of PHM.