Refinement of the gonadotropin releasing hormone receptor I homology model by applying molecular dynamics.

Sexual maturation of human cells in ovaries and prostate is linked to the biochemical cascade initiated by the activation of cell receptors through the binding of Gonadotropin Releasing Hormone (GnRH). The GnRH receptors (GnRHR) are part of the rhodopsin G-protein coupled receptor (GPCR) family and consist of seven trans-membrane helical domains connected via extra- and intra-cellular segments. The GnRH-GnRHR complex has been implicated in various forms of prostate and ovarian cancer. The lack of any structural data about the GnRH receptor impedes the design of antagonists for use in cancer treatment. The aim of the study is to devise a model of GnRHR to be used further for the design of improved peptide/non-peptide GnRH analogues and, to our knowledge provide new structural information regarding the extracellular loop 2 (ECL2) that acts a regulator of ligand entry to GnRHR. The common structural characteristics, of the members of the rhodopsin family of GPCRs, have been employed for the construction of a homology model for GnRHR. Structural information from the human ß2-adrenergic receptor, as well as rhodopsins have been used in order to create a theoretical model for GnRHR. Furthermore, molecular dynamics (MD) simulations have been employed for the refinement of the model and to explore the impact of the bilayer membrane in GnRHR conformation.

Theoretical modelling of epigenetically modified DNA sequences.

We report herein a set of calculations designed to examine the effects of epigenetic modifications on the structure of DNA. The incorporation of methyl, hydroxymethyl, formyl and carboxy substituents at the 5-position of cytosine is shown to hardly affect the geometry of CG base pairs, but to result in rather larger changes to hydrogen-bond and stacking binding energies, as predicted by dispersion-corrected density functional theory (DFT) methods. The same modifications within double-stranded GCG and ACA trimers exhibit rather larger structural effects, when including the sugar-phosphate backbone as well as sodium counterions and implicit aqueous solvation. In particular, changes are observed in the buckle and propeller angles within base pairs and the slide and roll values of base pair steps, but these leave the overall helical shape of DNA essentially intact. The structures so obtained are useful as a benchmark of faster methods, including molecular mechanics (MM) and hybrid quantum mechanics/molecular mechanics (QM/MM) methods. We show that previously developed MM parameters satisfactorily reproduce the trimer structures, as do QM/MM calculations which treat bases with dispersion-corrected DFT and the sugar-phosphate backbone with AMBER. The latter are improved by inclusion of all six bases in the QM region, since a truncated model including only the central CG base pair in the QM region is considerably further from the DFT structure. This QM/MM method is then applied to a set of double-stranded DNA heptamers derived from a recent X-ray crystallographic study, whose size puts a DFT study beyond our current computational resources. These data show that still larger structural changes are observed than in base pairs or trimers, leading us to conclude that it is important to model epigenetic modifications within realistic molecular contexts.

Relationships between electron density and magnetic properties in water-bridged dimetal complexes.

The electron densities in two analogous dimetallic transition metal compounds, namely, [M2(µ-OH2)((t)BuCOO)4((t)BuCOOH)2(C5H5N)2] (M = Co(1), Ni(2)), were determined from combined X-ray and neutron single-crystal diffraction at 100 K. Excellent correspondence between the thermal parameters from X- and N-derived atomic displacement parameters is found, indicating high-quality X-ray data and a successful separation of thermal and electronic effects. Topological analysis of electron densities derived from high-resolution X-ray diffraction, as well as density functional theory calculations, shows no direct metal-metal bonding in either compound, while the total energy density at the bond critical points suggests stronger metal-oxygen interactions for the Ni system, in correspondence with its shorter bond distances. The analysis also allows for estimation of the relative strength of binding of terminal and bridging ligands to the metals, showing that the bridging water molecule is more strongly bound than terminal carboxylic acid, but less so than bridging carboxylates. Recently, modeling of magnetic and spectroscopic data in both of these systems has shown weak ferromagnetic interactions between the metal atoms. Factors related to large zero-field splitting effects complicate the magnetic analysis in both compounds, albeit to a much greater degree in 1. The current results support the conclusion drawn from previous magnetic and spectroscopic measurements that there is no appreciable direct communication between metal centers.

Understanding the structural and dynamic consequences of DNA epigenetic modifications: computational insights into cytosine methylation and hydroxymethylation.

We report a series of molecular dynamics (MD) simulations of up to a microsecond combined simulation time designed to probe epigenetically modified DNA sequences. More specifically, by monitoring the effects of methylation and hydroxymethylation of cytosine in different DNA sequences, we show, for the first time, that DNA epigenetic modifications change the molecule's dynamical landscape, increasing the propensity of DNA toward different values of twist and/or roll/tilt angles (in relation to the unmodified DNA) at the modification sites. Moreover, both the extent and position of different modifications have significant effects on the amount of structural variation observed. We propose that these conformational differences, which are dependent on the sequence environment, can provide specificity for protein binding.

Experimental and theoretical charge-density study of a tetranuclear cobalt carbonyl complex.

Details of the complex bonding environment present in the molecular centre of an alkyne-bridged dicobalt complex have been examined using a combination of experimental and theoretical charge-density modelling for two compounds which share a central Co(2)C(2) tetrahedral moiety as their common motif. Topological analysis of the experimental electron density illustrates the problem of separating the Co-C bond-critical points (b.c.p.s) from the intervening ring-critical point (r.c.p.), due largely to the flat nature of the electron density in the CoC(2) triangles. Such a separation of critical points is immediately obtained from a topological analysis of the theoretical electron density as well as from the multipole-projected theoretical density; however, the addition of random noise to the theoretical structure factors prior to multipole modelling leads to a failure in consistently distinguishing two b.c.p.s and one r.c.p. in such close proximity within the particular environment of this Co(2)C(2) centre.

Locus-specific microemulsion catalysts for sulfur mustard (HD) chemical warfare agent decontamination.

The rates of catalytic oxidative decontamination of the chemical warfare agent (CWA) sulfur mustard (HD, bis(2-chlororethyl) sulfide) and a range (chloroethyl) sulfide simulants of variable lipophilicity have been examined using a hydrogen peroxide-based microemulsion system. SANS (small-angle neutron scattering), SAXS (small-angle X-ray scattering), PGSE-NMR (pulsed-gradient spin-echo NMR), fluorescence quenching, and electrospray mass spectroscopy (ESI-MS) were implemented to examine the distribution of HD, its simulants, and their oxidation/hydrolysis products in a model oil-in-water microemulsion. These measurements not only present a means of interpreting decontamination rates but also a rationale for the design of oxidation catalysts for these toxic materials. Here we show that by localizing manganese-Schiff base catalysts at the oil droplet-water interface or within the droplet core, a range of (chloroethyl) sulfides, including HD, spanning some 7 orders of octanol-water partition coefficient (K(ow)), may be oxidized with equal efficacy using dilute (5 wt. % of aqueous phase) hydrogen peroxide as a noncorrosive, environmentally benign oxidant (e.g., t(1/2) (HD) approximately 18 s, (2-chloroethyl phenyl sulfide, C(6)H(5)SCH(2)CH(2)Cl) approximately 15 s, (thiodiglycol, S(CH(2)CH(2)OH)(2)) approximately 19 s {20 degrees C}). Our observations demonstrate that by programming catalyst lipophilicity to colocalize catalyst and substrate, the inherent compartmentalization of the microemulsion can be exploited to achieve enhanced rates of reaction or to exert control over product selectivity. A combination of SANS, ESI-MS and fluorescence quenching measurements indicate that the enhanced catalytic activity is due to the locus of the catalyst and not a result of partial hydrolysis of the substrate.

Experimental and theoretical charge density study of chemical bonding in a Co dimer complex.

The charge density of Co2(CO)6(HC[triple bond]CC6H10OH) (1) in the crystalline state has been determined using multipolar refinement of single-crystal X-ray diffraction data collected (i) with a synchrotron source at very low temperatures (15 K) and (ii) using a conventional source with the crystal at intermediate temperature (100 K). The X-ray charge density model is augmented by complete active space and density functional theory calculations. Topological analyses of the different charge distributions show that the two Co atoms are not bonded to each other in the quantum theory of atoms in molecules (QTAIM) sense of the word. However, the behavior of the source function and the total energy density indicate that there is some bond-like character in the Co-Co interaction. The bridging alkyne fragment provides an unusual bonding situation, with extremely small electron density differences between the two Co-C bond critical points and the "CoC2" ring critical point. Thus, the structure is close to a topological catastrophe point. Comparison of the results obtained from the two diffraction data sets and ab initio theory suggests that the topology of the experimental electron density in this special atomic environment is highly sensitive to subtle effects of measurement errors and potential shortcomings of the multipole model, or to effects of the crystal field. Thus, even the two identical molecules in the asymmetric unit show altered bonding patterns.

Probing the skin permeation of fish oil/EPA and ketoprofen 1. NMR spectroscopy and molecular modelling.

The complexation of EPA with ketoprofen was probed in order to rationalise co-operative skin permeation enhancement behaviour observed previously. The modulation of aromatic protons of ketoprofen was determined using (1)H NMR spectra from different formulations containing varying concentrations of fish oil and a control saturated triglyceride. Molecular modelling of possible complexes of ketoprofen with constituents of fish oil was performed. NMR data revealed a dose-dependent change in chemical shift in the aromatic protons of ketoprofen on addition of fish oil and/or EPA. Similar patterns were observed in both cases, although the free fatty acid induced changes in more protons. Molecular modelling results indicate quite large binding energies of all complexes considered, varying between ca. 90 and 160 kJ mol(-1). The geometries of these complexes shows strong O-H...O hydrogen bonds in all cases, and in the case of the complex of ketoprofen with free EPA there is also some evidence of C-H... pi and/or pi-pi interactions, giving rise to regiospecifically solvated complexes. If strongly bound ketoprofen:EPA complexes can form, then the permeation enhancement of EPA by ketoprofen could be attributed to such a complex. Once the complex is formed, the triglyceride/free fatty acid could aid permeation of associated ketoprofen into the lipophilic stratum corneum via the pull effect. Once permeated, the more hydrophilic ketoprofen could aid the permeation of the triglyceride/free fatty acid through the epidermis, again via the pull effect. This could explain the synergistic permeation enhancement seen with these compounds.

Synthesis, structural characterization, and theoretical studies of complexes of magnesium and calcium with gallium heterocycles.

The magnesium- and calcium-gallium heterocycle complexes [Mg{Ga[(ArNCH)2]}2(THF)3] and [Ca{Ga[(ArNCR)2]}2(THF)4], R = H or Me, Ar = C6H3Pr(i)2-2,6, have been prepared via the reduction of [I2Ga{(ArNCR)2}] with the group 2 metal in tetrahydrofuran. The mechanisms of the reactions have been elucidated, and the crystal structures of the complexes exhibit the first structurally authenticated Ga-Mg and Ga-Ca bonds in molecular species. Theoretical studies suggest that the heterocycle-group 2 metal interactions have significant ionic character.

Four-membered group 13 metal(I) N-heterocyclic carbene analogues: synthesis, characterization, and theoretical studies.

The synthesis, spectroscopic and structural characterization of the monomeric, four-membered group 13 metal(I) heterocycles ([:M{eta2-N,N'-(Ar)NC(NCy2)N(Ar)}], M = Ga or In, Ar = C6H3Pri2-2,6) and an isomeric thallium complex are reported. Theoretical studies on these complexes, which are analogues of four-membered N-heterocyclic carbenes, suggest they should act as good sigma-donor ligands.

Synthesis, characterisation and theoretical studies of amidinato-indium(I) and thallium(I) complexes: isomers of neutral group 13 metal(I) carbene analogues.

The synthesis and characterisation of the monomeric amidinato-indium(I) and thallium(I) complexes, [M(Piso)].PisoH, M = In or Tl, Piso- = [ArNC(Bu(t))NAr]-, Ar = C6H3Pr(i)2-2,6, are reported. These complexes, in which the metal centre is chelated by the amidinate ligand in an N,eta3-arene-fashion, can be considered as isomers of four-membered group 13 metal(I) carbene analogues. Theoretical studies have compared the relative energies of both isomeric forms of a model complex, [In{PhNC(H)NPh}].

Analogies between the reactivities of an anionic gallium(I) heterocycle and N-heterocyclic carbenes toward metallocenes.

The synthesis, spectroscopic and structural characterization of the novel nickel-gallium(I) heterocycle complex, [{Ga[N(Ar)C(H)]2}2Ni(mu-Cp)K(tmeda)(mu-Cp)K(mu-C7H8)0.5]infinity, Ar = C6H3Pri2-2,6, are reported. The compound is polymeric in the solid state and reacts with an N-heterocyclic carbene to give the neutral, square planar complex, trans-[Ni{C[N(Me)C(Me)]2}2{Ga[N(Ar)C(H)]2}2]. Analogies between the reactivities of the gallium(I) heterocycle and isoelectronic N-heterocyclic carbenes are discussed.