Showing papers by "James Alexis Platts published in 2015"

Further evidence on the importance of fluorous-fluorous interactions in supramolecular chemistry: a combined structural and computational study

Abstract: The solid-state structures of CF3(CF2)5CH2CO2H and a fluorous triazole are reported, both of which display a wide variety and large number of noncovalent interactions in their packing. The solid-state structure of CF3(CF2)5CH2CO2H is stabilized by multiple F···F contacts but only one C–H···F–C interaction, as well as O–H···O and C–H···O hydrogen bonds. In contrast to other reported structures, the torsion angles in the fluorous chain are close to 180°, which means that the fluorine atoms are eclipsed. A DFT study of the interactions in both compounds show that F···F interactions, along with stacking and C–H···F and C–H···O contacts, are individually weakly energetically stabilizing, but collectively, they can give rise to interaction energies of up to 13 kcal mol–1. A topological approach to the interactions using atoms-in-molecules (AIM) theory reveals that there are bond critical points between the C–F···F–C interactions as well as C–F···H–C interactions that are not recognized when using only the van d...

Phosphorescent, Cyclometalated Cinchophen-Derived Platinum Complexes: Syntheses, Structures, and Electronic Properties.

Abstract: The syntheses of nine new monometallic heteroleptic platinum complexes [Pt(L1–4)(acac)], [Pt(L1)(hmacac/hfacac)], [PtCl(L1)(py)], [Pt(L1)(8-Q)], [Pt(L1)(bpy)](PF6) (where L1 = 2-phenyl-4-ethyl-quinolinecarboxylate; L2/L3 = N-functionalization of 2-phenyl-N-aryl/alkyl-quinoline-4-carboxamides; L4 = 2-phenyl-4-quinolinecarboxylic acid (cinchophen); acac = acetylacetonato; hmacac =2,2,6,6-tetramethyl-3,5-heptanedionate; hfacac = hexafluoroacetylacetonate; py = pyridine; 8-Q = 8-quinolinato; bpy =2,2′-bipyridine) are described from precursor dimeric Pt(II) species via an intermediate DMSO adduct of the general form [PtCl(L1–4)(DMSO)]. Single crystal X-ray diffraction studies were undertaken on three complexes, [Pt(L1)(acac)], [PtCl(L1)(DMSO)], and [Pt(L1)(bpy)](PF6). The structures show that the complexes each adopt a distorted square planar geometry (most severely in the case of [Pt(L1)(bpy)](PF6)) with indications of intermolecular Pt–Pt interactions in one example. The complexes were investigated using 195Pt{1H} NMR spectroscopy, revealing varied chemical shifts that were strongly dependent upon the specific coordination environment of Pt(II). Luminescence studies showed the complexes possess a phosphorescent character with tunable emission wavelengths between 605 and 641 nm and luminescent lifetimes up to ∼450 ns. Supporting TD-DFT studies provided descriptions of the HOMO and LUMO energy levels of the key complex types, confirming an MLCT contribution to the lowest energy absorption that generally correlated well with the experimental spectra. The contribution of the Pt(5d) center to the calculated HOMOs was strongly ligand dependent, whereas the LUMOs are generally localized over the quinoline component of the cyclometalated ligand.

Experimental and theoretical charge density distribution in Pigment Yellow 101.

Abstract: The charge density distribution in 2,2′-dihydroxy-1,1′-naphthalazine (Pigment Yellow 101; P.Y.101) has been determined using high-resolution X-ray diffraction and multipole refinement, along with density functional theory calculations. Topological analysis of the resulting densities highlights the localisation of single/double bonds in the central CN–NC moiety of the molecule in its ground state. The density in the N–N is examined in detail, where we show that very small differences between experiment and theory are amplified by use of the Laplacian of the density. Quantification of hydrogen bonds highlights the importance of the intramolecular N–H⋯O interaction, known to be vital for retention of fluorescence in the solid state, relative to the many but weak intermolecular contacts located. However, a popular method for deriving H-bond strengths from density data appears to struggle with the intramolecular N–H⋯O interaction. We also show that theoretical estimation of anisotropic displacements for hydrogen atoms brings little benefit overall, and degrades agreement with experiment for one intra-molecular contact.

Structure determination of bound nitrogen-based adducts with copper(II) acetylacetonato; an EPR, ENDOR and DFT study

Abstract: The adducts of bis(acetylacetonato)–copper(II), [Cu(acac)2], formed with a range of nitrogen heterocycles including pyridine (2), methylpyridines (3,4,5), amino-methylpyridines (6,7) and diazines (8,9,10) were investigated in frozen solution using X-band EPR and 1H ENDOR spectroscopy. The small perturbations to the EPR spin Hamiltonian parameters (g and CuA) were consistent with the axial coordination of the nitrogen bases to Cu(II), and found to be dependent on both the basicity and steric influence of the coordinating substrate. The detailed structure of two adducts was then investigated by angular selective 1H ENDOR and DFT. For the [Cu(acac)2](pyridine) adduct, axial coordination of the substrate was found to occur via the pyridine nitrogen as expected, producing a characteristic 1H hyperfine coupling (HAi = −2.6, −2.04, 4.7 MHz; β = 36°; aiso = 0.2 MHz) arising from the ortho-1H in the ring 2 or 6 position. These results were confirmed by DFT. However, in the [Cu(acac)2](2-amino-6-methyl-pyridine) adduct, the ENDOR data revealed a substantially different 1H hyperfine coupling (HAi = −4.52, −3.35, 6.47 MHz; β = 14°; aiso = −0.47 MHz) arising from the –NH2 amino protons. Analysis of this experimentally derived tensor in conjunction with the calculated DFT tensors, revealed that the 2-amino-6-methyl-pyridine substrate binds to Cu(II) via the exocyclic amino pyridine nitrogen, but with a tilt angle of 20° of the pyridine ring away from the geometry optimised structure. These results reveal how important structural information on the coordination geometry of Cu(II) adducts can be obtained by 1H ENDOR, but only when the complete angular dependency profile of the ENDOR data is thoroughly considered.

Computational evidence for structural consequences of kiteplatin damage on DNA

Abstract: The reaction of the potential anticancer drug kiteplatin, cis-[PtCl2(cis-1,4-DACH)], with oligomers of single- and double-stranded DNA ranging from 2 to 12 base pairs in length was performed as a model for DNA interaction. The potential for conformational flexibility of single-stranded adducts was examined with density functional theory (DFT) and compared with data from 1H-NMR 1D and 2D spectroscopy. This indicates the presence of multiple conformations of an adduct with d(GpG), but only one form of the adduct with d(TGGT). The importance of a suitable theoretical model, and in particular basis set, in reproducing experimental data is demonstrated. The DFT theoretical model was extended to platinated base pair step (GG/CC), allowing a comparison to the related compounds cisplatin and oxaliplatin. Adducts of kiteplatin with larger fragments of double-stranded DNA, including tetramer, octamer, and dodecamer, were studied theoretically using hybrid quantum mechanics/molecular mechanics methods. Structural parameters of all the base-paired models were evaluated and binding energies calculated in gas phase and in solution; these are compared across the series and also with the related complexes cisplatin and oxaliplatin, thus revealing insights into how kiteplatin binds to DNA and similarities and differences between this and related compounds.

Cationic, luminescent cyclometalated iridium(III) complexes based on substituted 2-phenylthiazole ligands

Abstract: Ten cationic heteroleptic iridium(III) complexes, [Ir(emptz)2(N^N)](PF6) were prepared from a cyclometalated iridium bridged-chloride dimer involving two ethyl-4-methylphenylthiazole-5-carboxylate (emptz) ligands. One X-ray crystallographic study was undertaken where the ancillary N^N ligand was 4,7-diphenyl-1,10-phenanthroline and revealed the anticipated structure, showing a distorted octahedral coordination geometry at Ir(III). The complexes were visibly luminescent with modestly structured emission at 540–590 nm and lifetimes (60–340 ns) consistent with phosphorescence. TD-DFT calculations suggest that strong MLCT character contributes to the visible absorption characteristics, whilst the moderately structured emission profiles indicate a 3MLCT/3IL admixture of states to the phosphorescence.

DNA fragment conformations in adducts with Kiteplatin

Abstract: The anticancer activity of cisplatin is triggered by its formation of intrastrand adducts involving adjacent G residues of DNA. To obtain information on the different conformers that can be formed, carrier ligands such as 2,2′-bipiperidine, which provide large steric bulk near the platinum coordination plane and decrease the dynamic motion about the Pt–N7 bonds, were introduced (“retro-modelling” approach). In the present study we investigate the effect of cis-1,4-diaminocyclohexane (cis-1,4-DACH) on the formation, stability, and stereochemistry of (cis-1,4-DACH)Pt(ss-oligo) adducts (ss-oligo = d(GpG) with 3′- and/or 5′-substituents). Interesting features of this ligand, absent in previous retro-modelling studies, include the large bite angle (expected to impede the ease of interconversion between possible conformers), the presence of two protons on each nitrogen (a characteristic associated with antitumor activity), and the absence of chiral centres. The use of cis-1,4-DACH has made it possible to detect different conformers in a system containing a primary diamine carrier ligand associated with anticancer activity and to confirm the previous hypothesis that the coexistence of different conformers established in studies of retro models having relatively bulky ligands is not an artefact resulting from carrier-ligand bulk. Moreover, the data for the (cis-1,4-DACH)Pt(d(GpG)) and (cis-1,4-DACH)Pt(d(GGTTT)) adducts indicate that at a temperature close to the physiological one (40 °C) HH1 and ΔHT1 conformers are present in comparable amounts. In contrast, at low temperature (close to 0 °C) the equilibrium shifts dramatically toward the more stable HH1 conformer (for the (cis-1,4-DACH)Pt(d(TGGT)) adduct the HH1 conformer is always dominant, even at high temperature). Notably, (cis-1,4-DACH)PtCl2 (Kiteplatin) has been recently reinvestigated and found to be particularly active against colorectal cancer (including oxaliplatin-resistant phenotypes).

Theoretical modelling of epigenetically modified DNA sequences.

Abstract: 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.

Improving catalyst activity in secondary amine catalysed transformations

Abstract: The effect on catalyst performance of altering substituents at the 2-position of the Macmillan imidazolidinone has been examined. Condensation of L-phenylalanine N-methyl amide with acetophenone derivatives results in a series of imidazolidinones whose salts can be used to accelerate the Diels–Alder cycloaddition. Electron withdrawing groups significantly increase the overall rate of cycloaddition without compromise in selectivity. The most effective catalyst was shown to be efficient for a variety of substrates and the applicability of this catalyst to alternative secondary amine catalysed transformations is also discussed.

Stabilization of Al(III) solutions by complexation with cacodylic acid: speciation and binding features

Abstract: Aluminium ions are believed to play a role in a number of neurological and skeletal disorders in the human body. The study of the biological processes and molecular mechanisms that underlie these pathological disorders is rendered a difficult task due to the wide variety of complex species that result from the hydrolysis of Al3+ ions. In addition, this ion displays a pronounced tendency to precipitate as a hydroxide, so certain complexing agents should be envisaged to stabilize Al(III) solutions in near physiological conditions. In this work, we show that the common buffer cacodylic acid (dimethylarsinic acid, HCac) interacts with Al(III) to give stable complexes, even at pH 7. After preliminary analyses of the speciation of the metal ion and also of the ligand, a systematic study of the formation of different Al/Cac complexes at different pH values has been conducted. UV-Vis titrations, mass spectrometry NMR measurements and DTF calculations were performed to enlighten the details of the speciation and stoichiometry of Al/Cac complexes. The results altogether show that Al/Cac dimer complexes prevail, but monomer and trimer forms are also present. Interestingly, it was found that cacodylate promotes the formation of such relatively simple complexes, even under conditions where the polymeric form, Al13O4(OH)247+, should predominate. The results obtained can help to shed some light into the reactivity of aluminium ions in biological environments.

Stereoelectronic control of photophysics: red and yellow axial and equatorial anomers of a rhenium-quinoline complex

Abstract: A novel quinoline-substituted pyrimidine ligand forms two different coloured complexes upon reaction with Re(CO)5Br. These compounds display distinct photophysical properties that are dictated by their stereochemistry.

Correction: Experimental and theoretical charge density distribution in Pigment Yellow 101

Abstract: Correction for ‘Experimental and theoretical charge density distribution in Pigment Yellow 101’ by Jonathan J. Du et al., Phys. Chem. Chem. Phys., 2015, DOI: 10.1039/c4cp04302b.