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Displaying Results 3176 - 3200 of 3821 on page 128 of 153
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Conformations of myoglobin-derived peptides at the air-water interface
(2016)
Cheung, David L.
Conformations of myoglobin-derived peptides at the air-water interface
(2016)
Cheung, David L.
Abstract:
Simulation files, analysis scripts, and output data to accompany article: Cheung, David L. (2016). Conformations of Myoglobin-Derived Peptides at the Air–Water Interface. Langmuir, 32(18), 4405-4414. doi: 10.1021/acs.langmuir.5b04619
http://hdl.handle.net/10379/6214
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Chemical and electrical characterisation of the segregation of Al from a CuAl alloy (90%:10% wt) with thermal anneal
(2016)
Byrne, Conor; Brady, Anita; Walsh, Lee; McCoy, Anthony; Bogan, Justin; McGlynn, Enda; V...
Chemical and electrical characterisation of the segregation of Al from a CuAl alloy (90%:10% wt) with thermal anneal
(2016)
Byrne, Conor; Brady, Anita; Walsh, Lee; McCoy, Anthony; Bogan, Justin; McGlynn, Enda; Vijayaraghavan, Rajani K.; Hughes, Greg
Abstract:
A copper-aluminium (CuAl) alloy (90% : 10% wt) has been investigated in relation to segregation of the alloying element Al, from the alloy bulk during vacuum anneal treatments. X-ray photoelectron spectroscopy (XPS) measurements were used to track the surface enrichment of Al segregating from the alloy bulk during in situ ultra-high vacuum anneals. Secondary ion mass spectroscopy (SIMS) indicates a build-up of Al at the surface of the annealed alloy relative to the bulk composition. Metal oxide semiconductor (MOS) CuAl/ SiO2/Si structures show a shift in flatband voltage upon thermal anneal consistent with the segregation of the Al to the alloy/SiO2 interface. Electrical four point probe measurements indicates that the segregation of Al from the alloy bulk following thermal annealing results in a decrease in film resistivity. X-ray diffraction data shows evidence for significant changes in crystal structure upon annealing, providing further evidence for expulsion of Al from the allo...
http://doras.dcu.ie/21116/
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Design, synthesis and evaluation of organocatalysts in 1,4-conjugate additions to nitroolefins and alkylidene malonates
(2012)
Gavin, Declan P.
Design, synthesis and evaluation of organocatalysts in 1,4-conjugate additions to nitroolefins and alkylidene malonates
(2012)
Gavin, Declan P.
Abstract:
A family of cinchona-based and thiourea pyrrolidine-based organocatalysts were synthesised and fully characterised. Their catalytic activity and selectivity in 1,4-conjugate additions involving the Michael acceptor, nitrostyrene, was evaluated. Thiourea catalysts based upon the cinchona alkaloid framework were found to exhibit excellent activity and enantioselectivity (up to 95% yield and 97% ee) at loadings of 10 mol% when 1,3-diketones were employed as the pronucleophile. This result demonstrated that a thiourea cinchona catalyst was much more efficient at catalysing this Michael addition than previously reported. The same thiourea organocatalysts were employed in the first successful Michael addition of the sterically challenging dipivaloylmethane to β-nitrostyrene. Thiourea catalysts based upon the pyrrolidine motif were also employed in the Michael addition of cyclohexanone to nitrostyrene, furnishing up to 97% yield and 48% ee . The organocatalysed conjugate addition reactions...
http://eprints.maynoothuniversity.ie/4764/
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Enhanced photostability of a Ruthenium(II) Polypyridyl Complex under highly oxidizing aqueous conditions by its partial inclusion into a cyclodextrin
(2016)
Farràs, Pau; Waller, Helen; Benniston, Andrew C.
Enhanced photostability of a Ruthenium(II) Polypyridyl Complex under highly oxidizing aqueous conditions by its partial inclusion into a cyclodextrin
(2016)
Farràs, Pau; Waller, Helen; Benniston, Andrew C.
Abstract:
The complex [Ru(bpy)2L]2+, where bpy=2,2′-bipyridine, L=4-(phenylethynyl)-2,2′-bipyridine, was prepared in its racemic and resolved forms (Δ and Λ). The phenylethynyl unit on the bipyridine for the complex acts as a binding site for α-cyclodextrin in water (1:1 complex, K=3390 L mol−1) or β-cyclodextrin (2:1 complex, K1=887 L mol−1, K2=8070 L mol−1). The presence of the cyclodextrin provides partial protection to the complex under light-activated water oxidation conditions.
P.F. gratefully acknowledges the Royal Society for the Newton Fellowship and for the financial support.
2017-01-08
http://hdl.handle.net/10379/5948
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Demonstration of Promoted Zinc Schlenk Equilibria, their Equilibrium Values and Derived Reactivity
(2007)
Blake, Alexander J.; Shannon, Jonathan; Stephens, John C.; Woodward, Simon
Demonstration of Promoted Zinc Schlenk Equilibria, their Equilibrium Values and Derived Reactivity
(2007)
Blake, Alexander J.; Shannon, Jonathan; Stephens, John C.; Woodward, Simon
Abstract:
The presence of promoted Schlenk equilibria for organozinc halide species has been explicitly demonstrated by 13C NMR studies. Thus, addition of methylaluminoxane (MeAlO)n, MAO, to RZnX (R=Et, Bn, ArCH2, (CH2)3CO2Et; X=Cl, Br) leads to the formation of ZnR2 and ZnX2⋅MAO. For EtZnCl, equilibration of ZnEt2 and ZnX2⋅MAO is rapid at −35 °C; a K value of 0.19 M−1 indicates the equilibrium favours ZnEt2 (0.75–3.0 equiv MAO). Use of RZnX/MAO mixtures allows copper-catalysed 1,4-addition to 2-cyclohexenone to be achieved, but a competing cascade reaction (two subsequent Michael additions and an intramolecular aldol reaction) leads to novel tetracyclic by-products (characterised crystallographically in one case). Activation of EtZnCl is also achieved by ZnMe2 addition and the presence of intermediate EtZnMe was observed by 13C NMR spectroscopy (at equilibrium, K≈1). Asymmetric conjugate addition in this system can be realised (up to 92 % ee for additions to 2-cyclohexenone).
http://eprints.maynoothuniversity.ie/7706/
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Computational Development of Selective nNOS Inhibitors: Binding Modes and Pharmacokinetic Considerations
(2015)
Curtin, A.M.; Kinsella, Gemma K.; Stephens, John C.
Computational Development of Selective nNOS Inhibitors: Binding Modes and Pharmacokinetic Considerations
(2015)
Curtin, A.M.; Kinsella, Gemma K.; Stephens, John C.
Abstract:
Neuronal nitric oxide synthase (nNOS) produces the key signalling mediator nitric oxide, (NO). This gaseous, free radical molecule modulates a vast array of biological processes, from vascular pressure to immune responses and neurological signalling cascades. Overproduction of NO has been implicated in conditions including Alzheimer’s disease, Parkinson’s disease and schizophrenia. Inhibition of nNOS therefore offers a potential therapeutic approach for treatment of these conditions. This endeavour is made more complex by the fact that there are two other isoforms of nitric oxide synthase (NOS), endothelial NOS (eNOS) and inducible NOS (iNOS). The selectivity of nNOS inhibitors is therefore a key concern for therapeutic development. This review explores recent advances in the field of selective nNOS inhibition. A particular focus is placed on computational approaches towards the rational design of selective nNOS ligands with improved pharmacokinetic properties. These ligands have be...
http://eprints.maynoothuniversity.ie/7701/
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Macrocyclic squaramides: anion receptors with high sulfate binding affinity and selectivity in aqueous media
(2016)
Qin, Lei; Hartley, Anna; Turner, Peter; Elmes, Robert B.P.; Jolliffe, Katrina A.
Macrocyclic squaramides: anion receptors with high sulfate binding affinity and selectivity in aqueous media
(2016)
Qin, Lei; Hartley, Anna; Turner, Peter; Elmes, Robert B.P.; Jolliffe, Katrina A.
Abstract:
A number of macrocyclic squaramide-containing receptors (MSQs) have been designed and synthesised and their interaction with a range of inorganic anions was studied in solution by 1H NMR spectroscopy and ESI-HRMS. The binding data revealed remarkable binding of sulfate in aqueous mixtures from 0.5 to 50% v/v H2O/DMSO-d6. The larger [3]-MSQs were found to better match the size and shape of the sulfate ion than the [2]-MSQs, providing high affinity and selectivity for sulfate while other tetrahedral divalent anions such as selenate, phosphate species and chromate have substantially lower binding affinities. In mixtures of anions mimicking the composition of either nuclear waste or plasma, the [3]-MSQs were still able to bind sulfate ions with high affinity.
http://eprints.maynoothuniversity.ie/7720/
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Contribution of the empirical dispersion correction on the conformation of short alanine peptides obtained by gas-phase QM calculations
(2013)
Fadda, Elisa; Woods, Robert J.
Contribution of the empirical dispersion correction on the conformation of short alanine peptides obtained by gas-phase QM calculations
(2013)
Fadda, Elisa; Woods, Robert J.
Abstract:
In this work we analyze the effect of the inclusion of an empirical dispersion term to standard DFT (DFT-D) in the prediction of the conformational energy of the alanine dipeptide (Ala2) and in assessing the relative stabilities of short polyalanine peptides in helical conformations, i.e., α and 310 helices, from Ala4 to Ala16. The Ala2 conformational energies obtained with the dispersion-corrected GGA functional B97-D are compared to previously published high level MP2 data. Meanwhile, the B97-D performance on larger polyalanine peptides is compared to MP2, B3LYP and RHF calculations obtained at a lower level of theory. Our results show that electron correlation affects the conformational energies of short peptides with a weight that increases with the peptide length. Indeed, while the contribution of vdW forces is significant for larger peptides, in the case of Ala2 it is negligible when compared to solvent effects. Even for short peptides, the inclusion of an empirical dispersion...
http://eprints.maynoothuniversity.ie/7732/
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Molecular basis of proton uptake in single and double mutants of cytochrome c oxidase
(2011)
Henry, Rowan M.; Caplan, David; Fadda, Elisa; Pomès, Régis
Molecular basis of proton uptake in single and double mutants of cytochrome c oxidase
(2011)
Henry, Rowan M.; Caplan, David; Fadda, Elisa; Pomès, Régis
Abstract:
Cytochrome c oxidase, the terminal enzyme of the respiratory chain, utilizes the reduction of dioxygen into water to pump protons across the mitochondrial inner membrane. The principal pathway of proton uptake into the enzyme, the D channel, is a 2.5 nm long channel-like cavity named after a conserved, negatively charged aspartic acid (D) residue thought to help recruiting protons to its entrance (D132 in the first subunit of the S. sphaeroides enzyme). The single-point mutation of D132 to asparagine (N), a neutral residue, abolishes enzyme activity. Conversely, replacing conserved N139, one-third into the D channel, by D, induces a decoupled phenotype, whereby oxygen reduction proceeds but not proton pumping. Intriguingly, the double mutant D132N/N139D, which conserves the charge of the D channel, restores the wild-type phenotype. We use molecular dynamics simulations and electrostatic calculations to examine the structural and physical basis for the coupling of proton pumping and ...
http://eprints.maynoothuniversity.ie/7734/
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Adding glycolipid functionality to model membranes – phase behaviour of a synthetic glycolipid in a phospholipid membrane
(2014)
Migas, Urszula M.; Abbey, Lorna; Velasco-Torrijos, Trinidad; McManus, Jennifer J.
Adding glycolipid functionality to model membranes – phase behaviour of a synthetic glycolipid in a phospholipid membrane
(2014)
Migas, Urszula M.; Abbey, Lorna; Velasco-Torrijos, Trinidad; McManus, Jennifer J.
Abstract:
Glycolipid phase behaviour is less well understood than for many phospholipids, but due to their structural and functional diversity, glycolipids represent an important group of amphiphiles from which biological function is derived. Here we have incorporated a synthetic glycolipid in binary mixtures with DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) into giant unilamellar vesicles (GUVs) at biologically relevant concentrations and observed the phase behaviour of the lipid mixtures for a range of glycolipid concentrations. At low concentrations, the glycolipid is fully dispersed in the GUV membrane. At glycolipid molar concentrations above 10%, the formation of lipid tubules is observed, and is consistent with the formation of a columnar lipid phase. Lipid tubules are observed in aqueous and oil solvents, suggesting that both hexagonal and inverted hexagonal lipid arrangements can be formed. This work may offer insights into the biological function of glycolipids and the challenges...
http://eprints.maynoothuniversity.ie/7755/
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Vacuum Ultraviolet Spectroscopy and Photochemistry of Zinc Dihydride and Related Molecules in Low-Temperature Matrices
(2013)
Henchy, Chris; Gilmartin, Una; McCaffrey, John G.
Vacuum Ultraviolet Spectroscopy and Photochemistry of Zinc Dihydride and Related Molecules in Low-Temperature Matrices
(2013)
Henchy, Chris; Gilmartin, Una; McCaffrey, John G.
Abstract:
Optical absorption spectra of thin film samples, formed by the codeposition of zinc vapor with D2 and CH4, have been recorded with synchrotron radiation. With sufficiently low metal vapor flux, samples deposited at 4 K were found to consist exclusively of isolated zinc atoms for both solids. The atomic absorption bands in the quantum solids D2 and CH4 were found to exhibit large bandwidths, behavior related to the high lattice frequencies of these low mass solids. The reactivity of atomic zinc was promoted with (1)P state photolysis leading to the first recording of electronic absorption spectra for the molecules ZnD2 and CH3ZnH in the vacuum ultraviolet (VUV) region. (3)P state luminescence of atomic zinc observed in the Zn/CH4 system points to the involvement of the spin triplet state in the relaxation of CH3ZnH system as it evolves into the C3v ground state. This state is not involved in the relaxation of the higher symmetry molecule ZnD2. Time dependent density functional theory...
http://eprints.maynoothuniversity.ie/7764/
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A DFT study of reversed isotope shifts in H/D substitution of free-base porphyrin and related free-base tetrapyrroles
(2012)
Henchy, Christopher; Murray, Ciaran; Crepin, Claudine; McCaffrey, John G.
A DFT study of reversed isotope shifts in H/D substitution of free-base porphyrin and related free-base tetrapyrroles
(2012)
Henchy, Christopher; Murray, Ciaran; Crepin, Claudine; McCaffrey, John G.
Abstract:
DFT/B3LYP calculations are used to analyse the occurrence of reverse isotope shift ratios (ISR) in H/D substitution of the free-base tetrapyrroles, in situations where the frequency ratio νH/νD is less than 1. The reverse ISR effect is found to be most evident in the out-of-plane bending modes (b2g and b3u symmetry) involving some N–H motion for the four molecules studied, viz., porphine (H2P), tetraaza-porphine (H2TAP), tetrabenzo-porphine (H2TBP), and phthalocyanine (H2Pc). It was analysed by following the evolution of the normal mode frequencies with incremental variation of the H atom masses from 1 to 2 amu. This method allows direct, unambiguous mode correlations to be established between the light and the heavy isotopologues. When the NH(D) motion is predominant, the H to D frequency evolution decreases in a continuous manner for a particular normal mode. In the case of two modes of the same symmetry and whose frequencies are similar, their frequency evolutions could cross, de...
http://eprints.maynoothuniversity.ie/7766/
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Structure-function analyses of the interactions between Rab11 and Rab14 small GTPases with their shared effector Rab coupling protein (RCP)
(2015)
BOND, URSULA; KHAN, AMIR
Structure-function analyses of the interactions between Rab11 and Rab14 small GTPases with their shared effector Rab coupling protein (RCP)
(2015)
BOND, URSULA; KHAN, AMIR
Abstract:
Rab GTPases recruit effector proteins, via their GTP-dependent switch regions, to distinct subcellular compartments. Rab11 and Rab25 are closely related small GTPases that bind to common effectors termed the Rab11 family of interacting proteins (FIPs). The FIPs are organized into two subclasses (class I and class II) based on sequence and domain organization, and both subclasses contain a highly conserved Rab-binding domain at their C termini. Yeast two-hybrid and biochemical studies have revealed that the more distantly related Rab14 also interacts with class I FIPs. Here, we perform detailed structural, thermodynamic, and cellular analyses of the interactions between Rab14 and one of the class I FIPs, the Rab-coupling protein (RCP), to clarify the molecular aspects of the interaction. We find that Rab14 indeed binds to RCP, albeit with reduced affinity relative to conventional Rab11-FIP and Rab25-FIP complexes. However, in vivo, Rab11 recruits RCP onto biological membranes. Furthe...
http://hdl.handle.net/2262/78782
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Molecular Interactions of Human Plasminogen with Fibronectin-binding Protein B (FnBPB), a Fibrinogen/Fibronectin-binding Protein from Staphylococcus aureus.
(2016)
GEOGHEGAN, JOAN; FOSTER, TIMOTHY
Molecular Interactions of Human Plasminogen with Fibronectin-binding Protein B (FnBPB), a Fibrinogen/Fibronectin-binding Protein from Staphylococcus aureus.
(2016)
GEOGHEGAN, JOAN; FOSTER, TIMOTHY
Abstract:
Staphylococcus aureus is a commensal bacterium that has the ability to cause superficial and deep-seated infections. Like several other invasive pathogens, S. aureus can capture plasminogen from the human host where it can be converted to plasmin by host plasminogen activators or by endogenously expressed staphylokinase. This study demonstrates that sortase-anchored cell wall-associated proteins are responsible for capturing the bulk of bound plasminogen. Two cell wall-associated proteins, the fibrinogen- and fibronectin-binding proteins A and B, were found to bind plasminogen, and one of them, FnBPB, was studied in detail. Plasminogen captured on the surface of S. aureus- or Lactococcus lactis-expressing FnBPB could be activated to the potent serine protease plasmin by staphylokinase and tissue plasminogen activator. Plasminogen bound to recombinant FnBPB with a KD of 0.532 ?m as determined by surface plasmon resonance. Plasminogen binding did not to occur by the same mechanism thr...
http://hdl.handle.net/2262/78772
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Chemotactic ionic liquid droplets: striving to mimic nature
(2016)
Delaney, Colm; Francis, Wayne; Florea, Larisa; Diamond, Dermot
Chemotactic ionic liquid droplets: striving to mimic nature
(2016)
Delaney, Colm; Francis, Wayne; Florea, Larisa; Diamond, Dermot
Abstract:
Chemotaxis, the ability of cells to move in response to certain stimuli, forms the basis for a family of signalling proteins, known as Chemokines. Their ability to control immune responses and cell migrations has proven a fascinating topic for chemists who try to find synthetic analogues to mimic this behaviour. Herein we report the movement of ionic liquid (IL) droplets, based on trihexyl(tetradecyl)phosphonium chloride ([P6,6,6,14]Cl), which exhibit chemotactic behaviour. These IL droplets can be moved spontaneously and guided to specific destinations in the presence of ionic strength gradients.[1] In addition, signalling and seeking [P6,6,6,14]+ droplets can also be developed which chemotactically find each other in open fluidic networks. In this study the signal droplet, which is stationary, releases a chemical signal that creates a chemical gradient inside the fluidic channel. In response to this signal, the seeker droplet is enabled to chemotactically find the signal droplet...
http://doras.dcu.ie/21280/
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Emerging nanonisation technologies: tailoring crystalline versus amorphous nanomaterials
(2015)
HEALY, ANNE
Emerging nanonisation technologies: tailoring crystalline versus amorphous nanomaterials
(2015)
HEALY, ANNE
Abstract:
The overall pharmaceutical market is changing. A more personalised medicine approach is replacing the concept of blockbuster drugs and the ?one size fits all? model. The two main forces that fuel the growth of nano-enabled drug technologies are the low aqueous solubility of new chemical entities and the pharmaceutical market itself, as the development of novel drug delivery systems can extend the drug patent lifetime. Classical solubilisation techniques, such as salt formation and the use of cyclodextrins can only be applied to drugs with ionisable groups or specific molecular weight ranges in order to fit in the cavity of the cyclodextrin. However, drug nanonisation, or particle size reduction into the nanosize range, is a versatile technique that can be applied to a wide range of pharmaceutical compounds. Nano-drugs exhibit higher surface area per unit of volume, which leads to faster dissolution kinetics and hence potentially improved bioavailability. Marketed nano-drugs are most...
http://hdl.handle.net/2262/78792
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Pushing up the magnetisation values for iron oxide nanoparticles: Via zinc doping: X-ray studies on the particle's sub-nano structure of different synthesis routes
(2016)
NICOLOSI, VALERIA
Pushing up the magnetisation values for iron oxide nanoparticles: Via zinc doping: X-ray studies on the particle's sub-nano structure of different synthesis routes
(2016)
NICOLOSI, VALERIA
Abstract:
The maximum magnetisation (saturation magnetisation) obtainable for iron oxide nanoparticles can be increased by doping the nanocrystals with non-magnetic elements such as zinc. Herein, we closely study how only slightly different synthesis approaches towards such doped nanoparticles strongly influence the resulting sub-nano/atomic structure. We compare two co-precipitation approaches, where we only vary the base (NaOH versus NH3), and a thermal decomposition route. These methods are the most commonly applied ones for synthesising doped iron oxide nanoparticles. The measurable magnetisation change upon zinc doping is about the same for all systems. However, the sub-nano structure, which we studied with M?ssbauer and X-ray absorption near edge spectroscopy, differs tremendously. We found evidence that a much more complex picture has to be drawn regarding what happens upon Zn doping compared to what textbooks tell us about the mechanism. Our work demonstrates that it is crucial to stu...
http://hdl.handle.net/2262/78785
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Monte Carlo configuration interaction with perturbation corrections for dissociation energies of first row diatomic molecules: C-2, N-2, O-2, CO, and NO
(2014)
Kelly, Thomas P.; Perera, Ajith; Bartlett, Rodney J.; Greer, James C.
Monte Carlo configuration interaction with perturbation corrections for dissociation energies of first row diatomic molecules: C-2, N-2, O-2, CO, and NO
(2014)
Kelly, Thomas P.; Perera, Ajith; Bartlett, Rodney J.; Greer, James C.
Abstract:
Dissociation energies for the diatomic molecules C2, N2, O2, CO, and NO are estimated using the Monte Carlo configuration interaction (MCCI) and augmented by a second order perturbation theory correction. The calculations are performed using the correlation consistent polarized valence “triple zeta” atomic orbital basis and resulting dissociation energies are compared to coupled cluster calculations including up to triple excitations (CCSDT) and Full Configuration Interaction Quantum Monte Carlo (FCIQMC) estimates. It is found that the MCCI method readily describes the correct behavior for dissociation for the diatomics even when capturing only a relatively small fraction (∼80%) of the correlation energy. At this level only a small number of configurations, typically O(103) from a FCI space of dimension O(1014), are required to describe dissociation. Including the perturbation correction to the MCCI estimates, the difference in dissociation energies with respect to CCSDT ranges betw...
http://hdl.handle.net/10468/3490
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Conformational and structural studies of meso monosubstituted metalloporphyrins - Edge-on molecular interactions of porphyrins in crystals
(2016)
SENGE, MATHIAS
Conformational and structural studies of meso monosubstituted metalloporphyrins - Edge-on molecular interactions of porphyrins in crystals
(2016)
SENGE, MATHIAS
Abstract:
A series of meso monosubstituted metalloporphyrins were synthesized to assess the structural chemistry of porphyrins with only one substituent. The structures of four nickel(II) and zinc(II) complexes with either alkyl or aryl residues indicate primarily planar macrocycles. This gives rise to a different type of ?-interactions in the crystal and the formation of dimeric, trimeric or tetrameric porphyrin units that function as building blocks for the overall crystal structure. Notably, some structures exhibit a unique edge-on packing of porphyrins, while the molecules of (5-n-butylporphyrinato)nickel(II) forms an unusual bilayer type structure where rows of two porphyrin macrocycles are separated by the alkyl residues arranged in a head-to-head fashion. This adds to the canon of intermolecular porphyrin packing arrangements and is of relevance for the preparation of ordered nanoscopic porphyrin devices.
http://hdl.handle.net/2262/78921
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Contribution of bacteriochlorophyll conformation to the distribution of site-energies in the FMO protein
(2016)
SENGE, MATHIAS
Contribution of bacteriochlorophyll conformation to the distribution of site-energies in the FMO protein
(2016)
SENGE, MATHIAS
Abstract:
The structural data for the Fenna-Matthews-Olson (FMO) protein indicate that the bacteriochlorophylls (BChls) display a significant degree of conformational heterogeneity of their peripheral substituents and the protein-induced nonplanar skeletal deformations of the tetrapyrrole macrocycle. As electronic properties of chromophores are altered by such differences, a conformational effect may influence the site-energies of specific pigments and thus play a role in mediating the excitation energy transfer dynamics, but this has not yet been established. The difficulty of assessing this question is shown to be partly the result of the inability of the sequential truncation approach usually employed to account for interactions between the conformations of the macrocycle and its substituents and an alternative approach is suggested. By assigning the BChl atoms to meaningful atom groups and performing all possible permutations of partial optimizations in a full-factorial design, where each...
http://hdl.handle.net/2262/78919
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A two-pronged attack on DNA: Targeting guanine quadruplexes with nonplanar porphyrins and DNA-binding small molecules
(2016)
ROZAS, ISABEL; SENGE, MATHIAS
A two-pronged attack on DNA: Targeting guanine quadruplexes with nonplanar porphyrins and DNA-binding small molecules
(2016)
ROZAS, ISABEL; SENGE, MATHIAS
Abstract:
Cancer therapy requires the identification and selective targeting of cancer?specific effectors. DNA is considered to be a chemotherapeutic target for cancer because of its involvement in cellular proliferation. In addition to the well?known double?stranded structures (A, B, Z?DNA), DNA can form a number of multi?stranded structures (triplexes, quadruplexes, i?motifs) that have distinct biological relevance. In particular, guanine quadruplexes (GQs) are four?stranded nucleic acid structures formed by guanine?rich sequences that fold into non?canonical secondary structures [1]. They consist of two or more G?tetrads which form when four guanine residues connected by hydrogen bonds are held in a planar arrangement and stabilized further by cations such as Na+ and K+. Although GQs can take numerous conformations, there are common features among the GQ structures that may be harnessed to develop small?molecules that bind to them [2]. GQs are present in biologically important regions, suc...
http://hdl.handle.net/2262/78917
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Nucleophilic Aromatic Substitution on Pentafluorophenyl-Substituted Dipyrranes and Tetrapyrroles as a Route to Multifunctionalized Chromophores for Potential Application in Photodynamic Therapy
(2016)
SENGE, MATHIAS
Nucleophilic Aromatic Substitution on Pentafluorophenyl-Substituted Dipyrranes and Tetrapyrroles as a Route to Multifunctionalized Chromophores for Potential Application in Photodynamic Therapy
(2016)
SENGE, MATHIAS
Abstract:
The application of porphyrinoids in biomedical fields like photodynamic therapy (PDT) requires the introduction of functional groups to adjust their solubility in the biological environment and to allow a coupling to other active moieties or carrier systems. A valuable motif in this regard is the pentafluorophenyl (PFP)- substituent, as the PFP-group easily undergoes a regiospecific nucleophilic replacement (SNAr) of the para-fluorine atom by a number of nucleophiles. Here, it is shown that - alternatively to an amino-substitution on the final porphyrinoid or BODIPY - the precursor 5-(PFP)-dipyrrane can be modified with amines (or alcohols). These dipyrranes were transformed into amino-substituted BODIPYs. Condensation of these dipyrranes with aldehydes gives access to trans-A2B2-porphyrins and -A2B-corroles. Using pentafluorobenzaldehyde another para-fluorine atom can be introduced enabling the synthesis of multifunctionalized tetrapyrroles. Furthermore, alkoxy- and amino-substitut...
http://hdl.handle.net/2262/78914
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Lewis acid induced anomerization of se-glycosides. Application to synthesis of alpha-Se-GalCer
(2016)
McDonagh, Anthony W.; Mahon, Mary F.; Murphy, Paul V.
Lewis acid induced anomerization of se-glycosides. Application to synthesis of alpha-Se-GalCer
(2016)
McDonagh, Anthony W.; Mahon, Mary F.; Murphy, Paul V.
Abstract:
The TiCl4 induced anomerization of selenium glycosides of galacturonic acid derivatives is reported. The reaction was successful for galacturonic acid when various alkyl, alkenyl, alkynyl, saccharide, steroid, and lipid groups were attached to the anomeric Se atom. An increased amount of TiCl4 and/or higher temperature were needed to ensure completion of the reaction in some cases. Yields were higher for reactions carried out at higher dilution. The reaction was applied to the synthesis of Se-based mimics of the potent immunostimulant alpha-GalCer (KRN7000).
The research was supported by the Irish Research Council (PhD Scholarship to A.McD.) and NUI Galway (College of Science PhD scholarship to A.McD.). This publication has also emanated in part from research supported by Science Foundation Ireland (SFI, Grant Number 12/IA/1398) and is cofunded under the European Regional Development Fund under Grant Number 14/SP/2710.
2017-01-22
http://hdl.handle.net/10379/5940
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An investigation into the photochemistry of, and the electrochemically induced CO-loss from, [(CO)5MC(OMe)Me](M = Cr or W) using low-temperature matrix isolation, picosecond infrared spectroscopy, cyclic voltammetry, and time-dependent density functional theory
(2015)
McMahon, Suzanne; Amirjalayer, Saeed; Buma, Wybren J.; Halpin, Yvonne; Long, Conor; Roo...
An investigation into the photochemistry of, and the electrochemically induced CO-loss from, [(CO)5MC(OMe)Me](M = Cr or W) using low-temperature matrix isolation, picosecond infrared spectroscopy, cyclic voltammetry, and time-dependent density functional theory
(2015)
McMahon, Suzanne; Amirjalayer, Saeed; Buma, Wybren J.; Halpin, Yvonne; Long, Conor; Rooney, A. Denise; Woutersenc, Sander; Pryce, Mary T.
Abstract:
The photophysics and photochemistry of [(CO)5MC(OMe)Me] (M = Cr or W) were investigated using picosecond time-resolved infrared spectroscopy (M = Cr or W), low-temperature matrix isolation techniques (M = Cr), and time-dependent density functional calculations (M = Cr or W). These studies provide unambiguous evidence for the photochemical formation of a long-lived, 18-electron metallaketene species capable of acting as a synthetically useful intermediate. For the Cr complex, an intermediate metallacyclopropanone singlet excited state was detected on the reaction path to the metallaketene species. This metallacyclopropanone excited state species has a lifetime of less than 100 ps and a characteristic bridging carbonyl band at 1770 cm−1. The tungsten ketene species was also detected but in contrast to the chromium system, this forms directly from a low-lying triplet excited state. The electrochemical release of CO showed a greater efficiency for the chromium complex when compared to t...
http://eprints.maynoothuniversity.ie/7810/
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Phosphate Diester Cleavage, DNA Interaction and Cytotoxic Activity of a Bimetallic Bis(1,4,7-triazacyclononane) Zinc Complex
(2014)
Montagner, Diego; Gandin, Valentina; Marzano, Cristina; Erxleben, Andrea
Phosphate Diester Cleavage, DNA Interaction and Cytotoxic Activity of a Bimetallic Bis(1,4,7-triazacyclononane) Zinc Complex
(2014)
Montagner, Diego; Gandin, Valentina; Marzano, Cristina; Erxleben, Andrea
Abstract:
The dinuclear zinc complex [Zn2{bcmp(-H)}(μ-Cl)](ClO4)2· H2O {bcmp = 2,6-bis(1,4,7-triazacyclonon-1-ylmethyl)-4- methylphenol} has been synthesized and structurally characterized. The DNA binding affinity was assessed by ethidium bromide fluorescence quenching experiments. The complex relaxes supercoiled pUC19 DNA into the nicked form at low micromolar concentration. Mechanistic studies were carried out using the DNA and RNA models bis(2,4-dinitrophenyl) phosphate (BDNPP) and 2-hydroxypropyl p-nitrophenyl phosphate (HPNP). A detailed kinetic analysis suggested that the bridging OH group of the solution species [Zn2{bcmp(-H)}(μ-OH)]2+ acts as the nucleophile in the hydrolysis of BDNPP, while in the case of HPNP, the bridging OH group acts as a general base and seems to shift to a terminal position upon substrate coordination. Finally, the cytotoxicity profile of the dinuclear zinc(II) complex was assessed. The complex showed promising in vitro antitumour activity against pancreatic a...
http://eprints.maynoothuniversity.ie/7816/
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