Mixed ligand complexation of some transition metal ions in solution and solid state: Spectral characterization, antimicrobial, antioxidant, DNA cleavage activities and molecular modeling

NASA Astrophysics Data System (ADS)

Shobana, Sutha; Dharmaraja, Jeyaprakash; Selvaraj, Shanmugaperumal

2013-04-01

Equilibrium studies of Ni(II), Cu(II) and Zn(II) mixed ligand complexes involving a primary ligand 5-fluorouracil (5-FU; A) and imidazoles viz., imidazole (him), benzimidazole (bim), histamine (hist) and L-histidine (his) as co-ligands(B) were carried out pH-metrically in aqueous medium at 310 ± 0.1 K with I = 0.15 M (NaClO4). In solution state, the stoichiometry of MABH, MAB and MAB2 species have been detected. The primary ligand(A) binds the central M(II) ions in a monodentate manner whereas him, bim, hist and his co-ligands(B) bind in mono, mono, bi and tridentate modes respectively. The calculated Δ log K, log X and log X' values indicate higher stability of the mixed ligand complexes in comparison to binary species. Stability of the mixed ligand complex equilibria follows the Irving-Williams order of stability. In vitro biological evaluations of the free ligand(A) and their metal complexes by well diffusion technique show moderate activities against common bacterial and fungal strains. Oxidative cleavage interaction of ligand(A) and their copper complexes with CT DNA is also studied by gel electrophoresis method in the presence of oxidant. In vitro antioxidant evaluations of the primary ligand(A), CuA and CuAB complexes by DPPH free radical scavenging model were carried out. In solid, the MAB type of M(II)sbnd 5-FU(A)sbnd his(B) complexes were isolated and characterized by various physico-chemical and spectral techniques. Both the magnetic susceptibility and electronic spectral analysis suggest distorted octahedral geometry. Thermal studies on the synthesized mixed ligand complexes show loss of coordinated water molecule in the first step followed by decomposition of the organic residues subsequently. XRD and SEM analysis suggest that the microcrystalline nature and homogeneous morphology of MAB complexes. Further, the 3D molecular modeling and analysis for the mixed ligand MAB complexes have also been carried out.

Energy cascades, excited state dynamics, and photochemistry in cob(III)alamins and ferric porphyrins.

PubMed

Rury, Aaron S; Wiley, Theodore E; Sension, Roseanne J

2015-03-17

Porphyrins and the related chlorins and corrins contain a cyclic tetrapyrrole with the ability to coordinate an active metal center and to perform a variety of functions exploiting the oxidation state, reactivity, and axial ligation of the metal center. These compounds are used in optically activated applications ranging from light harvesting and energy conversion to medical therapeutics and photodynamic therapy to molecular electronics, spintronics, optoelectronic thin films, and optomagnetics. Cobalt containing corrin rings extend the range of applications through photolytic cleavage of a unique axial carbon-cobalt bond, permitting spatiotemporal control of drug delivery. The photochemistry and photophysics of cyclic tetrapyrroles are controlled by electronic relaxation dynamics including internal conversion and intersystem crossing. Typically the electronic excitation cascades through ring centered ππ* states, ligand to metal charge transfer (LMCT) states, metal to ligand charge transfer (MLCT) states, and metal centered states. Ultrafast transient absorption spectroscopy provides a powerful tool for the investigation of the electronic state dynamics in metal containing tetrapyrroles. The UV-visible spectrum is sensitive to the oxidation state, electronic configuration, spin state, and axial ligation of the central metal atom. Ultrashort broadband white light probes spanning the range from 270 to 800 nm, combined with tunable excitation pulses, permit the detailed unravelling of the time scales involved in the electronic energy cascade. State-of-the-art theoretical calculations provide additional insight required for precise assignment of the states. In this Account, we focus on recent ultrafast transient absorption studies of ferric porphyrins and corrin containing cob(III)alamins elucidating the electronic states responsible for ultrafast energy cascades, excited state dynamics, and the resulting photoreactivity or photostability of these compounds. Iron tetraphenyl porphyrin chloride (Fe((III))TPPCl) exhibits picosecond decay to a metal centered d → d* (4)T state. This state decays on a ca. 16 ps time scale in room temperature solution but persists for much longer in a cryogenic glass. The photoreactivity of the (4)T state may lead to novel future applications for these compounds. In contrast, the nonplanar cob(III)alamins contain two axial ligands to the central cobalt atom. The upper axial ligand can be an alkyl group as in the two biologically active coenzymes or a nonalkyl ligand such as -CN in cyanocobalamin (vitamin B12) or -OH in hydroxocobalamin. The electronic structure, energy cascade, and bond cleavage of these compounds is sensitive to the details of the axial ligand. Nonalkylcobalamins exhibit ultrafast internal conversion to a low-lying state of metal to ligand or ligand to metal charge transfer character. The compounds are generally photostable with ground state recovery complete on a time scale of 2-7 ps in room temperature aqueous solution. Alkylcobalamins exhibit ultrafast internal conversion to an S1 state of d/π → π* character. Most compounds undergo bond cleavage from this state with near unit quantum yield within ∼100 ps. Recent theoretical calculations provide a potential energy surface accounting for these observations. Conformation dependent mixing of the corrin π and cobalt d orbitals plays a significant role in the observed photochemistry and photophysics.

Chiral allene-containing phosphines in asymmetric catalysis

PubMed Central

Cai, Feng; Pu, Xiaotao; Qi, Xiangbing; Lynch, Vincent; Radha, Akella; Ready, Joseph M.

2011-01-01

Traditionally, ligands used in asymmetric catalysis have contained either stereogenic atoms or hindered single bonds (atropisomerism), or both. Here we demonstrate that allenes, chiral 1,2-dienes, appended with basic functionality can serve as ligands for transition metals. We describe an allene-containing bisphosphine that, when coordinated to Rh(I), promotes the asymmetric addition of aryl boronic acids to α-keto esters with high enantioselectivity. Solution and solid-state structural analysis reveals that one olefin of the allene can coordinate to transition metals generating bi- and tri-dentate ligands. PMID:21972824

Hybrid organic-inorganic inks flatten the energy landscape in colloidal quantum dot solids.

PubMed

Liu, Mengxia; Voznyy, Oleksandr; Sabatini, Randy; García de Arquer, F Pelayo; Munir, Rahim; Balawi, Ahmed Hesham; Lan, Xinzheng; Fan, Fengjia; Walters, Grant; Kirmani, Ahmad R; Hoogland, Sjoerd; Laquai, Frédéric; Amassian, Aram; Sargent, Edward H

2017-02-01

Bandtail states in disordered semiconductor materials result in losses in open-circuit voltage (V oc ) and inhibit carrier transport in photovoltaics. For colloidal quantum dot (CQD) films that promise low-cost, large-area, air-stable photovoltaics, bandtails are determined by CQD synthetic polydispersity and inhomogeneous aggregation during the ligand-exchange process. Here we introduce a new method for the synthesis of solution-phase ligand-exchanged CQD inks that enable a flat energy landscape and an advantageously high packing density. In the solid state, these materials exhibit a sharper bandtail and reduced energy funnelling compared with the previous best CQD thin films for photovoltaics. Consequently, we demonstrate solar cells with higher V oc and more efficient charge injection into the electron acceptor, allowing the use of a closer-to-optimum bandgap to absorb more light. These enable the fabrication of CQD solar cells made via a solution-phase ligand exchange, with a certified power conversion efficiency of 11.28%. The devices are stable when stored in air, unencapsulated, for over 1,000 h.

Ultrafast photochemistry of polyatomic molecules containing labile halogen atoms in solution

NASA Astrophysics Data System (ADS)

Mereshchenko, Andrey S.

Because breaking and making of chemical bonds lies at the heart of chemistry, this thesis focuses on dynamic studies of labile molecules in solutions using ultrafast transient absorption spectroscopy. Specifically, my interest is two-fold: (i) novel reaction intermediates of polyhalogenated carbon, boron and phosphorus compounds; (ii) photophysics and photochemistry of labile copper(II) halide complexes. Excitation of CH2Br2, CHBr3, BBr 3, and PBr3 into n(Br)sigma*(X-Br) states, where X=C, B, or P, leads to direct photoisomerization with formation of isomers having Br-Br bonds as well as rupture of one of X-Br bonds with the formation of a Br atom and a polyatomic radical fragment, which subsequently recombine to form similar isomer products. Nonpolar solvation stabilizes the isomers, consistent with intrinsic reaction coordinate calculations of the isomer ground state potential energy surfaces at the density functional level of theory, and consequently, the involvement of these highly energetic species on chemically-relevant time scales needs to be taken into account. Monochlorocomplexes in methanol solutions promoted to the ligand-to-metal charge transfer (LMCT) excited state predominantly undergo internal conversion via back electron transfer, giving rise to vibrationally hot ground-state parent complexes. Copper-chloride homolitical bond dissociation yielding the solvated copper(I) and Cl- atom/solvent CT complexes constitutes a minor pathway. Insights into ligand substitution mechanisms were acquired by monitoring the recovery of monochloro complexes at the expense of two unexcited dichloro- and unsubstituted forms of Cu(II) complexes also present in the solution. Detailed description of ultrafast excited-state dynamics of CuCl 42- complexes in acetonitrile upon excitation into all possible Ligand Field (LF) excited states and two most intense LMCT transitions is reported. The LF states were found to be nonreactive with lifetimes remarkably longer than those for copper(II) complexes studied so far, in particular, copper blue proteins. The highest 2A1 and lowest 2E LF states relax directly to the ground electronic state whereas the intermediate 2B1 LF state relaxes stepwise through the 2E state. The LMCT excited states are short-lived undergoing either ionic dissociation (CuCl3- + Cl-) or cascading relaxation through the manifold of vibrationally hot LF states to the ground state.

Synthesis and fluorescence properties of some difluoroboron β-diketonate complexes and composite containing PMMA

NASA Astrophysics Data System (ADS)

Xing, Dongye; Hou, Yanjun; Niu, Haijun

2018-03-01

A series of difluoroboron β-diketonate complexes, containing the indon-β-diketonate ligand carrying methyl or methoxyl substituents was synthesized. The crystal structures of the complexes were confirmed by single crystal X-ray diffraction studies. The fluorescence properties of compounds were studied in solution state, solid state and on PMMA polymer matrix. The photophysical data of compounds 2a-2d exhibited strong fluorescence and photostability under the ultraviolet light (Hg lamp). The complex 2b showed higher fluorescence intensity in solution state as compared to other complexes of the series. The complexes 2c and 2d showed higher fluorescence intensity in the solid state, which are ascribed to the stronger π-π interactions between ligands in the solid state. The introduction of methoxyl or methyl groups on the benzene rings enhanced the absorption intensity, emission intensity, quantum yields and fluorescence lifetimes due to their electron-donating nature. Furthermore, the complex 2b was doped into the PMMA to produce hybrid materials, where the PMMA matrix acted as sensitizer for the central boron ion to enhance the fluorescence emission intensity and quantum yields.

Palladium complexes with simple iminopyridines as catalysts for polyketone synthesis.

PubMed

Rosar, V; Dedeic, D; Nobile, T; Fini, F; Balducci, G; Alessio, E; Carfagna, C; Milani, B

2016-10-07

Four iminopyridines (N-N') differing in the nature of the substituents on the iminic carbon and on the ortho positions of the aryl ring (H or CH3) on the iminic nitrogen were used for the synthesis of neutral and monocationic palladium(ii) complexes of general formulae [Pd(CH3)Cl(N-N')] and [Pd(CH3)(NCCH3)(N-N')][PF6]. The detailed NMR characterization in solution highlighted that: (i) for both series of complexes, the Pd-CH3 signal is progressively shifted to a lower frequency on increasing the number of methyl groups on the ligand skeleton; (ii) for the neutral derivatives, the chemical shift of the (15)N NMR signals, determined through {(1)H,(15)N}-HMBC spectra, is significantly affected by the coordination to palladium; (iii) the coordination induced shift (CIS) of the nitrogen atom trans to the CH3 ligand is smaller than the other. The structure in the solid state for the neutral derivatives with all the four ligands was solved, pointing out that: (iv) the Pd-C bond distance increases with the basicity of the nitrogen-donor ligand; (v) the Pd-N bond distance correlates well with the CIS value. The combining of the solution and solid state structural features allows stating that: (vi) the Pd-CH3 singlet is a good probe for the electron donor capability of the ligand; (vii) the CIS value might be used as a probe for the strength of the Pd-N bond. All monocationic complexes generated active catalysts for the CO/vinyl arene copolymerization, leading to prevailingly syndiotactic polyketones. The catalyst performances, both in terms of catalyst productivity and polymer molecular weight, correlate well with the precatalyst structural features.

On the interaction of luminol with human serum albumin: Nature and thermodynamics of ligand binding

NASA Astrophysics Data System (ADS)

Moyon, N. Shaemningwar; Mitra, Sivaprasad

2010-09-01

The mechanism and thermodynamic parameters for the binding of luminol (LH 2) with human serum albumin was explored by steady state and picosecond time-resolved fluorescence spectroscopy. It was shown that out of two possible LH 2 conformers present is solution, only one is accessible for binding with HSA. The thermodynamic parameters like enthalpy (Δ H) and entropy (Δ S) change corresponding to the ligand binding process were also estimated by performing the experiment at different temperatures. The ligand replacement experiment with bilirubin confirms that LH 2 binds into the sub-domain IIA of the protein.

Synthesis and reactivity of TADDOL-based chiral Fe(II) PNP pincer complexes-solution equilibria between κ(2)P,N- and κ(3)P,N,P-bound PNP pincer ligands.

PubMed

Holzhacker, Christian; Stöger, Berthold; Carvalho, Maria Deus; Ferreira, Liliana P; Pittenauer, Ernst; Allmaier, Günter; Veiros, Luis F; Realista, Sara; Gil, Adrià; Calhorda, Maria José; Müller, Danny; Kirchner, Karl

2015-08-07

Treatment of anhydrous FeX2 (X = Cl, Br) with 1 equiv. of the asymmetric chiral PNP pincer ligands PNP-R,TAD (R = iPr, tBu) with an R,R-TADDOL (TAD) moiety afforded complexes of the general formula [Fe(PNP)X2]. In the solid state these complexes adopt a tetrahedral geometry with the PNP ligand coordinated in κ(2)P,N-fashion, as shown by X-ray crystallography and Mössbauer spectroscopy. Magnetization studies led to a magnetic moment very close to 4.9μB reflecting the expected four unpaired d-electrons (quintet ground state). In solution there are equilibria between [Fe(κ(3)P,N,P-PNP-R,TAD)X2] and [Fe(κ(2)P,N-PNP-R,TAD)X2] complexes, i.e., the PNP-R,TAD ligand is hemilabile. At -50 °C these equilibria are slow and signals of the non-coordinated P-TAD arm of the κ(2)P,N-PNP-R,TAD ligand can be detected by (31)P{(1)H} NMR spectroscopy. Addition of BH3 to a solution of [Fe(PNP-iPr,TAD)Cl2] leads to selective boronation of the pendant P-TAD arm shifting the equilibrium towards the four-coordinate complex [Fe(κ(2)P,N-PNP-iPr,TAD(BH3))Cl2]. DFT calculations corroborate the existence of equilibria between four- and five-coordinated complexes. Addition of CO to [Fe(PNP-iPr,TAD)X2] in solution yields the diamagnetic octahedral complexes trans-[Fe(κ(3)P,N,P-PNP-iPr,TAD)(CO)X2], which react further with Ag(+) salts in the presence of CO to give the cationic complexes trans-[Fe(κ(3)P,N,P-PNP-iPr,TAD)(CO)2X](+). CO addition most likely takes place at the five coordinate complex [Fe(κ(3)P,N,P-PNP-iPr,TAD)X2]. The mechanism for the CO addition was also investigated by DFT and the most favorable path obtained corresponds to the rearrangement of the pincer ligand first from a κ(2)P,N- to a κ(3)P,N,P-coordination mode followed by CO coordination to [Fe(κ(3)P,N,P-PNP-iPr,TAD)X2]. Complexes bearing tBu substituents do not react with CO. Moreover, in the solid state none of the tetrahedral complexes are able to bind CO.

Synthesis, characterization, and photophysical properties of a thiophene-functionalized bis(pyrazolyl) pyridine (BPP) tricarbonyl rhenium(I) complex.

PubMed

Lytwak, Lauren A; Stanley, Julie M; Mejía, Michelle L; Holliday, Bradley J

2010-09-07

A bromo tricarbonyl rhenium(I) complex with a thiophene-functionalized bis(pyrazolyl) pyridine ligand (L), ReBr(L)(CO)(3) (1), has been synthesized and characterized by variable temperature and COSY 2-D (1)H NMR spectroscopy, single-crystal X-ray diffraction, and photophysical methods. Complex 1 is highly luminescent in both solution and solid-state, consistent with phosphorescence from an emissive (3)MLCT excited state with an additional contribution from a LC (3)(pi-->pi*) transition. The single-crystal X-ray diffraction structure of the title ligand is also reported.

Atomistic Description of Thiostannate-Capped CdSe Nanocrystals: Retention of Four-Coordinate SnS4 Motif and Preservation of Cd-Rich Stoichiometry

PubMed Central

2016-01-01

Colloidal semiconductor nanocrystals (NCs) are widely studied as building blocks for novel solid-state materials. Inorganic surface functionalization, used to displace native organic capping ligands from NC surfaces, has been a major enabler of electronic solid-state devices based on colloidal NCs. At the same time, very little is known about the atomistic details of the organic-to-inorganic ligand exchange and binding motifs at the NC surface, severely limiting further progress in designing all-inorganic NCs and NC solids. Taking thiostannates (K4SnS4, K4Sn2S6, K6Sn2S7) as typical examples of chalcogenidometallate ligands and oleate-capped CdSe NCs as a model NC system, in this study we address these questions through the combined application of solution 1H NMR spectroscopy, solution and solid-state 119Sn NMR spectroscopy, far-infrared and X-ray absorption spectroscopies, elemental analysis, and by DFT modeling. We show that through the X-type oleate-to-thiostannate ligand exchange, CdSe NCs retain their Cd-rich stoichiometry, with a stoichiometric CdSe core and surface Cd adatoms serving as binding sites for terminal S atoms of the thiostannates ligands, leading to all-inorganic (CdSe)core[Cdm(Sn2S7)yK(6y-2m)]shell (taking Sn2S76– ligand as an example). Thiostannates SnS44– and Sn2S76– retain (distorted) tetrahedral SnS4 geometry upon binding to NC surface. At the same time, experiments and simulations point to lower stability of Sn2S64– (and SnS32–) in most solvents and its lower adaptability to the NC surface caused by rigid Sn2S2 rings. PMID:25597625

Electrogenerated chemiluminescence. 58. Ligand-sensitized electrogenerated chemiluminescence in europium labels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Richter, M.M.; Bard, A.J.

The electrochemistry and electrogenerated chemiluminescence (ECL) of a series of europium chelates, cryptates, and mixed-ligand chelate/cryptand complexes were studied. The complexes were of the following general forms: EuL{sub 4}{sup -}, where L = {beta}-diketonate, a bis-chelating ligand (such as dibenzoylmethide), added as salts (A)EuL{sub 4}, where A= tetrabutylammonium ion or piperidinium ion (pipH{sup +}); Eu(crypt){sup 3+}, where crypt = a cryptand ligand, e.g., 4,7,13,16,21-pentaoxa-1,10-diazabicyclo[8,8,5]-tricosa ne; and Eu(crypt)(L){sup 2+} for the mixed-ligand systems. ECL was obtained for the chelates and mixed-ligand systems by reducing the complexes at a Pt electrode in the presence of peroxydisulfate in acetonitrile solutions and was attributedmore » to the electron-transfer reaction between the reduced bound ligands and SO{sub 4}{sup .-}, followed by intramolecular excitation transfer from the excited ligand orbitals to the metal-centered 4f states. No ECL was observed under the same conditions for the europium complexes incorporating only the cryptand ligands in aqueous solution. The ECL spectra matched the photoluminescence spectra with a narrow emission band observed at 612 nm, corresponding to a metal-centered 4f-4f transition. The ECL efficiencies for the ECL-active species were low, about 10{sup -1}-10{sup -4}% of that of the Ru-(bpy){sub 3}{sup 2+}/S{sub 2}O{sub 8}{sup 2-} system under similar conditions. 38 refs., 6 figs., 2 tabs.« less

Molecular and electronic structures of mononuclear iron complexes using strongly electron-donating ligands and their oxidized forms.

PubMed

Strautmann, Julia B H; George, Serena DeBeer; Bothe, Eberhard; Bill, Eckhard; Weyhermüller, Thomas; Stammler, Anja; Bögge, Hartmut; Glaser, Thorsten

2008-08-04

The ligand L (2-) (H 2L = N, N'-dimethyl- N, N'-bis(3,5-di- t-butyl-2-hydroxybenzyl)-1,2-diaminoethane) has been employed for the synthesis of two mononuclear Fe (III) complexes, namely, [LFe(eta (2)-NO 3)] and [LFeCl]. L (2-) is comprised of four strongly electron-donating groups (two tert-amines and two phenolates) that increase the electron density at the coordinated ferric ions. This property should facilitate oxidation of the complexes, that is, stabilization of the oxidized species. The molecular structures in the solid state have been established by X-ray diffraction studies. [LFeCl] is five-coordinate in a square-pyramidal coordination environment with the ligand adopting a trans-conformation, while [LFe(eta (2)-NO 3)] is six-coordinate in a distorted octahedral environment with the ligand in a beta-cis conformation. The electronic structures have been studied using magnetization, EPR, Mossbauer (with and without applied field), UV-vis-NIR, and X-ray absorption spectroscopies, which demonstrate highly anisotropic covalency from the strong sigma- and pi-donating phenolates. This analysis is supported by DFT calculations on [LFeCl]. The variations of the well-understood spectroscopic data in the solid state to the spectroscopic data in solution have been used to obtain insight in the molecular structure of the two complexes in solution. While the molecular structures of the solid states are retained in solutions of nonpolar aprotic solvents, there is, however, one common molecular structure in all protic polar solvents. The analysis of the LMCT transitions and the rhombicity E/ D clearly establish that both compounds exhibit a beta-cis conformation in these protic polar solvents. These two open coordination sites, cis to each other, allow access for two potential ligands in close proximity. Electrochemical analysis establishes two reversible oxidation waves for [LFeCl] at +0.55 V and +0.93 V vs Fc (+)/Fc and one reversible oxidation wave at +0.59 V with an irreversible oxidation at +1.07 V vs Fc (+)/Fc for [LFe(eta (2)-NO 3)]. The one- and the two-electron oxidations of [LFeCl] by chronoamperometry have been followed spectroscopically. The increase of a strong band centered at 420 nm indicates the formulation of [LFeCl] (+) as a Fe (III) monophenoxyl radical complex and of [LFeCl] (2+) as a Fe (III) bisphenoxyl radical complex. These studies imply that the ligand L (2-) is capable of providing a flexible coordination geometry with two binding sites for substrates and the allocation of two oxidation equivalents on the ligand.

Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software.

PubMed

Riniker, Sereina; Christ, Clara D; Hansen, Halvor S; Hünenberger, Philippe H; Oostenbrink, Chris; Steiner, Denise; van Gunsteren, Wilfred F

2011-11-24

The calculation of the relative free energies of ligand-protein binding, of solvation for different compounds, and of different conformational states of a polypeptide is of considerable interest in the design or selection of potential enzyme inhibitors. Since such processes in aqueous solution generally comprise energetic and entropic contributions from many molecular configurations, adequate sampling of the relevant parts of configurational space is required and can be achieved through molecular dynamics simulations. Various techniques to obtain converged ensemble averages and their implementation in the GROMOS software for biomolecular simulation are discussed, and examples of their application to biomolecules in aqueous solution are given. © 2011 American Chemical Society

Site-Selective Benzannulation of N-Heterocycles in Bidentate Ligands Leads to Blue-Shifted Emission from [( P^N)Cu]2(μ-X)2 Dimers.

PubMed

Mondal, Rajarshi; Lozada, Issiah B; Davis, Rebecca L; Williams, J A Gareth; Herbert, David E

2018-05-07

Benzannulated bidentate pyridine/phosphine ( P^N) ligands bearing quinoline or phenanthridine (3,4-benzoquinoline) units have been prepared, along with their halide-bridged, dimeric Cu(I) complexes of the form [( P^N)Cu] 2 (μ-X) 2 . The copper complexes are phosphorescent in the orange-red region of the spectrum in the solid-state under ambient conditions. Structural characterization in solution and the solid-state reveals a flexible conformational landscape, with both diamond-like and butterfly motifs available to the Cu 2 X 2 cores. Comparing the photophysical properties of complexes of (quinolinyl)phosphine ligands with those of π-extended (phenanthridinyl)phosphines has revealed a counterintuitive impact of site-selective benzannulation. Contrary to conventional assumptions regarding π-extension and a bathochromic shift in the lowest energy absorption maxima, a blue shift of nearly 40 nm in the emission wavelength is observed for the complexes with larger ligand π-systems, which is assigned as phosphorescence on the basis of emission energies and lifetimes. Comparison of the ground-state and triplet excited state structures optimized from DFT and TD-DFT calculations allows attribution of this effect to a greater rigidity for the benzannulated complexes resulting in a higher energy emissive triplet state, rather than significant perturbation of orbital energies. This study reveals that ligand structure can impact photophysical properties for emissive molecules by influencing their structural rigidity, in addition to their electronic structure.

Vanadium(IV/V) complexes of Triapine and related thiosemicarbazones: Synthesis, solution equilibrium and bioactivity.

PubMed

Kowol, Christian R; Nagy, Nóra V; Jakusch, Tamás; Roller, Alexander; Heffeter, Petra; Keppler, Bernhard K; Enyedy, Éva A

2015-11-01

The stoichiometry and thermodynamic stability of vanadium(IV/V) complexes of Triapine and two related α(N)-heterocyclic thiosemicarbazones (TSCs) with potential antitumor activity have been determined by pH-potentiometry, EPR and (51)V NMR spectroscopy in 30% (w/w) dimethyl sulfoxide/water solvent mixtures. In all cases, mono-ligand complexes in different protonation states were identified. Dimethylation of the terminal amino group resulted in the formation of vanadium(IV/V) complexes with considerably higher stability. Three of the most stable complexes were also synthesized in solid state and comprehensively characterized. The biological evaluation of the synthesized vanadium complexes in comparison to the metal-free ligands in different human cancer cell lines revealed only minimal influence of the metal ion. Thus, in addition the coordination ability of salicylaldehyde thiosemicarbazone (STSC) to vanadium(IV/V) ions was investigated. The exchange of the pyridine nitrogen of the α(N)-heterocyclic TSCs to a phenolate oxygen in STSC significantly increased the stability of the complexes in solution. Finally, this also resulted in increased cytotoxicity activity of a vanadium(V) complex of STSC compared to the metal-free ligand. Copyright © 2015 Elsevier Inc. All rights reserved.

Comparing alchemical and physical pathway methods for computing the absolute binding free energy of charged ligands.

PubMed

Deng, Nanjie; Cui, Di; Zhang, Bin W; Xia, Junchao; Cruz, Jeffrey; Levy, Ronald

2018-06-13

Accurately predicting absolute binding free energies of protein-ligand complexes is important as a fundamental problem in both computational biophysics and pharmaceutical discovery. Calculating binding free energies for charged ligands is generally considered to be challenging because of the strong electrostatic interactions between the ligand and its environment in aqueous solution. In this work, we compare the performance of the potential of mean force (PMF) method and the double decoupling method (DDM) for computing absolute binding free energies for charged ligands. We first clarify an unresolved issue concerning the explicit use of the binding site volume to define the complexed state in DDM together with the use of harmonic restraints. We also provide an alternative derivation for the formula for absolute binding free energy using the PMF approach. We use these formulas to compute the binding free energy of charged ligands at an allosteric site of HIV-1 integrase, which has emerged in recent years as a promising target for developing antiviral therapy. As compared with the experimental results, the absolute binding free energies obtained by using the PMF approach show unsigned errors of 1.5-3.4 kcal mol-1, which are somewhat better than the results from DDM (unsigned errors of 1.6-4.3 kcal mol-1) using the same amount of CPU time. According to the DDM decomposition of the binding free energy, the ligand binding appears to be dominated by nonpolar interactions despite the presence of very large and favorable intermolecular ligand-receptor electrostatic interactions, which are almost completely cancelled out by the equally large free energy cost of desolvation of the charged moiety of the ligands in solution. We discuss the relative strengths of computing absolute binding free energies using the alchemical and physical pathway methods.

Photochemistry of monodentate and bidentate carbonato complexes of rhodium (3). [applications to spacecraft fuel cells

NASA Technical Reports Server (NTRS)

Sheridan, P. S.

1980-01-01

A scheme for the photochemical fixation of water is proposed which involves a five-step reaction sequence; the first step involves the 2 electron reduction of a metal by a coordinated carbonate ligand, with corresponding oxidation of the carbonate to CO2 and O2. Ligand field photolysis of trans- (RH(en)2 H2O CO3) ClO4, and (Rh(en)2 CO3) CLO4 have been studied in the solid state and in aqueous solution at various pH values. Both salts are photoinert in the solid phase, but are quite photoreactive in aqueous solution. In solution, the monodentate ion undergoes efficient isomerization to a mixture of cis and trans - (Rh(en)2 H2O CO3)+, presumably with water exchange. A minor pH increase upon photolysis is evidence of inefficient carbonate (CO3 =) release, with formation of (Rh(en)2 (H2O)2)3+. In contrast, aqueous solutions of the bidentate carbonato complex undergo efficient pH decrease upon ligand field photolysis. Changes in the electronic spectrum (200-500 nm) and pH changes indicate that the desired redox is occurring. The pH increase is due to the aqueous behavior of CO2.

The use of amphipols for solution NMR studies of membrane proteins: advantages and constraints as compared to other solubilizing media.

PubMed

Planchard, Noelya; Point, Élodie; Dahmane, Tassadite; Giusti, Fabrice; Renault, Marie; Le Bon, Christel; Durand, Grégory; Milon, Alain; Guittet, Éric; Zoonens, Manuela; Popot, Jean-Luc; Catoire, Laurent J

2014-10-01

Solution-state nuclear magnetic resonance studies of membrane proteins are facilitated by the increased stability that trapping with amphipols confers to most of them as compared to detergent solutions. They have yielded information on the state of folding of the proteins, their areas of contact with the polymer, their dynamics, water accessibility, and the structure of protein-bound ligands. They benefit from the diversification of amphipol chemical structures and the availability of deuterated amphipols. The advantages and constraints of working with amphipols are discussed and compared to those associated with other non-conventional environments, such as bicelles and nanodiscs.

Metal-organic complexes in geochemical processes: Estimation of standard partial molal thermodynamic properties of aqueous complexes between metal cations and monovalent organic acid ligands at high pressures and temperatures

NASA Astrophysics Data System (ADS)

Shock, Everetr L.; Koretsky, Carla M.

1995-04-01

Regression of standard state equilibrium constants with the revised Helgeson-Kirkham-Flowers (HKF) equation of state allows evaluation of standard partial molal entropies ( overlineSo) of aqueous metal-organic complexes involving monovalent organic acid ligands. These values of overlineSo provide the basis for correlations that can be used, together with correlation algorithms among standard partial molal properties of aqueous complexes and equation-of-state parameters, to estimate thermodynamic properties including equilibrium constants for complexes between aqueous metals and several monovalent organic acid ligands at the elevated pressures and temperatures of many geochemical processes which involve aqueous solutions. Data, parameters, and estimates are given for 270 formate, propanoate, n-butanoate, n-pentanoate, glycolate, lactate, glycinate, and alanate complexes, and a consistent algorithm is provided for making other estimates. Standard partial molal entropies of association ( Δ -Sro) for metal-monovalent organic acid ligand complexes fall into at least two groups dependent upon the type of functional groups present in the ligand. It is shown that isothermal correlations among equilibrium constants for complex formation are consistent with one another and with similar correlations for inorganic metal-ligand complexes. Additional correlations allow estimates of standard partial molal Gibbs free energies of association at 25°C and 1 bar which can be used in cases where no experimentally derived values are available.

The role of ligand covalency in the selective activation of metalloenediynes for Bergman cyclization

PubMed Central

Porter, Meghan R.; Zaleski, Jeffrey M.

2017-01-01

One of the key concerns with the development of radical-generating reactive therapeutics is the ability to control the activation event within a biological environment. To that end, a series of quinoline-metal-loenediynes of the form M(QuiED)·2Cl (M = Cu(II), Fe(II), Mg(II), or Zn(II)) and their independently synthesized cyclized analogs have been prepared in an effort to elucidate Bergman cyclization (BC) reactivity differences in solution. HRMS(ESI) establishes a solution stoichiometry of 1:1 metal to ligand with coordination of one chloride counter ion to the metal center. EPR spectroscopy of Cu(QuiED)·2Cl and Cu (QuiBD)·2Cl denotes an axially-elongated tetragonal octahedron (g║ > g⊥ > 2.0023) with a dx2–y2 ground state, while the electronic absorption spectrum reveals a pπ Cl→Cu(II) LMCT feature at 19,000 cm −1, indicating a solution structure with three nitrogens and a chloride in the equatorial plane with the remaining quinoline nitrogen and solvent in the axial positions. Investigations into the BC activity reveal formation of the cyclized product from the Cu(II) and Fe(II) complexes after 12 h at 45 °C in solution, while no product is observed for the Mg(II) or Zn(II) complexes under identical conditions. The basis of this reactivity difference has been found to be a steric effect leading to metal–ligand bond elongation and thus, a retardation of solution reactivity. These results demonstrate how careful consideration of ligand and complex structure may allow for a degree of control and selective activation of these reactive agents. PMID:28931964

The role of ligand covalency in the selective activation of metalloenediynes for Bergman cyclization.

PubMed

Porter, Meghan R; Zaleski, Jeffrey M

2016-01-08

One of the key concerns with the development of radical-generating reactive therapeutics is the ability to control the activation event within a biological environment. To that end, a series of quinoline-metal-loenediynes of the form M( QuiED )·2Cl (M = Cu(II), Fe(II), Mg(II), or Zn(II)) and their independently synthesized cyclized analogs have been prepared in an effort to elucidate Bergman cyclization (BC) reactivity differences in solution. HRMS(ESI) establishes a solution stoichiometry of 1:1 metal to ligand with coordination of one chloride counter ion to the metal center. EPR spectroscopy of Cu( QuiED )·2Cl and Cu ( QuiBD )·2Cl denotes an axially-elongated tetragonal octahedron ( g ║ > g ⊥ > 2.0023) with a d x 2 - y 2 ground state, while the electronic absorption spectrum reveals a pπ Cl→Cu(II) LMCT feature at 19,000 cm -1 , indicating a solution structure with three nitrogens and a chloride in the equatorial plane with the remaining quinoline nitrogen and solvent in the axial positions. Investigations into the BC activity reveal formation of the cyclized product from the Cu(II) and Fe(II) complexes after 12 h at 45 °C in solution, while no product is observed for the Mg(II) or Zn(II) complexes under identical conditions. The basis of this reactivity difference has been found to be a steric effect leading to metal-ligand bond elongation and thus, a retardation of solution reactivity. These results demonstrate how careful consideration of ligand and complex structure may allow for a degree of control and selective activation of these reactive agents.

Solution XAS Analysis for Exploring the Active Species in Homogeneous Vanadium Complex Catalysis

NASA Astrophysics Data System (ADS)

Nomura, Kotohiro; Mitsudome, Takato; Tsutsumi, Ken; Yamazoe, Seiji

2018-06-01

Selected examples in V K-edge X-ray Absorption Near Edge Structure (XANES) analysis of a series of vanadium complexes containing imido ligands (possessing metal-nitrogen double bond) in toluene solution have been introduced, and their pre-edge and the edge were affected by their structures and nature of ligands. Selected results in exploring the oxidation states of the active species in ethylene dimerization/polymerization using homogeneous vanadium catalysts [consisting of (imido)vanadium(V) complexes and Al cocatalysts] by X-ray absorption spectroscopy (XAS) analyses have been introduced. It has been demonstrated that the method should provide more clear information concerning the active species in situ, especially by combination with the other methods (NMR and ESR spectra, X-ray crystallographic analysis, and reaction chemistry), and should be powerful tool for study of catalysis mechanism as well as for the structural analysis in solution.

Conserved conformational selection mechanism of Hsp70 chaperone-substrate interactions

PubMed Central

Velyvis, Algirdas; Zoltsman, Guy; Rosenzweig, Rina; Bouvignies, Guillaume

2018-01-01

Molecular recognition is integral to biological function and frequently involves preferred binding of a molecule to one of several exchanging ligand conformations in solution. In such a process the bound structure can be selected from the ensemble of interconverting ligands a priori (conformational selection, CS) or may form once the ligand is bound (induced fit, IF). Here we focus on the ubiquitous and conserved Hsp70 chaperone which oversees the integrity of the cellular proteome through its ATP-dependent interaction with client proteins. We directly quantify the flux along CS and IF pathways using solution NMR spectroscopy that exploits a methyl TROSY effect and selective isotope-labeling methodologies. Our measurements establish that both bacterial and human Hsp70 chaperones interact with clients by selecting the unfolded state from a pre-existing array of interconverting structures, suggesting a conserved mode of client recognition among Hsp70s and highlighting the importance of molecular dynamics in this recognition event. PMID:29460778

Magnetic Levitation as a Platform for Competitive Protein-Ligand Binding Assays

PubMed Central

Shapiro, Nathan D.; Soh, Siowling; Mirica, Katherine A.; Whitesides, George M.

2012-01-01

This paper describes a method based on magnetic levitation (MagLev) that is capable of indirectly measuring the binding of unlabeled ligands to unlabeled protein. We demonstrate this method by measuring the affinity of unlabeled bovine carbonic anhydrase (BCA) for a variety of ligands (most of which are benzene sulfonamide derivatives). This method utilizes porous gel beads that are functionalized with a common aryl sulfonamide ligand. The beads are incubated with BCA and allowed to reach an equilibrium state in which the majority of the immobilized ligands are bound to BCA. Since the beads are less dense than the protein, protein binding to the bead increases the overall density of the bead. This change in density can be monitored using MagLev. Transferring the beads to a solution containing no protein creates a situation where net protein efflux from the bead is thermodynamically favorable. The rate at which protein leaves the bead for the solution can be calculated from the rate at which the levitation height of the bead changes. If another small molecule ligand of BCA is dissolved in the solution, the rate of protein efflux is accelerated significantly. This paper develops a reaction-diffusion (RD) model to explain both this observation, and the physical-organic chemistry that underlies it. Using this model, we calculate the dissociation constants of several unlabeled ligands from BCA, using plots of levitation height versus time. Notably, although this method requires no electricity, and only a single piece of inexpensive equipment, it can measure accurately the binding of unlabeled proteins to small molecules over a wide range of dissociation constants (Kd’s within the range of ~ 10 nM to 100 µM are measured easily). Assays performed using this method generally can be completed within a relatively short time period (20 minutes – 2 hours). A deficiency of this system is that it is not, in its present form, applicable to proteins with molecular weight greater than approximately 65 kDa. PMID:22686324

Magnetic levitation as a platform for competitive protein-ligand binding assays.

PubMed

Shapiro, Nathan D; Soh, Siowling; Mirica, Katherine A; Whitesides, George M

2012-07-17

This paper describes a method based on magnetic levitation (MagLev) that is capable of indirectly measuring the binding of unlabeled ligands to unlabeled protein. We demonstrate this method by measuring the affinity of unlabeled bovine carbonic anhydrase (BCA) for a variety of ligands (most of which are benzene sulfonamide derivatives). This method utilizes porous gel beads that are functionalized with a common aryl sulfonamide ligand. The beads are incubated with BCA and allowed to reach an equilibrium state in which the majority of the immobilized ligands are bound to BCA. Since the beads are less dense than the protein, protein binding to the bead increases the overall density of the bead. This change in density can be monitored using MagLev. Transferring the beads to a solution containing no protein creates a situation where net protein efflux from the bead is thermodynamically favorable. The rate at which protein leaves the bead for the solution can be calculated from the rate at which the levitation height of the bead changes. If another small molecule ligand of BCA is dissolved in the solution, the rate of protein efflux is accelerated significantly. This paper develops a reaction-diffusion (RD) model to explain both this observation, and the physical-organic chemistry that underlies it. Using this model, we calculate the dissociation constants of several unlabeled ligands from BCA, using plots of levitation height versus time. Notably, although this method requires no electricity, and only a single piece of inexpensive equipment, it can measure accurately the binding of unlabeled proteins to small molecules over a wide range of dissociation constants (K(d) values within the range from ~10 nM to 100 μM are measured easily). Assays performed using this method generally can be completed within a relatively short time period (20 min-2 h). A deficiency of this system is that it is not, in its present form, applicable to proteins with molecular weight greater than approximately 65 kDa.

Ligand manipulation of charge transfer excited state relaxation and spin crossover in [Fe(2,2'-bipyridine) 2(CN) 2

DOE PAGES

Kjaer, Kasper S.; Zhang, Wenkai; Alonso-Mori, Roberto; ...

2017-07-06

Here, we have used femtosecond resolution UV-visible and Kβ x-ray emission spectroscopy to characterize the electronic excited state dynamics of [Fe(bpy) 2(CN) 2], where bpy=2,2'-bipyridine, initiated by metal-to-ligand charge transfer (MLCT) excitation. The excited-state absorption in the transient UV-visible spectra, associated with the 2,2'-bipyridine radical anion, provides a robust marker for the MLCT excited state, while the transient Kβ x-ray emission spectra provide a clear measure of intermediate and high spin metal-centered excited states. From these measurements, we conclude that the MLCT state of [Fe(bpy) 2(CN) 2] undergoes ultrafast spin crossover to a metal-centered quintet excited state through a shortmore » lived metal-centered triplet transient species. These measurements of [Fe(bpy) 2(CN) 2] complement prior measurement performed on [Fe(bpy) 3] 2+ and [Fe(bpy)(CN) 4] 2– in dimethylsulfoxide solution and help complete the chemical series [Fe(bpy) N(CN) 6–2N] 2N-4, where N = 1–3. The measurements confirm that simple ligand modifications can significantly change the relaxation pathways and excited state lifetimes and support the further investigation of light harvesting and photocatalytic applications of 3 d transition metal complexes.« less

Ligand manipulation of charge transfer excited state relaxation and spin crossover in [Fe(2,2'-bipyridine) 2(CN) 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kjaer, Kasper S.; Zhang, Wenkai; Alonso-Mori, Roberto

Here, we have used femtosecond resolution UV-visible and Kβ x-ray emission spectroscopy to characterize the electronic excited state dynamics of [Fe(bpy) 2(CN) 2], where bpy=2,2'-bipyridine, initiated by metal-to-ligand charge transfer (MLCT) excitation. The excited-state absorption in the transient UV-visible spectra, associated with the 2,2'-bipyridine radical anion, provides a robust marker for the MLCT excited state, while the transient Kβ x-ray emission spectra provide a clear measure of intermediate and high spin metal-centered excited states. From these measurements, we conclude that the MLCT state of [Fe(bpy) 2(CN) 2] undergoes ultrafast spin crossover to a metal-centered quintet excited state through a shortmore » lived metal-centered triplet transient species. These measurements of [Fe(bpy) 2(CN) 2] complement prior measurement performed on [Fe(bpy) 3] 2+ and [Fe(bpy)(CN) 4] 2– in dimethylsulfoxide solution and help complete the chemical series [Fe(bpy) N(CN) 6–2N] 2N-4, where N = 1–3. The measurements confirm that simple ligand modifications can significantly change the relaxation pathways and excited state lifetimes and support the further investigation of light harvesting and photocatalytic applications of 3 d transition metal complexes.« less

Ligand manipulation of charge transfer excited state relaxation and spin crossover in [Fe(2,2′-bipyridine)2(CN)2

PubMed Central

Kjær, Kasper S.; Zhang, Wenkai; Alonso-Mori, Roberto; Bergmann, Uwe; Chollet, Matthieu; Hadt, Ryan G.; Hartsock, Robert W.; Harlang, Tobias; Kroll, Thomas; Kubiček, Katharina; Lemke, Henrik T.; Liang, Huiyang W.; Liu, Yizhu; Nielsen, Martin M.; Robinson, Joseph S.; Solomon, Edward I.; Sokaras, Dimosthenis; van Driel, Tim B.; Weng, Tsu-Chien; Zhu, Diling; Persson, Petter; Wärnmark, Kenneth; Sundström, Villy; Gaffney, Kelly J.

2017-01-01

We have used femtosecond resolution UV-visible and Kβ x-ray emission spectroscopy to characterize the electronic excited state dynamics of [Fe(bpy)2(CN)2], where bpy=2,2′-bipyridine, initiated by metal-to-ligand charge transfer (MLCT) excitation. The excited-state absorption in the transient UV-visible spectra, associated with the 2,2′-bipyridine radical anion, provides a robust marker for the MLCT excited state, while the transient Kβ x-ray emission spectra provide a clear measure of intermediate and high spin metal-centered excited states. From these measurements, we conclude that the MLCT state of [Fe(bpy)2(CN)2] undergoes ultrafast spin crossover to a metal-centered quintet excited state through a short lived metal-centered triplet transient species. These measurements of [Fe(bpy)2(CN)2] complement prior measurement performed on [Fe(bpy)3]2+ and [Fe(bpy)(CN)4]2− in dimethylsulfoxide solution and help complete the chemical series [Fe(bpy)N(CN)6–2N]2N-4, where N = 1–3. The measurements confirm that simple ligand modifications can significantly change the relaxation pathways and excited state lifetimes and support the further investigation of light harvesting and photocatalytic applications of 3d transition metal complexes. PMID:28653021

Painting proteins with covalent labels: what's in the picture?

PubMed

Fitzgerald, Michael C; West, Graham M

2009-06-01

Knowledge about the structural and biophysical properties of proteins when they are free in solution and/or in complexes with other molecules is essential for understanding the biological processes that proteins regulate. Such knowledge is also important to drug discovery efforts, particularly those focused on the development of therapeutic agents with protein targets. In the last decade a variety of different covalent labeling techniques have been used in combination with mass spectrometry to probe the solution-phase structures and biophysical properties of proteins and protein-ligand complexes. Highlighted here are five different mass spectrometry-based covalent labeling strategies including: continuous hydrogen/deuterium (H/D) exchange labeling, hydroxyl radical-mediated footprinting, SUPREX (stability of unpurified proteins from rates of H/D exchange), PLIMSTEX (protein-ligand interaction by mass spectrometry, titration, and H/D exchange), and SPROX (stability of proteins from rates of oxidation). The basic experimental protocols used in each of the above-cited methods are summarized along with the kind of biophysical information they generate. Also discussed are the relative strengths and weaknesses of the different methods for probing the wide range of conformational states that proteins and protein-ligand complexes can adopt when they are in solution.

Butterfly deformation modes in a photoexcited pyrazolate-bridged Pt complex measured by time-resolved x-ray scattering in solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haldrup, Kristoffer; Dohn, Asmus O.; Shelby, Megan L.

2016-08-27

Pyrazolate-bridged di-nuclear Pt complexes represent a series of molecules with tunable absorption and emission properties that can be directly modulated by structural factors, such as the Pt-Pt distance. However, direct experimental information regarding the structure of the emissive triplet excited state has remained scarce. Using time-resolved wide angle X-ray scattering (WAXS), the molecular structure of the triplet excited state for one of the complexes [Pt(ppy)(μ-tBu 2pz)] 2 was obtained in a dilute (0.5 mM) toluene solution utilizing the monochromatic X-ray beamline 11IDD of the Advanced Photon Source. The excited state structural analysis was carried out based on the results frommore » both transient WAXS measurements and DFT calculations to shed light on the primary structural changes, in particular the Pt-Pt distance and ligand rotation taking place following the photo-excitation of [Pt(ppy)(μ-tBu 2pz)] 2 in toluene solution. We find that in the triplet excited state a pronounced contraction along the Pt-Pt axis has taken place accompanied by rotational motions of ppy ligands toward one another. Our results suggest that the contraction is larger than what has previously been reported, but are in good agreement with recent theoretical efforts and suggest the ppy moieties as targets for rational synthesis aimed at tuning the excited-state structure and properties« less

Multiligand Metal-Phenolic Assembly from Green Tea Infusions.

PubMed

Rahim, Md Arifur; Björnmalm, Mattias; Bertleff-Zieschang, Nadja; Ju, Yi; Mettu, Srinivas; Leeming, Michael G; Caruso, Frank

2018-03-07

The synthesis of hybrid functional materials using the coordination-driven assembly of metal-phenolic networks (MPNs) is of interest in diverse areas of materials science. To date, MPN assembly has been explored as monoligand systems (i.e., containing a single type of phenolic ligand) where the phenolic components are primarily obtained from natural sources via extraction, isolation, and purification processes. Herein, we demonstrate the fabrication of MPNs from a readily available, crude phenolic source-green tea (GT) infusions. We employ our recently introduced rust-mediated continuous assembly strategy to prepare these GT MPN systems. The resulting hollow MPN capsules contain multiple phenolic ligands and have a shell thickness that can be controlled through the reaction time. These multiligand MPN systems have different properties compared to the analogous MPN systems reported previously. For example, the Young's modulus (as determined using colloidal-probe atomic force microscopy) of the GT MPN system presented herein is less than half that of MPN systems prepared using tannic acid and iron salt solutions, and the disassembly kinetics are faster (∼50%) than other, comparable MPN systems under identical disassembly conditions. Additionally, the use of rust-mediated assembly enables the formation of stable capsules under conditions where the conventional approach (i.e., using iron salt solutions) results in colloidally unstable dispersions. These differences highlight how the choice of phenolic ligand and its source, as well as the assembly protocol (e.g., using solution-based or solid-state iron sources), can be used to tune the properties of MPNs. The strategy presented herein expands the toolbox of MPN assembly while also providing new insights into the nature and robustness of metal-phenolic interfacial assembly when using solution-based or solid-state metal sources.

Structural direction of hybrid organic-inorganic materials: Synthesis of vanadium oxyfluoride, copper vanadate, and copper molybdate solid state materials through solvuthermal and solution methods

NASA Astrophysics Data System (ADS)

Deburgomaster, Paul

The vast structural complexity of inorganic oxides with structure directing organocations, nitrogen containing ligands and organophosphonate ligands was explored. The hydrothermal reaction conditions utilized herein include the variables of temperature, pH, fill volume and stoichiometry. The systems studied included: (1) the complex materials rendered from reactions of organoamine cations on the structure of vanadium oxides, oxyfluorides and fluorides. As with other systems, the influence of the mineralizer HF was not limited to pH as fluorine incorporation was not uncommon. In specific cases this coincided with reduction of vanadium sites. (2) The copper-organonitrogen ligand/vanadium oxide/aromatic phosphonate system has been studied. The rigid aromatic di- and tri-phosphonate tethers have provided a series of materials which are structurally distinct from the previously investigated aliphatic series. The inclusion of copper-coordinated nitrogen bi- and tri-dentate ligands also provided structural diversity. Product composition was highly influenced by the HF/V ratio. A similar study was conducted with the ligand 1,4-carboxy-phenylphosphonic acid. (3) The preparation of a series of bimetallic organic-inorganic hybrid materials of the M(II)/VxOy/organonitrogen ligand class was further evidence of the utility of thermodynamically driven hydrothermal synthesis. (4) While decomposition of the spherical Keplerate molybdenum clusters is encountered under hydrothermal conditions, this highly soluble form of molybdate was investigated for the development of hybrid organic-inorganic room temperature solution synthesis.

Photooxidation of Diimine Dithiolate Platinium(II) Complexes Induced by Charge Transfer to Diimine Excitation.

PubMed

Zhang, Yin; Ley, Kevin D.; Schanze, Kirk S.

1996-11-20

A photochemical and photophysical investigation was carried out on (tbubpy)Pt(II)(dpdt) and (tbubpy)Pt(II)(edt) (1 and 2, respectively, where tbubpy = 4,4'-di-tert-butyl-2,2'-bipyridine, dpdt = meso-1,2-diphenyl-1,2-ethanedithiolate and edt = 1,2-ethanedithiolate). Luminescence and transient absorption studies reveal that these complexes feature a lowest excited state with Pt(S)(2) --> tbubpy charge transfer to diimine character. Both complexes are photostable in deoxygenated solution; however, photolysis into the visible charge transfer band in air-saturated solution induces moderately efficient photooxidation. Photooxidation of 1 produces the dehydrogenation product (tbubpy)Pt(II)(1,2-diphenyl-1,2-ethenedithiolate) (4). By contrast, photooxidation of 2 produces S-oxygenated complexes in which one or both thiolate ligands are converted to sulfinate (-SO(2)R) ligands. Mechanistic photochemical studies and transient absorption spectroscopy reveal that photooxidation occurs by (1) energy transfer from the charge transfer to diimine excited state of 1 to (3)O(2) to produce (1)O(2) and (2) reaction between (1)O(2) and the ground state 1. Kinetic data indicates that excited state 1 produces (1)O(2) efficiently and that reaction between ground state 1 and (1)O(2) occurs with k approximately 3 x 10(8) M(-)(1) s(-)(1).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neu, Mary Patricia

The coordination chemistry and solution behavior of the toxic ions lead(II) and plutonium(IV, V, VI) have been investigated. The ligand pK as and ligand-lead(II) stability constants of one hydroxamic acid and four thiohydroaxamic acids were determined. Solution thermodynamic results indicate that thiohydroxamic acids are more acidic and slightly better lead chelators than hydroxamates, e.g., N-methylthioaceto-hydroxamic acid, pK a = 5.94, logβ 120 = 10.92; acetohydroxamic acid, pK a = 9.34, logβ 120 = 9.52. The syntheses of lead complexes of two bulky hydroxamate ligands are presented. The X-ray crystal structures show the lead hydroxamates are di-bridged dimers with irregular five-coordinatemore » geometry about the metal atom and a stereochemically active lone pair of electrons. Molecular orbital calculations of a lead hydroxamate and a highly symmetric pseudo octahedral lead complex were performed. The thermodynamic stability of plutonium(IV) complexes of the siderophore, desferrioxamine B (DFO), and two octadentate derivatives of DFO were investigated using competition spectrophotometric titrations. The stability constant measured for the plutonium(IV) complex of DFO-methylterephthalamide is logβ 120 = 41.7. The solubility limited speciation of 242Pu as a function of time in near neutral carbonate solution was measured. Individual solutions of plutonium in a single oxidation state were added to individual solutions at pH = 6.0, T = 30.0, 1.93 mM dissolved carbonate, and sampled over intervals up to 150 days. Plutonium solubility was measured, and speciation was investigated using laser photoacoustic spectroscopy and chemical methods.« less

Analysis of Cytochrome P450 CYP119 Ligand-dependent Conformational Dynamics by Two-dimensional NMR and X-ray Crystallography*

PubMed Central

Basudhar, Debashree; Madrona, Yarrow; Kandel, Sylvie; Lampe, Jed N.; Nishida, Clinton R.; de Montellano, Paul R. Ortiz

2015-01-01

Defining the conformational states of cytochrome P450 active sites is critical for the design of agents that minimize drug-drug interactions, the development of isoform-specific P450 inhibitors, and the engineering of novel oxidative catalysts. We used two-dimensional 1H,15N HSQC chemical shift perturbation mapping of 15N-labeled Phe residues and x-ray crystallography to examine the ligand-dependent conformational dynamics of CYP119. Active site Phe residues were most affected by the binding of azole inhibitors and fatty acid substrates, in agreement with active site localization of the conformational changes. This was supported by crystallography, which revealed movement of the F-G loop with various azoles. Nevertheless, the NMR chemical shift perturbations caused by azoles and substrates were distinguishable. The absence of significant chemical shift perturbations with several azoles revealed binding of ligands to an open conformation similar to that of the ligand-free state. In contrast, 4-phenylimidazole caused pronounced NMR changes involving Phe-87, Phe-144, and Phe-153 that support the closed conformation found in the crystal structure. The same closed conformation is observed by NMR and crystallography with a para-fluoro substituent on the 4-phenylimidazole, but a para-chloro or bromo substituent engendered a second closed conformation. An open conformation is thus favored in solution with many azole ligands, but para-substituted phenylimidazoles give rise to two closed conformations that depend on the size of the para-substituent. The results suggest that ligands selectively stabilize discrete cytochrome P450 conformational states. PMID:25670859

Cyclometalated platinum(ii) complexes of 2,2'-bipyridine N-oxide containing a 1,1'-bis(diphenylphosphino)ferrocene ligand: structural, computational and electrochemical studies.

PubMed

Shahsavari, Hamid R; Fereidoonnezhad, Masood; Niazi, Maryam; Mosavi, S Talaat; Habib Kazemi, Sayed; Kia, Reza; Shirkhan, Shima; Abdollahi Aghdam, Siamak; Raithby, Paul R

2017-02-14

The preparation and characterization of new heteronuclear-platinum(ii) complexes containing a 1,1'-bis(diphenylphosphino)ferrocene (dppf) ligand are described. The reaction of the known starting complex [PtMe(κ 2 N,C-bipyO-H)(SMe 2 )], A, in which bipyO-H is a cyclometalated rollover 2,2'-bipyridine N-oxide, with the dppf ligand in a 2 : 1 ratio or an equimolar ratio led to the formation of the corresponding binuclear complex [Pt 2 Me 2 (κ 2 N,C-bipyO-H) 2 (μ-dppf)], 1, or the mononuclear complex [PtMe(κ 1 C-bipyO-H)(dppf)], 2, respectively. According to the reaction conditions, the dppf ligand in 1 and 2 behaves as either a bridging or chelating ligand. All complexes were characterized by NMR spectroscopy. The solid-state structure of 2 was determined by the single-crystal X-ray diffraction method and it was shown that the chelating dppf ligand in this complex was arranged in a "synclinal-staggered" conformation. Also, the occurrence of intermolecular C-H Cp O bipyO-H interactions in the solid-state gave rise to an extended 1-D network. The electronic absorption spectra and the electrochemical behavior of these complexes are discussed. Density functional theory (DFT) was used for geometry optimization of the singlet states in solution and for electronic structure calculations. The analysis of the molecular orbital (MO) compositions in terms of occupied and unoccupied fragment orbitals in 2 was performed.

Effect of axial ligands on the molecular configurations, stability, reactivity, and photodynamic activities of silicon phthalocyanines.

PubMed

Luan, Liqiang; Ding, Lanlan; Shi, Jiawei; Fang, Wenjuan; Ni, Yuxing; Liu, Wei

2014-12-01

To demonstrate the effect of axial ligands on the structure-activity relationship, a series of axially substituted silicon phthalocyanines (SiPcs) have been synthesized with changes to the axial ligands. The reactivity of the axial ligand upon shielding by the phthalocyanine ring current, along with their stability, photophysical, and photodynamic therapy (PDT) activities were compared and evaluated for the first time. As revealed by single-crystal XRD analysis, rotation of the axial -OMe ligands was observed in SiPc 3, which resulted in two molecular configurations coexisting synchronously in both the solid and solution states and causing a split of the phthalocyanine α protons in the (1)H NMR spectra that is significantly different from all SiPcs reported so far. The remarkable photostability, good singlet oxygen quantum yield, and efficient in vitro photodynamic activity synergistically show that compound 3 is one of the most promising photosensitizers for PDT. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andersson, Gunther G., E-mail: gunther.andersson@flinders.edu.au, E-mail: vladimir.golovko@canterbury.ac.nz, E-mail: greg.metha@adelaide.edu.au; Al Qahtani, Hassan S.; Golovko, Vladimir B., E-mail: gunther.andersson@flinders.edu.au, E-mail: vladimir.golovko@canterbury.ac.nz, E-mail: greg.metha@adelaide.edu.au

Chemically made, atomically precise phosphine-stabilized clusters Au{sub 9}(PPh{sub 3}){sub 8}(NO{sub 3}){sub 3} were deposited on titania and silica from solutions at various concentrations and the samples heated under vacuum to remove the ligands. Metastable induced electron spectroscopy was used to determine the density of states at the surface, and X-ray photoelectron spectroscopy for analysing the composition of the surface. It was found for the Au{sub 9} cluster deposited on titania that the ligands react with the titania substrate. Based on analysis using the singular value decomposition algorithm, the series of MIE spectra can be described as a linear combination ofmore » 3 base spectra that are assigned to the spectra of the substrate, the phosphine ligands on the substrate, and the Au clusters anchored to titania after removal of the ligands. On silica, the Au clusters show significant agglomeration after heat treatment and no interaction of the ligands with the substrate can be identified.« less

Oil-soluble and water-soluble BTPhens and their europium complexes in octanol/water solutions: interface crossing studied by MD and PMF simulations.

PubMed

Benay, G; Wipff, G

2013-01-31

Bistriazinyl-phenantroline "BTPhen" ligands L display the remarkable feature to complex trivalent lanthanide and actinide ions, with a marked selectivity for the latter. We report on molecular dynamics studies of tetrasubstituted X(4)BTPhens: L(4+) (X = (+)Et(3)NCH(2)-), L(4-) (X = (-)SO(3)Ph-), and L(0) (X = CyMe(4)) and their complexes with Eu(III) in binary octanol/water solutions. Changes in free energies upon interface crossing are also calculated for typical solutes by potential of mean force PMF simulations. The ligands and their complexes partition, as expected, to either the aqueous or the oil phase, depending on the "solubilizing" group X. Furthermore, most of them are found to be surface active. The water-soluble L(4+) and L(4-) ligands and their (L)Eu(NO(3))(3) complexes adsorb at the aqueous side of the interface, more with L(4-) than with L(4+). The oil soluble ligand L(0) is not surface active in its endo-endo form but adsorbs on the oil side of the interface in its most polar endo-exo form, as well as in its protonated L(0)H(+) and complexed (L(0))Eu(NO(3))(3) states. Furthermore, comparing PMFs of the Eu(III) complexes with and without nitric acid shows that acidifying the aqueous phase has different effects, depending on the ligand charge. In particular, acid promotes the Eu(III) extraction by L(0) via the (L(0))(2)Eu(NO(3))(2+) complex, as observed experimentally. Overall, the results point to the importance of interfacial adsorption for the liquid-liquid extraction of trivalent lanthanide and actinide cations by BTPhens and analogues.

Multivalent ligand-receptor-mediated interaction of small filled vesicles with a cellular membrane

NASA Astrophysics Data System (ADS)

Zhdanov, Vladimir P.

2017-07-01

The ligand-receptor-mediated contacts of small sub-100-nm-sized lipid vesicles (or nanoparticles) with the cellular membrane are of interest in the contexts of cell-to-cell communication, endocytosis of membrane-coated virions, and drug (RNA) delivery. In all these cases, the interior of vesicles is filled by biologically relevant content. Despite the diversity of such systems, the corresponding ligand-receptor interaction possesses universal features. One of them is that the vesicle-membrane contacts can be accompanied by the redistribution of ligands and receptors between the contact and contact-free regions. In particular, the concentrations of ligands and receptors may become appreciably higher in the contact regions and their composition may there be different compared to that in the suspended state in the solution. A statistical model presented herein describes the corresponding distribution of various ligands and receptors and allows one to calculate the related change of the free energy with variation of the vesicle-engulfment extent. The results obtained are used to clarify the necessary conditions for the vesicle-assisted pathway of drug delivery.

Vibrational spectroscopic study of nickel (II) formate, Ni(HCO 2) 2, and its aqueous solution

NASA Astrophysics Data System (ADS)

Edwards, H. G. M.; Knowles, A.

1992-04-01

A vibrational spectroscopic study of nickel (II) formate and its aqueous solution has been made. The vibrations characteristic of a formato—nickel complex have been assigned and it is concluded that the species Ni(HCO 2) +(HCO 2) - exists in the solid state, with monodentate ligand-to-metal bonding. The Raman spectrum of an aqueous solution of nickel (II) formate indicates that complete dissociation of the formato—nickel (II) species occurs to formate ions and nickel (II) hexa-aquo ions. Comparisons are made with other nickel (II) carboxylates.

Mononuclear nickel (II) and copper (II) coordination complexes supported by bispicen ligand derivatives: Experimental and computational studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, Nirupama; Niklas, Jens; Poluektov, Oleg

2017-01-01

The synthesis, characterization and density functional theory calculations of mononuclear Ni and Cu complexes supported by the N,N’-Dimethyl-N,N’-bis-(pyridine-2-ylmethyl)-1,2-diaminoethane ligand and its derivatives are reported. The complexes were characterized by X-ray crystallography as well as by UV-visible absorption spectroscopy and EPR spectroscopy. The solid state structure of these coordination complexes revealed that the geometry of the complex depended on the identity of the metal center. Solution phase characterization data are in accord with the solid phase structure, indicating minimal structural changes in solution. Optical spectroscopy revealed that all of the complexes exhibit color owing to d-d transition bands in the visiblemore » region. Magnetic parameters obtained from EPR spectroscopy with other structural data suggest that the Ni(II) complexes are in pseudo-octahedral geometry and Cu(II) complexes are in a distorted square pyramidal geometry. In order to understand in detail how ligand sterics and electronics affect complex topology detailed computational studies were performed. The series of complexes reported in this article will add significant value in the field of coordination chemistry as Ni(II) and Cu(II) complexes supported by tetradentate pyridyl based ligands are rather scarce.« less

Application of chiral critical clusters to assymetric synthesis

DOEpatents

Ferrieri, Richard A.

2002-01-01

Disclosed is a composition, a method of making and a method of using critical clusters for asymmetric synthesis using substantially optically-pure chiral solvent molecules in a supercritical fluid. The solvent molecules are capable of forming a multipoint hydrogen bonded solvate as they encage at least one solute molecule. The encaged solute molecule is capable of reacting to form an optically active chiral center. In another aspect, there is disclosed a method of directing the position of bonding between a solute molecule and a ligand involving encaging the solute molecule and the ligand with polar solvent molecules in a supercritical fluid under conditions of temperature and pressure sufficient to change electric charge distribution in the solute molecule. In yet another aspect, disclosed is a method of making pharmaceutical compounds involving encaging a solute molecule, which is capable of forming a chiral center, and a ligand with polar solvent molecules in a supercritical fluid under conditions of temperature and pressure sufficient to change electric charge distribution of the solute molecule. The solute molecule and ligand are then reacted whereby the ligand bonds to the solute molecule forming a chiral center. Also disclosed is a method for racemic resolution using critical clusters involving encaging racemic mixtures of solute molecules with substantially optically-pure chiral solvent molecules in a supercritical fluid under conditions of temperature and pressure sufficient to form critical clusters. The solvent molecules are capable of multipoint hydrogen bonding with the solute molecules. The encaged solute molecules are then nonenzymatically reacted to enhance the optical purity of the solute molecules.

Iron chelating ligand for iron overload diseases.

PubMed

Ozbolat, G; Tuli, A

2018-01-01

Iron overloads are a serious clinical condition in the health of humans and are therefore a key target in drug development. In this study, iron(III) complex of 8-hydroxyquinoline-5 sulphonic acid was synthesized and structurally characterized in its solid state and solution state by FT-IR, UV-Vis, elemental analysis, magnetic susceptibility and 1H-NMR. The catalase activities of complex were investigated. It was showed that the complex has the catalase activity. It is suggested that this type of complex may constitute a new and interesting basis for the future search for new and more potential drugs. The electrochemical behaviour patterns of the ligand and complex were examined as supporting electrolyte and platinum electrode for cyclic voltammetry. The electrochemistry studies showed that the reductions in free ligand and complex take place differently.The cytotoxicity was evaluated by MTT assay. The complex exhibited a very high cytotoxic activity and showed a cytotoxic effect that was much better than that of the ligand.The observed cytotoxicity could be pursued to obtain a potential drug. These results indicate that using the 8-hydroxyquinoline-5 sulphonic acid for this aim in further studies is appropriate (Tab. 1, Fig. 4, Ref. 18). Text in PDF www.elis.sk.

Mass spectrometry-based monitoring of millisecond protein–ligand binding dynamics using an automated microfluidic platform

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cong, Yongzheng; Katipamula, Shanta; Trader, Cameron D.

2016-01-01

Characterizing protein-ligand binding dynamics is crucial for understanding protein function and developing new therapeutic agents. We have developed a novel microfluidic platform that features rapid mixing of protein and ligand solutions, variable incubation times, and on-chip electrospray ionization to perform label-free, solution-based monitoring of protein-ligand binding dynamics. This platform offers many advantages including automated processing, rapid mixing, and low sample consumption.

Highly versatile heteroditopic ligand scaffolds for accommodating group 8, 9 & 11 heterobimetallic complexes.

PubMed

Gatus, Mark R D; Bhadbhade, Mohan; Messerle, Barbara A

2017-10-24

Two highly versatile xanthene scaffolds containing pairs of heteroditopic ligands were found to be capable of accommodating a range of transition metal ions, including Au(i), Ir(i), Ir(iii), Rh(i), and Ru(ii) to generate an array of heterobimetallic complexes. The metal complexes were fully characterised and proved to be stable in the solid and solution state, with no observed metal-metal scrambling. Heterobimetallic complexes containing the Rh(i)/Ir(i) combinations were tested as catalysts for the two-step dihydroalkoxylation reaction of alkynediols and sequential hydroamination/hydrosilylation reaction of alkynamines.

Analysis of cytochrome P450 CYP119 ligand-dependent conformational dynamics by two-dimensional NMR and X-ray crystallography.

PubMed

Basudhar, Debashree; Madrona, Yarrow; Kandel, Sylvie; Lampe, Jed N; Nishida, Clinton R; de Montellano, Paul R Ortiz

2015-04-17

Defining the conformational states of cytochrome P450 active sites is critical for the design of agents that minimize drug-drug interactions, the development of isoform-specific P450 inhibitors, and the engineering of novel oxidative catalysts. We used two-dimensional (1)H,(15)N HSQC chemical shift perturbation mapping of (15)N-labeled Phe residues and x-ray crystallography to examine the ligand-dependent conformational dynamics of CYP119. Active site Phe residues were most affected by the binding of azole inhibitors and fatty acid substrates, in agreement with active site localization of the conformational changes. This was supported by crystallography, which revealed movement of the F-G loop with various azoles. Nevertheless, the NMR chemical shift perturbations caused by azoles and substrates were distinguishable. The absence of significant chemical shift perturbations with several azoles revealed binding of ligands to an open conformation similar to that of the ligand-free state. In contrast, 4-phenylimidazole caused pronounced NMR changes involving Phe-87, Phe-144, and Phe-153 that support the closed conformation found in the crystal structure. The same closed conformation is observed by NMR and crystallography with a para-fluoro substituent on the 4-phenylimidazole, but a para-chloro or bromo substituent engendered a second closed conformation. An open conformation is thus favored in solution with many azole ligands, but para-substituted phenylimidazoles give rise to two closed conformations that depend on the size of the para-substituent. The results suggest that ligands selectively stabilize discrete cytochrome P450 conformational states. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Analysis of Cytochrome P450 CYP119 Ligand-dependent Conformational Dynamics by Two-dimensional NMR and X-ray Crystallography

DOE PAGES

Basudhar, Debashree; Madrona, Yarrow; Kandel, Sylvie; ...

2015-02-10

Defining the conformational states of cytochrome P450 active sites is critical for the design of agents that minimize drug-drug interactions, the development of isoform-specific P450 inhibitors, and the engineering of novel oxidative catalysts. In this paper, we used two-dimensional 1H,15N HSQC chemical shift perturbation mapping of 15N-labeled Phe residues and x-ray crystallography to examine the ligand-dependent conformational dynamics of CYP119. Active site Phe residues were most affected by the binding of azole inhibitors and fatty acid substrates, in agreement with active site localization of the conformational changes. This was supported by crystallography, which revealed movement of the F-G loop withmore » various azoles. Nevertheless, the NMR chemical shift perturbations caused by azoles and substrates were distinguishable. The absence of significant chemical shift perturbations with several azoles revealed binding of ligands to an open conformation similar to that of the ligand-free state. In contrast, 4-phenylimidazole caused pronounced NMR changes involving Phe-87, Phe-144, and Phe-153 that support the closed conformation found in the crystal structure. The same closed conformation is observed by NMR and crystallography with a para-fluoro substituent on the 4-phenylimidazole, but a para-chloro or bromo substituent engendered a second closed conformation. An open conformation is thus favored in solution with many azole ligands, but para-substituted phenylimidazoles give rise to two closed conformations that depend on the size of the para-substituent. Finally, the results suggest that ligands selectively stabilize discrete cytochrome P450 conformational states.« less

Analysis of Cytochrome P450 CYP119 Ligand-dependent Conformational Dynamics by Two-dimensional NMR and X-ray Crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Basudhar, Debashree; Madrona, Yarrow; Kandel, Sylvie

Defining the conformational states of cytochrome P450 active sites is critical for the design of agents that minimize drug-drug interactions, the development of isoform-specific P450 inhibitors, and the engineering of novel oxidative catalysts. In this paper, we used two-dimensional 1H,15N HSQC chemical shift perturbation mapping of 15N-labeled Phe residues and x-ray crystallography to examine the ligand-dependent conformational dynamics of CYP119. Active site Phe residues were most affected by the binding of azole inhibitors and fatty acid substrates, in agreement with active site localization of the conformational changes. This was supported by crystallography, which revealed movement of the F-G loop withmore » various azoles. Nevertheless, the NMR chemical shift perturbations caused by azoles and substrates were distinguishable. The absence of significant chemical shift perturbations with several azoles revealed binding of ligands to an open conformation similar to that of the ligand-free state. In contrast, 4-phenylimidazole caused pronounced NMR changes involving Phe-87, Phe-144, and Phe-153 that support the closed conformation found in the crystal structure. The same closed conformation is observed by NMR and crystallography with a para-fluoro substituent on the 4-phenylimidazole, but a para-chloro or bromo substituent engendered a second closed conformation. An open conformation is thus favored in solution with many azole ligands, but para-substituted phenylimidazoles give rise to two closed conformations that depend on the size of the para-substituent. Finally, the results suggest that ligands selectively stabilize discrete cytochrome P450 conformational states.« less

Structural Basis for Activation of Fatty Acid-binding Protein 4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gillilan,R.; Ayers, S.; Noy, N.

2007-01-01

Fatty acid-binding protein 4 (FABP4) delivers ligands from the cytosol to the nuclear receptor PPAR{gamma} in the nucleus, thereby enhancing the transcriptional activity of the receptor. Notably, FABP4 binds multiple ligands with a similar affinity but its nuclear translocation is activated only by specific compounds. To gain insight into the structural features that underlie the ligand-specificity in activation of the nuclear import of FABP4, we solved the crystal structures of the protein complexed with two compounds that induce its nuclear translocation, and compared these to the apo-protein and to FABP4 structures bound to non-activating ligands. Examination of these structures indicatesmore » that activation coincides with closure of a portal loop phenylalanine side-chain, contraction of the binding pocket, a subtle shift in a helical domain containing the nuclear localization signal of the protein, and a resultant change in oligomeric state that exposes the nuclear localization signal to the solution. Comparisons of backbone displacements induced by activating ligands with a measure of mobility derived from translation, libration, screw (TLS) refinement, and with a composite of slowest normal modes of the apo state suggest that the helical motion associated with the activation of the protein is part of the repertoire of the equilibrium motions of the apo-protein, i.e. that ligand binding does not induce the activated configuration but serves to stabilize it. Nuclear import of FABP4 can thus be understood in terms of the pre-existing equilibrium hypothesis of ligand binding.« less

Deuterium kinetic isotope effects on the dissociation of a protein-fatty acid complex in the gas phase.

PubMed

Liu, Lan; Michelsen, Klaus; Kitova, Elena N; Schnier, Paul D; Brown, Alex; Klassen, John S

2012-04-04

Deuterium kinetic isotope effects (KIEs) are reported for the first time for the dissociation of a protein-ligand complex in the gas phase. Temperature-dependent rate constants were measured for the loss of neutral ligand from the deprotonated ions of the 1:1 complex of bovine β-lactoglobulin (Lg) and palmitic acid (PA), (Lg + PA)(n-) → Lg(n-) + PA, at the 6- and 7- charge states. At 25 °C, partial or complete deuteration of the acyl chain of PA results in a measurable inverse KIE for both charge states. The magnitude of the KIEs is temperature dependent, and Arrhenius analysis of the rate constants reveals that deuteration of PA results in a decrease in activation energy. In contrast, there is no measurable deuterium KIE for the dissociation of the (Lg + PA) complex in aqueous solution at pH 8. Deuterium KIEs were calculated using conventional transition-state theory with an assumption of a late dissociative transition state (TS), in which the ligand is free of the binding pocket. The vibrational frequencies of deuterated and non-deuterated PA in the gas phase and in various solvents (n-hexane, 1-chlorohexane, acetone, and water) were established computationally. The KIEs calculated from the corresponding differences in zero-point energies account qualitatively for the observation of an inverse KIE but do not account for the magnitude of the KIEs nor their temperature dependence. It is proposed that the dissociation of the (Lg + PA) complex in aqueous solution also proceeds through a late TS in which the acyl chain is extensively hydrated such that there is no significant differential change in the vibrational frequencies along the reaction coordinate and, consequently, no significant KIE.

The Role of Interfacial Water in Protein-Ligand Binding: Insights from the Indirect Solvent Mediated Potential of Mean Force.

PubMed

Cui, Di; Zhang, Bin W; Matubayasi, Nobuyuki; Levy, Ronald M

2018-02-13

Classical density functional theory (DFT) can be used to relate the thermodynamic properties of solutions to the indirect solvent mediated part of the solute-solvent potential of mean force (PMF). Standard, but powerful numerical methods can be used to estimate the solute-solvent PMF from which the indirect part can be extracted. In this work we show how knowledge of the direct and indirect parts of the solute-solvent PMF for water at the interface of a protein receptor can be used to gain insights about how to design tighter binding ligands. As we show, the indirect part of the solute-solvent PMF is equal to the sum of the 1-body (energy + entropy) terms in the inhomogeneous solvation theory (IST) expansion of the solvation free energy. To illustrate the effect of displacing interfacial water molecules with particular direct/indirect PMF signatures on the binding of ligands, we carry out simulations of protein binding with several pairs of congeneric ligands. We show that interfacial water locations that contribute favorably or unfavorably at the 1-body level (energy + entropy) to the solvation free energy of the solute can be targeted as part of the ligand design process. Water locations where the indirect PMF is larger in magnitude provide better targets for displacement when adding a functional group to a ligand core.

Is It Reliable to Take the Molecular Docking Top Scoring Position as the Best Solution without Considering Available Structural Data?

PubMed

Ramírez, David; Caballero, Julio

2018-04-28

Molecular docking is the most frequently used computational method for studying the interactions between organic molecules and biological macromolecules. In this context, docking allows predicting the preferred pose of a ligand inside a receptor binding site. However, the selection of the “best” solution is not a trivial task, despite the widely accepted selection criterion that the best pose corresponds to the best energy score. Here, several rigid-target docking methods were evaluated on the same dataset with respect to their ability to reproduce crystallographic binding orientations, to test if the best energy score is a reliable criterion for selecting the best solution. For this, two experiments were performed: (A) to reconstruct the ligand-receptor complex by performing docking of the ligand in its own crystal structure receptor (defined as self-docking), and (B) to reconstruct the ligand-receptor complex by performing docking of the ligand in a crystal structure receptor that contains other ligand (defined as cross-docking). Root-mean square deviation (RMSD) was used to evaluate how different the obtained docking orientation is from the corresponding co-crystallized pose of the same ligand molecule. We found that docking score function is capable of predicting crystallographic binding orientations, but the best ranked solution according to the docking energy is not always the pose that reproduces the experimental binding orientation. This happened when self-docking was achieved, but it was critical in cross-docking. Taking into account that docking is typically used with predictive purposes, during cross-docking experiments, our results indicate that the best energy score is not a reliable criterion to select the best solution in common docking applications. It is strongly recommended to choose the best docking solution according to the scoring function along with additional structural criteria described for analogue ligands to assure the selection of a correct docking solution.

Dissolution kinetics and biodurability of tremolite particles in mimicked lung fluids: Effect of citrate and oxalate

NASA Astrophysics Data System (ADS)

Rozalen, Marisa; Ramos, M. Elena; Huertas, F. Javier; Fiore, Saverio; Gervilla, Fernando

2013-11-01

The effect of citrate and oxalate on tremolite dissolution rate was measured at 37 °C in non-stirred flow-through reactors, using modified Gamble's solutions at pH 4 (macrophages), 7.4 (interstitial fluids) and 5.5 (intermediate check point) containing 0, 0.15, 1.5 and 15 mmol L-1 of citrate or oxalate. The dissolution rates calculated from Si concentration in the output solutions without organic ligands depend on pH, decreasing when the pH increases from -13.00 (pH 4) to -13.35 (pH 7.4) mol g-1 s-1 and following a proton-promoted mechanism. The presence of both ligands enhances dissolution rates at every pH, increasing this effect when the ligand concentration increases. Citrate produces a stronger effect as a catalyst than oxalate, mainly at more acidic pHs and enhances dissolution rates until 20 times for solutions with 15 mmol L-1 citrate. However, at pH 7.4 the effect is lighter and oxalate solutions (15 mmol L-1) only enhances dissolution rates eight times respect to free organic ligand solutions. Dissolution is promoted by the attack to protons and organic ligands to the tremolite surface. Magnesium speciation in oxalate and citrate solutions shows that Mg citrate complexes are more effective than oxalate ones during the alteration of tremolite in magrophages, but this tendency is the opposite for interstitial fluids, being oxalate magnesium complexes stronger. The biodurability estimations show that the destruction of the fibers is faster in acidic conditions (macrophages) than in the neutral solutions (interstitial fluid). At pH 4, both ligands oxalate and citrate reduce the residence time of the fibers with respect to that calculated in absence of ligands. Nevertheless, at pH 7.4 the presence of ligands does not reduce significantly the lifetime of the fibers.

Potassium Binding Adjacent to Cationic Transition-Metal Fragments: Unusual Heterobimetallic Adducts of a Calix[4]arene-Based Thione Ligand.

PubMed

Patchett, Ruth; Knighton, Richard C; Mattock, James D; Vargas, Alfredo; Chaplin, Adrian B

2017-11-20

The synthesis of cationic rhodium and iridium complexes of a bis(imidazole-2-thione)-functionalized calix[4]arene ligand and their surprising capacity for potassium binding are described. In both cases, uptake of the alkali metal into the calix[4]arene cavity occurs despite adverse electrostatic interactions associated with close proximity to the transition-metal fragment [Rh + ···K + = 3.715(1) Å; Ir + ···K + = 3.690(1) Å]. The formation and constituent bonding of these unusual heterobimetallic adducts have been interrogated through extensive solution and solid-state characterization, examination of the host-guest chemistry of the ligand and its upper-rim unfunctionalized calix[4]arene analogue, and use of density functional theory based energy decomposition analysis.

Influence of Countercation Hydration Enthalpies on the Formation of Molecular Complexes: A Thorium–Nitrate Example

DOE PAGES

Jin, Geng Bang; Lin, Jian; Estes, Shanna L.; ...

2017-11-17

Here, the influence of countercations (A n+) in directing the composition of monomeric metal–ligand (ML) complexes that precipitate from solution are often overlooked despite the wide usage of A n+ in materials synthesis. Herein, we describe a correlation between the composition of ML complexes and A + hydration enthalpies found for two related series of thorium (Th)–nitrate molecular compounds obtained by evaporating acidic aqueous Th–nitrate solutions in the presence of A + counterions. Analyses of their chemical composition and solid-state structures demonstrate that A + not only affects the overall solid-state packing of the Th–nitrato complexes but also influences themore » composition of the Th–nitrato monomeric anions themselves. Trends in composition and structure are found to correlate with A + hydration enthalpies, such that the A + with smaller hydration enthalpies associate with less hydrated and more anionic Th–nitrato complexes. This perspective, broader than the general assumption of size and charge as the dominant influence of A n+, opens a new avenue for the design and synthesis of targeted metal–ligand complexes.« less

Influence of Countercation Hydration Enthalpies on the Formation of Molecular Complexes: A Thorium–Nitrate Example

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Geng Bang; Lin, Jian; Estes, Shanna L.

Here, the influence of countercations (A n+) in directing the composition of monomeric metal–ligand (ML) complexes that precipitate from solution are often overlooked despite the wide usage of A n+ in materials synthesis. Herein, we describe a correlation between the composition of ML complexes and A + hydration enthalpies found for two related series of thorium (Th)–nitrate molecular compounds obtained by evaporating acidic aqueous Th–nitrate solutions in the presence of A + counterions. Analyses of their chemical composition and solid-state structures demonstrate that A + not only affects the overall solid-state packing of the Th–nitrato complexes but also influences themore » composition of the Th–nitrato monomeric anions themselves. Trends in composition and structure are found to correlate with A + hydration enthalpies, such that the A + with smaller hydration enthalpies associate with less hydrated and more anionic Th–nitrato complexes. This perspective, broader than the general assumption of size and charge as the dominant influence of A n+, opens a new avenue for the design and synthesis of targeted metal–ligand complexes.« less

Mn K-Edge XANES and Kβ XES Studies of Two Mn–Oxo Binuclear Complexes: Investigation of Three Different Oxidation States Relevant to the Oxygen-Evolving Complex of Photosystem II

PubMed Central

Visser, Hendrik; Anxolabéhère-Mallart, Elodie; Bergmann, Uwe; Glatzel, Pieter; Robblee, John H.; Cramer, Stephen P.; Girerd, Jean-Jacques; Sauer, Kenneth; Klein, Melvin P.; Yachandra, Vittal K.

2014-01-01

Two structurally homologous Mn compounds in different oxidation states were studied to investigate the relative influence of oxidation state and ligand environment on Mn K-edge X-ray absorption near-edge structure (XANES) and Mn Kβ X-ray emission spectroscopy (Kβ XES). The two manganese compounds are the di-μ-oxo compound [L′2MnIIIO2MnIVL′2](ClO4)3, where L′ is 1,10-phenanthroline (Cooper, S. R.; Calvin, M. J. Am. Chem. Soc. 1977, 99, 6623–6630) and the linear mono-μ-oxo compound [LMnIIIOMnIIIL](ClO4)2, where L− is the monoanionic N,N-bis(2-pyridylmethyl)-N′-salicylidene-1,2-diaminoethane ligand (Horner, O.; Anxolabéhère-Mallart, E.; Charlot, M. F.; Tchertanov, L.; Guilhem, J.; Mattioli, T. A.; Boussac, A.; Girerd, J.-J. Inorg. Chem. 1999, 38, 1222–1232). Preparative bulk electrolysis in acetonitrile was used to obtain higher oxidation states of the compounds: the MnIVMnIV species for the di-μ-oxo compound and the MnIIIMnIV and MnIVMnIV species for the mono-μ-oxo compound. IR, UV/vis, EPR, and EXAFS spectra were used to determine the purity and integrity of the various sample solutions. The Mn K-edge XANES spectra shift to higher energy upon oxidation when the ligand environment remains similar. However, shifts in energy are also observed when only the ligand environment is altered. This is achieved by comparing the di-μ-oxo and linear mono-μ-oxo Mn–Mn moieties in equivalent oxidation states, which represent major structural changes. The magnitude of an energy shift due to major changes in ligand environment can be as large as that of an oxidation-state change. Therefore, care must be exercised when correlating the Mn K-edge energies to manganese oxidation states without taking into account the nature of the ligand environment and the overall structure of the compound. In contrast to Mn K-edge XANES, Kβ XES spectra show less dependence on ligand environment. The Kβ1,3 peak energies are comparable for the di-μ-oxo and mono-μ-oxo compounds in equivalent oxidation states. The energy shifts observed due to oxidation are also similar for the two different compounds. The study of the different behavior of the XANES pre-edge and main-edge features in conjunction with Kβ XES provides significant information about the oxidation state and character of the ligand environment of manganese atoms. PMID:11459481

Physicochemical basis for the rapid time-action of LysB28ProB29-insulin: dissociation of a protein-ligand complex.

PubMed Central

Bakaysa, D. L.; Radziuk, J.; Havel, H. A.; Brader, M. L.; Li, S.; Dodd, S. W.; Beals, J. M.; Pekar, A. H.; Brems, D. N.

1996-01-01

The rate-limiting step for the absorption of insulin solutions after subcutaneous injection is considered to be the dissociation of self-associated hexamers to monomers. To accelerate this absorption process, insulin analogues have been designed that possess full biological activity and yet have greatly diminished tendencies to self-associate. Sedimentation velocity and static light scattering results show that the presence of zinc and phenolic ligands (m-cresol and/or phenol) cause one such insulin analogue, LysB28ProB29-human insulin (LysPro), to associate into a hexameric complex. Most importantly, this ligand-bound hexamer retains its rapid-acting pharmacokinetics and pharmacodynamics. The dissociation of the stabilized hexameric analogue has been studied in vitro using static light scattering as well as in vivo using a female pig pharmacodynamic model. Retention of rapid time-action is hypothesized to be due to altered subunit packing within the hexamer. Evidence for modified monomer-monomer interactions has been observed in the X-ray crystal structure of a zinc LysPro hexamer (Ciszak E et al., 1995, Structure 3:615-622). The solution state behavior of LysPro, reported here, has been interpreted with respect to the crystal structure results. In addition, the phenolic ligand binding differences between LysPro and insulin have been compared using isothermal titrating calorimetry and visible absorption spectroscopy of cobalt-containing hexamers. These studies establish that rapid-acting insulin analogues of this type can be stabilized in solution via the formation of hexamer complexes with altered dissociation properties. PMID:8976561

Discrimination of fluorescence light-up effects induced by pH and metal ion chelation on a spirocyclic derivative of rhodamine B.

PubMed

Leite, Andreia; Silva, Ana M G; Cunha-Silva, Luís; de Castro, Baltazar; Gameiro, Paula; Rangel, Maria

2013-05-07

In the present work we describe the structure and the spectroscopic characterization of a spirocyclic derivative of a rhodamine B ligand whose properties allow discrimination of light-up effects induced by metal ion chelation and variation of pH. Distinction of the two effects is important for the use of this type of ligand to detect and monitor metal ions in aqueous solutions. The synthesis of the ligand was performed in two steps, which involve the reaction of rhodamine B with hydrazine hydrate to form rhodamine B hydrazide followed by condensation with 2-pyridinecarboxaldehyde and was successfully optimized using a solvent free approach under microwave irradiation. The ligand was obtained in the expected spirolactam form and was characterized in the solid state by EA, MS and single-crystal X-ray diffraction. The ligand was characterized in solution by NMR and absorption and fluorescence spectroscopies and its properties were found to be sensitive to pH and concentration of iron(III). The study of the fluorescence properties at variable pH shows that the compound is fluorescent in the range 2 < pH < 4 with maximum intensity at pH 3 and allowed the determination of two pK(a) values (pK(a1) = 2.98, pK(a2) = 2.89) and establishment of the corresponding distribution diagram. The very low pK(a) values guarantee that above pH equal to 4 the ligand is mostly present in the fully non-protonated and non-fluorescent form L. The study of the interaction of the ligand with iron(iii) was performed in DMSO and DMSO-H(2)O to exclude the influence of pH and due to the low solubility of the compound. The results indicate that the presence of iron(III) triggers the opening of the spirolactam form of the ligand and the maximum intensity obtained at a metal : ligand ratio of 1 : 2 is consistent with the formation of an iron(III) complex with the tridentate ligand.

Probing the interaction of U (VI) with phosphonate-functionalized mesoporous silica using solid-state NMR spectroscopy

DOE PAGES

Uribe, Eva C.; Mason, Harris E.; Shusterman, Jennifer A.; ...

2016-05-30

The fundamental interaction of U (VI) with diethylphosphatoethyl triethoxysilane functionalized SBA-15 mesoporous silica is studied by macroscopic batch experiments and solid-state NMR spectroscopy. DPTS-functionalized silica has been shown to extract U (VI) from nitric acid solutions at or above pH 3. Extraction is dependent on pH and ionic strength. Single-pulse 31P NMR on U (VI) contacted samples revealed that U (VI)only interacts with a fraction of the ligands present on the surface. At pH 4 the U (VI) extraction capacity of the material is limited to 27–37% of the theoretical capacity, based on ligand loading. We combined single pulse 31Pmore » NMR on U (VI)-contacted samples with batch studies to measure a ligand-to-metal ratio of approximately 2 : 1 at pH 3 and 4. Batch studies and cross-polarization NMR measurements reveal that U (VI) binds to deprotonated phosphonate and/or silanol sites. We use 31P– 31P DQ-DRENAR NMR studies to compare the average dipolar coupling between phosphorus spins for both U (VI)-complexed and non-complexed ligand environments. Furthermore, these measurements reveal that U (VI) extraction is not limited by inadequate surface distribution of ligands, but rather by low stability of the surface phosphonate complex.« less

Probing the interaction of U (VI) with phosphonate-functionalized mesoporous silica using solid-state NMR spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Uribe, Eva C.; Mason, Harris E.; Shusterman, Jennifer A.

The fundamental interaction of U (VI) with diethylphosphatoethyl triethoxysilane functionalized SBA-15 mesoporous silica is studied by macroscopic batch experiments and solid-state NMR spectroscopy. DPTS-functionalized silica has been shown to extract U (VI) from nitric acid solutions at or above pH 3. Extraction is dependent on pH and ionic strength. Single-pulse 31P NMR on U (VI) contacted samples revealed that U (VI)only interacts with a fraction of the ligands present on the surface. At pH 4 the U (VI) extraction capacity of the material is limited to 27–37% of the theoretical capacity, based on ligand loading. We combined single pulse 31Pmore » NMR on U (VI)-contacted samples with batch studies to measure a ligand-to-metal ratio of approximately 2 : 1 at pH 3 and 4. Batch studies and cross-polarization NMR measurements reveal that U (VI) binds to deprotonated phosphonate and/or silanol sites. We use 31P– 31P DQ-DRENAR NMR studies to compare the average dipolar coupling between phosphorus spins for both U (VI)-complexed and non-complexed ligand environments. Furthermore, these measurements reveal that U (VI) extraction is not limited by inadequate surface distribution of ligands, but rather by low stability of the surface phosphonate complex.« less

Molecular simulations reveal that the long range fluctuations of human DPP III change upon ligand binding.

PubMed

Tomić, A; Berynskyy, M; Wade, R C; Tomić, S

2015-11-01

The experimentally determined structures of human dipeptidyl peptidase III (DPP III) for the wild-type protein and for the complex of its E451A mutant with the peptide substrate, tynorphin, differ significantly in their overall shape. The two domains of the enzyme are separated by a wide cleft in the structure of the ligand-free enzyme, while in the ligand-bound mutant they are very close to each other, and the protein structure is extremely compact. Here, we applied a range of molecular dynamics simulation techniques to investigate the DPP III conformational landscape and the influence of ligand binding on the protein structure and dynamics. We used conventional, accelerated and steered methods to simulate DPP III and its complexes with tynorphin and with the preferred, synthetic, substrate Arg-Arg-2-naphthylamide. We found that DPP III can adopt a number of different forms in solution. The compact forms are more stable, but the open and partially closed states, spanning a wide range of conformations, can more effectively recognize the substrate which preferentially binds to the five-stranded β-core of the lower DPP III domain. The simulations indicated the existence of a dynamic equilibrium between open and semi-closed states and revealed two ways that the protein can close, leading to two distinct compact structures. The way in which the protein closes depends on the presence of the ligand.

Photophysical properties of the series fac- and mer-(1-phenylisoquinolinato-N∧C2')(x)(2-phenylpyridinato-N∧C2')(3-x)iridium(III) (x = 1-3).

PubMed

Deaton, Joseph C; Young, Ralph H; Lenhard, Jerome R; Rajeswaran, Manju; Huo, Shouquan

2010-10-18

The photophysical properties of tris-cyclometalated iridium(III) complexes have been probed by chemical and geometric variation through the series fac- and mer-Ir(piq)(x)(ppy)(3-x) (x = 1-3; piq = 1-phenylisoquinolinato-N(∧)C(2'), ppy = 2-phenylpyridinato-N(∧)C(2')). The phosphorescent decays were recorded in solution at 295 K and in polymer films from 2 to 295 K. In the heteroleptic complexes, emission occurs based solely on the piq ligand(s), at least by the nanosecond time scale, as its excited states are the lowest energy. Because fac-Ir(piq)(3) and fac-Ir(ppy)(3) possess practically the same oxidation potential, comparison of photophysical properties through the series fac-Ir(piq)(x)(ppy)(3-x) (x = 1-3) revealed the effects of having one, two, or three emissive piq ligands with no confounding effects from differences in electron withdrawing or donating properties between the spectator ppy ligands and the piq ligands. Effects of placement of piq ligands in different coordination geometries were elucidated by comparisons to the mer series.

New Insights into Structure and Luminescence of Eu III and Sm III Complexes of the 3,4,3-LI(1,2-HOPO) Ligand

DOE PAGES

Daumann, Lena J.; Tatum, David S.; Snyder, Benjamin E. R.; ...

2015-01-21

We report the preparation and new insight into photophysical properties of luminescent hydroxypyridonate complexes [M IIIL] - (M = Eu or Sm) of the versatile 3,4,3-LI(1,2-HOPO) ligand (L). We report the crystal structure of this ligand with EuIII as well as insights into the coordination behavior and geometry in solution by using magnetic circular dichroism. In addition TD-DFT calculations were used to examine the excited states of the two different chromophores present in the 3,4,3-LI(1,2-HOPO) ligand. We find that the Eu III and Sm III complexes of this ligand undergo a transformation after in situ preparation to yield complexes withmore » higher quantum yield (QY) over time. We propose that the lower QY in the in situ complexes is not only due to water quenching but could also be due to a lower degree of f-orbital overlap (in a kinetic isomer) as indicated by magnetic circular dichroism measurements.« less

Ligand Rearrangements at Fe/S Cofactors: Slow Isomerization of a Biomimetic [2Fe-2S] Cluster.

PubMed

Bergner, Marie; Roy, Lisa; Dechert, Sebastian; Neese, Frank; Ye, Shengfa; Meyer, Franc

2017-04-18

Ligand exchange plays an important role in the biogenesis of Fe/S clusters, most prominently during cluster transfer from a scaffold protein to its target protein. Although in vivo and in vitro studies have provided some insight into this process, the microscopic details of the ligand exchange steps are mostly unknown. In this work, the kinetics of the ligand rearrangement in a biomimetic [2Fe-2S] cluster with mixed S/N capping ligands have been studied. Two geometrical isomers of the cluster are present in solution, and mechanistic insight into the isomerization process was obtained by variable-temperature 1 H NMR spectroscopy. Combined experimental and computational results reveal that this is an associative process that involves the coordination of a solvent molecule to one of the ferric ions. The cluster isomerizes at least two orders of magnitude faster in its protonated and mixed-valent states. These findings may contribute to a deeper understanding of cluster transfer and sensing processes occurring in Fe/S cluster biogenesis. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Volume-confined synthesis of ligand-free gold nanoparticles with tailored sizes for enhanced catalytic activity

NASA Astrophysics Data System (ADS)

Shaik, Firdoz; Zhang, Weiqing; Niu, Wenxin; Lu, Xianmao

2014-10-01

Ligand-free Au nanoparticles with controlled sizes are synthesized via a volume-confined method. In this synthesis, mesoporous hollow silica shells (mHSS) are used as nano-containers for the impregnation of HAuCl4 solution before they are separated from the bulk solution. With a simple heating process, the Au precursor confined within the cavity of the isolated hollow shells is converted into ligand-free Au nanoparticles. The size of the Au nanoparticles can be tuned precisely by loading HAuCl4 solution of different concentrations, or by using mHSS with different cavity volumes. The ligand-free Au nanoparticles demonstrate superior catalytic activity than sodium citrate-capped Au nanoparticles.

Rational Ligand Design for U(VI) and Pu(IV)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Szigethy, Geza

2009-08-12

Nuclear power is an attractive alternative to hydrocarbon-based energy production at a time when moving away from carbon-producing processes is widely accepted as a significant developmental need. Hence, the radioactive actinide power sources for this industry are necessarily becoming more widespread, which is accompanied by the increased risk of exposure to both biological and environmental systems. This, in turn, requires the development of technology designed to remove such radioactive threats efficiently and selectively from contaminated material, whether that be contained nuclear waste streams or the human body. Raymond and coworkers (University of California, Berkeley) have for decades investigated the interactionmore » of biologically-inspired, hard Lewis-base ligands with high-valent, early-actinide cations. It has been established that such ligands bind strongly to the hard Lewis-acidic early actinides, and many poly-bidentate ligands have been developed and shown to be effective chelators of actinide contaminants in vivo. Work reported herein explores the effect of ligand geometry on the linear U(IV) dioxo dication (uranyl, UO 2 2+). The goal is to utilize rational ligand design to develop ligands that exhibit shape selectivity towards linear dioxo cations and provides thermodynamically favorable binding interactions. The uranyl complexes with a series of tetradentate 3-hydroxy-pyridin-2-one (3,2-HOPO) ligands were studied in both the crystalline state as well as in solution. Despite significant geometric differences, the uranyl affinities of these ligands vary only slightly but are better than DTPA, the only FDA-approved chelation therapy for actinide contamination. The terepthalamide (TAM) moiety was combined into tris-beidentate ligands with 1,2- and 3,2-HOPO moieties were combined into hexadentate ligands whose structural preferences and solution thermodynamics were measured with the uranyl cation. In addition to achieving coordinative saturation, these ligands exhibited increased uranyl affinity compared to bis-Me-3,2-HOPO ligands. This result is due in part to their increased denticity, but is primarily the result of the presence of the TAM moiety. In an effort to explore the relatively unexplored coordination chemistry of Pu(IV) with bidentate moieties, a series of Pu(IV) complexes were also crystallized using bidentate hydroxypyridinone and hydroxypyrone ligands. The geometries of these complexes are compared to that of the analogous Ce(IV) complexes. While in some cases these showed the expected structural similarities, some ligand systems led to significant coordination changes. A series of crystal structure analyses with Ce(IV) indicated that these differences are most likely the result of crystallization condition differences and solvent inclusion effects.« less

Structural insights into the interaction of IL-33 with its receptors.

PubMed

Liu, Xi; Hammel, Michal; He, Yanfeng; Tainer, John A; Jeng, U-Ser; Zhang, Linqi; Wang, Shuying; Wang, Xinquan

2013-09-10

Interleukin (IL)-33 is an important member of the IL-1 family that has pleiotropic activities in innate and adaptive immune responses in host defense and disease. It signals through its ligand-binding primary receptor ST2 and IL-1 receptor accessory protein (IL-1RAcP), both of which are members of the IL-1 receptor family. To clarify the interaction of IL-33 with its receptors, we determined the crystal structure of IL-33 in complex with the ectodomain of ST2 at a resolution of 3.27 Å. Coupled with structure-based mutagenesis and binding assay, the structural results define the molecular mechanism by which ST2 specifically recognizes IL-33. Structural comparison with other ligand-receptor complexes in the IL-1 family indicates that surface-charge complementarity is critical in determining ligand-binding specificity of IL-1 primary receptors. Combined crystallography and small-angle X-ray-scattering studies reveal that ST2 possesses hinge flexibility between the D3 domain and D1D2 module, whereas IL-1RAcP exhibits a rigid conformation in the unbound state in solution. The molecular flexibility of ST2 provides structural insights into domain-level conformational change of IL-1 primary receptors upon ligand binding, and the rigidity of IL-1RAcP explains its inability to bind ligands directly. The solution architecture of IL-33-ST2-IL-1RAcP complex from small-angle X-ray-scattering analysis resembles IL-1β-IL-1RII-IL-1RAcP and IL-1β-IL-1RI-IL-1RAcP crystal structures. The collective results confer IL-33 structure-function relationships, supporting and extending a general model for ligand-receptor assembly and activation in the IL-1 family.

Characterization of Ce SUP 3+-tributyl phosphate coordination complexes produced by fused droplet electrospray ionization with a target capillary

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gary S. Groenewold; Jean-Jacques Gaumet

2011-12-01

Coordination complexes containing Ce(III) and tri-n-butyl phosphate (TBP) in the 1+, 2+ and 3+ charge states were generated using desorption electrospray ionization (DESI) mass spectrometry, in which the analyte solutions were supplied via a target capillary orthogonally situated with respect to the electrospray. Comparison with direct electrospray (ESI) showed that the same coordination complexes were produced in each experiment, and could be described by the general formula [Ce(NO3)m=0-2(TBP)n](3-m)+. This result indicates that DESI has utility for measuring metal speciation for metal ligand solutions where the gas-phase complexes generated by ESI have been correlated with solution speciation. Such an application wouldmore » be useful for analyses where it is desirable to limit the total amount of metal being handled, or that have solvent systems that are not readily amenable to ESI. Both the direct ESI and DESI mass spectra showed similar trends with respect to the TBP:Ce ratio, viz. high values tend to favor formation of a larger fraction of the 1+ species, and the 2+ and 3+ species become relatively more important as the ratio is decreased. Within individual charge state ion envelopes, lower TBP:Ce ratios produce coordination complexes with fewer ligands, a trend also seen using both approaches. These trends again point toward strong similarity between the direct ESI and DESI analyses of the metal-ligand solutions. The DESI experiments were less sensitive for measuring the coordination complexes compared to the direct ESI experiments, by a factor of 10 - 100 depending on whether minimum detectable concentration or absolute ion abundances were considered. Nevertheless, mid-picomolar quantities of coordination complexes were measured using the target capillary, indicating that sensitivity would be sufficient for measuring species in many industrial separations processes.« less

Conformational study on cyclic melanocortin ligands and new insight into their binding mode at the MC4 receptor.

PubMed

Grieco, Paolo; Brancaccio, Diego; Novellino, Ettore; Hruby, Victor J; Carotenuto, Alfonso

2011-09-01

The melanocortin receptors are involved in many physiological functions, including pigmentation, sexual function, feeding behavior, and energy homeostasis, making them potential targets to treat obesity, sexual dysfunction, etc. Understanding the basis of the ligand-receptor interactions is crucial for the design of potent and selective ligands for these receptors. The conformational preferences of the cyclic melanocortin ligands MTII (Ac-Nle(4)-c[Asp(5)-His(6)-DPhe(7)-Arg(8)-Trp(9)-Lys(10)]-NH(2)) and SHU9119 (Ac-Nle(4)-c[Asp(5)-His(6)-DNal(2')(7)-Arg(8)-Trp(9)-Lys(10)]-NH(2)), which show agonist and antagonist activity at the h-MC4R, respectively, were comprehensively investigated by solution NMR spectroscopy in different environments. In particular, water and water/DMSO (8:2) solutions were used as isotropic solutions and an aqueous solution of DPC (dodecylphosphocholine) micelles was used as a membrane mimetic environment. NMR-derived conformations of these two ligands were docked within h-MC4R models. NMR and docking studies revealed intriguing differences which can help explain the different activities of these two ligands. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

Peripheral halo-functionalization in [Cu(N^N)(P^P)]+ emitters: influence on the performances of light-emitting electrochemical cells.

PubMed

Brunner, Fabian; Martínez-Sarti, Laura; Keller, Sarah; Pertegás, Antonio; Prescimone, Alessandro; Constable, Edwin C; Bolink, Henk J; Housecroft, Catherine E

2016-09-27

A series of heteroleptic [Cu(N^N)(P^P)][PF 6 ] complexes is described in which P^P = bis(2-(diphenylphosphino)phenyl)ether (POP) or 4,5-bis(diphenylphosphino)-9,9-dimethylxanthene (xantphos) and N^N = 4,4'-diphenyl-6,6'-dimethyl-2,2'-bipyridine substituted in the 4-position of the phenyl groups with atom X (N^N = 1 has X = F, 2 has X = Cl, 3 has X = Br, 4 has X = I; the benchmark N^N ligand with X = H is 5). These complexes have been characterized by multinuclear NMR spectroscopy, mass spectrometry, elemental analyses and cyclic voltammetry; representative single crystal structures are also reported. The solution absorption spectra are characterized by high energy bands (arising from ligand-centred transitions) which are red-shifted on going from X = H to X = I, and a broad metal-to-ligand charge transfer band with λ max in the range 387-395 nm. The ten complexes are yellow emitters in solution and yellow or yellow-orange emitters in the solid-state. For a given N^N ligand, the solution photoluminescence (PL) spectra show no significant change on going from [Cu(N^N)(POP)] + to [Cu(N^N)(xantphos)] + ; introducing the iodo-functionality into the N^N domain leads to a red-shift in λ compared to the complexes with the benchmark N^N ligand 5. In the solid state, [Cu(1)(POP)][PF 6 ] and [Cu(1)(xantphos)][PF 6 ] (fluoro-substituent) exhibit the highest PL quantum yields (74 and 25%, respectively) with values of τ 1/2 = 11.1 and 5.8 μs, respectively. Light-emitting electrochemical cells (LECs) with [Cu(N^N)(P^P)][PF 6 ] complexes in the emissive layer have been tested. Using a block-wave pulsed current driving mode, the best performing device employed [Cu(1)(xantphos)] + and this showed a maximum luminance (Lum max ) of 129 cd m -2 and a device lifetime (t 1/2 ) of 54 h; however, the turn-on time (time to reach Lum max ) was 4.1 h. Trends in performance data reveal that the introduction of fluoro-groups is beneficial, but that the incorporation of heavier halo-substituents leads to poor devices, probably due to a detrimental effect on charge transport; LECs with the iodo-functionalized N^N ligand 4 failed to show any electroluminescence after 50 h.

Hydrodynamics of the VanA-type VanS histidine kinase: an extended solution conformation and first evidence for interactions with vancomycin

PubMed Central

Phillips-Jones, Mary K.; Channell, Guy; Kelsall, Claire J.; Hughes, Charlotte S.; Ashcroft, Alison E.; Patching, Simon G.; Dinu, Vlad; Gillis, Richard B.; Adams, Gary G.; Harding, Stephen E.

2017-01-01

VanA-type resistance to glycopeptide antibiotics in clinical enterococci is regulated by the VanSARA two-component signal transduction system. The nature of the molecular ligand that is recognised by the VanSA sensory component has not hitherto been identified. Here we employ purified, intact and active VanSA membrane protein (henceforth referred to as VanS) in analytical ultracentrifugation experiments to study VanS oligomeric state and conformation in the absence and presence of vancomycin. A combination of sedimentation velocity and sedimentation equilibrium in the analytical ultracentrifuge (SEDFIT, SEDFIT-MSTAR and MULTISIG analysis) showed that VanS in the absence of the ligand is almost entirely monomeric (molar mass M = 45.7 kDa) in dilute aqueous solution with a trace amount of high molar mass material (M ~ 200 kDa). The sedimentation coefficient s suggests the monomer adopts an extended conformation in aqueous solution with an equivalent aspect ratio of ~(12 ± 2). In the presence of vancomycin over a 33% increase in the sedimentation coefficient is observed with the appearance of additional higher s components, demonstrating an interaction, an observation consistent with our circular dichroism measurements. The two possible causes of this increase in s – either a ligand induced dimerization and/or compaction of the monomer are considered. PMID:28397853

Preparation and Structural Properties of InIII–H Complexes

PubMed Central

Sickerman, Nathaniel S.; Henry, Renée M.; Ziller, Joseph W.

2013-01-01

The use of the tripodal ligands tris[(N'-tert-butylureaylato)-N-ethyl]aminato ([H3buea]3−) and the sulfonamide-based N,N',N"-[2,2',2"-nitrilotris(ethane-2,1-diyl)]tris(2,4,6-trimethylbenzene-sulfonamidato) ([MST]3−) has led to the synthesis of two structurally distinct In(III)–OH complexes. The first example of a five-coordinate indium(III) complex with a terminal hydroxide ligand, K[InIIIH3buea(OH)], was prepared by addition of In(OAc)3 and water to a deprotonated solution of H6buea. X-ray diffraction analysis, as well as FTIR and 1H NMR spectroscopic methods, provided evidence for the formation of a monomeric In(III)–OH complex. The complex contains an intramolecular hydrogen bonding (H-bonding) network involving the In(III)–OH unit and [H3buea]3− ligand, which aided in isolation of the complex. Isotope labeling studies verified the source of the hydroxo ligand as water. Treatment of the [InIIIMST] complex with a mixture of 15-crown-5 ether and NaOH led to isolation of the complex [15-crown-5⊃NaI-(μ-OH)-InIIIMST], whose solid-state structure was confirmed using X-ray diffraction methods. Nuclear magnetic resonance studies on this complex suggest it retains its heterobimetallic structure in solution. PMID:25309019

Third-order nonlinear optical properties of soluble Cr(III)-dioxolene complexes

NASA Astrophysics Data System (ADS)

Noro, Shin-ichiro; Sassa, Takafumi; Aoyama, Tetsuya; Chang, Ho-Chol; Kitagawa, Susumu; Wada, Tatsuo

2004-10-01

We synthesized novel ligand-based mixed valence (LBMV) CrIII-dioxolene complexes, [Cr(X4SQ)(X4Cat)(4,4'-di-tert-butyl-2,2'-bpy)] (SQ = semiquinone, Cat = catecohol, 2,2'-bpy = 2,2'-bipyridine; X = Cl (2a) and Br (2b)) and [Cr(X4SQ)(X4Cat)(4,4'-dinonyl-2,2'-bpy)] (X = Cl (3a) and Br (3b)), and prepared thin films for investigating their third-order nonlinear optical (NLO) properties in terms of the mixed valence states. Electronic absorption spectra of these complexes in solution and solid states showed an intervalence charge-transfer (IVCT) band from Cat2- to SQ"- at the IR region, indicating of a coexistence of SQ and Cat ligands, namely, LBMV state of the complexes. These complexes were well soluble in nonpolar organic solvent, which allowed us to prepare thin films by spin coating. The obtained films showed the electronic absorption spectra similar to those in solution and were amorphous because of steric hindrance of halogen and alkyl substituents in o-dioxolene and 2,2'-bpy moieties, respectively. The x(3) values of the films of 3a and 3b with a thickness of 30 ~ 40 nm were determined for 1.0 × 10-12 esu at 1.907 μm.

Ligands Exchange Process on Gold Nanoparticles in Acetone Solution

NASA Astrophysics Data System (ADS)

Hu, C. L.; Mu, Y. Y.; Bian, Z. C.; Luo, Z. H.; Luo, K.; Huang, A. Z.

2018-05-01

The ligands exchange process on gold nanoparticles (GNPs) was proceeded by using hydrophobic group (PPh3) and hydrophilic group (THPO) in acetone solution. The FTIR and XPS results demonstrated that part of THPO was replaced by PPh3 which was dissolved in polar solution (acetone); the results were in accordance with the electrochemical analysis where the differential capacity decreased with increasing exchange time. After 12 h, the exchange process terminated and the final ratio of PPh3 and THPO was about 1.4: 1. This ratio remained unchanged although the PPh3 and THPO modified GNPs re-dispersed in the PPh3 acetone solution demonstrating the stable adsorption of both ligands after exchanging for 12 h. The TEM images showed that the gold nanoparticles were self-assembled from scattered to arranged morphology due to the existence of hydrophilic and hydrophobic ligands and led to Janus gold nanoparticles.

Analytical Solution of Steady State Equations for Chemical Reaction Networks with Bilinear Rate Laws

PubMed Central

Halász, Ádám M.; Lai, Hong-Jian; McCabe, Meghan M.; Radhakrishnan, Krishnan; Edwards, Jeremy S.

2014-01-01

True steady states are a rare occurrence in living organisms, yet their knowledge is essential for quasi-steady state approximations, multistability analysis, and other important tools in the investigation of chemical reaction networks (CRN) used to describe molecular processes on the cellular level. Here we present an approach that can provide closed form steady-state solutions to complex systems, resulting from CRN with binary reactions and mass-action rate laws. We map the nonlinear algebraic problem of finding steady states onto a linear problem in a higher dimensional space. We show that the linearized version of the steady state equations obeys the linear conservation laws of the original CRN. We identify two classes of problems for which complete, minimally parameterized solutions may be obtained using only the machinery of linear systems and a judicious choice of the variables used as free parameters. We exemplify our method, providing explicit formulae, on CRN describing signal initiation of two important types of RTK receptor-ligand systems, VEGF and EGF-ErbB1. PMID:24334389

Ligand-hole localization in oxides with unusual valence Fe

PubMed Central

Chen, Wei-Tin; Saito, Takashi; Hayashi, Naoaki; Takano, Mikio; Shimakawa, Yuichi

2012-01-01

Unusual high-valence states of iron are stabilized in a few oxides. A-site-ordered perovskite-structure oxides contain such iron cations and exhibit distinct electronic behaviors at low temperatures, e.g. charge disproportionation (4Fe4+ → 2Fe3+ + 2Fe5+) in CaCu3Fe4O12 and intersite charge transfer (3Cu2+ + 4Fe3.75+ → 3Cu3+ + 4Fe3+) in LaCu3Fe4O12. Here we report the synthesis of solid solutions of CaCu3Fe4O12 and LaCu3Fe4O12 and explain how the instabilities of their unusual valence states of iron are relieved. Although these behaviors look completely different from each other in simple ionic models, they can both be explained by the localization of ligand holes, which are produced by the strong hybridization of iron d and oxygen p orbitals in oxides. The localization behavior in the charge disproportionation of CaCu3Fe4O12 is regarded as charge ordering of the ligand holes, and that in the intersite charge transfer of LaCu3Fe4O12 is regarded as a Mott transition of the ligand holes. PMID:22690318

Extractant composition

DOEpatents

Smith, Barbara F.; Jarvinen, Gordon D.; Ryan, Robert R.

1990-01-01

An organic extracting solution useful for separating elements of the actinide series of the periodic table from elements of the lanthanide series, where both are in trivalent form. The extracting solution consists of a primary ligand and a secondary ligand, preferably in an organic solvent. The primary ligand is a substituted monothio-1,3-dicarbonyl, which includes a substituted 4-acyl-2-pyrazolin-5-thione, such as 4-benzoyl-2,4-dihydro-5-methyl-2-phenyl-3H-pyrazol-3-thione (BMPPT). The secondary ligand is a substituted phosphine oxide, such as trioctylphosphine oxide (TOPO).

Ultrafast kinetics of linkage isomerism in Na2[Fe(CN)5NO] aqueous solution revealed by time-resolved photoelectron spectroscopy

PubMed Central

Raheem, Azhr A.; Wilke, Martin; Borgwardt, Mario; Engel, Nicholas; Bokarev, Sergey I.; Grell, Gilbert; Aziz, Saadullah G.; Kühn, Oliver; Kiyan, Igor Yu.; Merschjann, Christoph; Aziz, Emad F.

2017-01-01

The kinetics of ultrafast photoinduced structural changes in linkage isomers is investigated using Na2[Fe(CN)5NO] as a model complex. The buildup of the metastable side-on configuration of the NO ligand, as well as the electronic energy levels of ground, excited, and metastable states, has been revealed by means of time-resolved extreme UV (XUV) photoelectron spectroscopy in aqueous solution, aided by theoretical calculations. Evidence of a short-lived intermediate state in the isomerization process and its nature are discussed, finding that the complete isomerization process occurs in less than 240 fs after photoexcitation. PMID:28713840

Contrasting coordination behavior of Group 12 perchlorate salts with an acyclic N3O2 donor ligand by X-ray crystallography and (1)H NMR.

PubMed

Tice, Daniel B; Pike, Robert D; Bebout, Deborah C

2016-08-09

An unbranched N3O2 ligand 2,6-bis[((2-pyridinylmethyl)oxy)methyl]pyridine (L1) was used to prepare new mononuclear heteroleptic Group 12 perchlorate complexes characterized by IR, (1)H NMR and X-ray crystallography. Racemic complexes with pentadentate L1 and one to four oxygens from either water or perchlorate bound to a metal ion were structurally characterized. Octahedral [Zn(L1)(OH2)](ClO4)2 (1) and pentagonal bipyramidal [Cd(L1)(OH2)(OClO3)]ClO4 (2) structures were found with lighter congeners. The polymorphic forms of [Hg(L1)(ClO4)2] characterized (3 in P1[combining macron] and 4 in P21/c) had a mix of monodentate, anisobidentate and bidentate perchlorates, providing the first examples of a tricapped trigonal prismatic Hg(ii) coordination geometry, as well as additional examples of a rare square antiprismatic Hg(ii) coordination geometry. Solution state (1)H NMR characterization of the Group 12 complexes in CD3CN indicated intramolecular reorganization remained rapid under conditions where intermolecular M-L1 exchange was slow on the chemical shift time scale for Zn(ii) and on the J(M(1)H) time scale for Cd(ii) and Hg(ii). Solution studies with more than one equivalent of ligand also suggested that a complex with a 1 : 2 ratio of M : L1 contributed significantly to solution equilibria with Hg(ii) but not the other metal ions. The behavior of related linear pentadentate ligands with Group 12 perchlorate salts is discussed.

Silver baits for the "miraculous draught" of amphiphilic lanthanide helicates.

PubMed

Terazzi, Emmanuel; Guénée, Laure; Varin, Johan; Bocquet, Bernard; Lemonnier, Jean-François; Emery, Daniel; Mareda, Jiri; Piguet, Claude

2011-01-03

The axial connection of flexible thioalkyls chains of variable length (n=1-12) within the segmental bis-tridentate 2-benzimidazole-8-hydroxyquinoline ligands [L12(Cn) -2 H](2-) provides amphiphilic receptors designed for the synthesis of neutral dinuclear lanthanides helicates. However, the stoichiometric mixing of metals and ligands in basic media only yields intricate mixtures of poorly soluble aggregates. The addition of Ag(I) in solution restores classical helicate architectures for n=3, with the quantitative formation of the discrete D(3) -symmetrical [Ln(2) Ag2(L12(C3) -2 H)(3) ](2+) complexes at millimolar concentration (Ln=La, Eu, Lu). The X-ray crystal structure supports the formation of [La(2) Ag(2) (L12(C3) -2 H)(3) ][OTf](2) , which exists in the solid state as infinite linear polymers bridged by S-Ag-S bonds. In contrast, molecular dynamics (MD) simulations in the gas phase and in solution confirm the experimental diffusion measurements, which imply the formation of discrete molecular entities in these media, in which the sulfur atoms of each lipophilic ligand are rapidly exchanged within the Ag(I) coordination sphere. Turned as a predictive tool, MD suggests that this Ag(I) templating effect is efficient only for n=1-3, while for n>3 very loose interactions occur between Ag(I) and the thioalkyl residues. The subsequent experimental demonstration that only 25 % of the total ligand speciation contributes to the formation of [Ln(2) Ag(2) (L12(C12) -2 H)(3) ](2+) in solution puts the bases for a rational approach for the design of amphiphilic helical complexes with predetermined molecular interfaces. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cationic Gold Clusters Ligated with Differently Substituted Phosphines: Effect of Substitution on Ligand Reactivity and Binding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Grant E.; Olivares, Astrid M.; Hill, David E.

2015-01-01

We present a systematic study of the effect of the number of methyl (Me) and cyclohexyl (Cy) functional groups in monodentate phosphine ligands on the solution-phase synthesis of ligated sub-nanometer gold clusters and their gas-phase fragmentation pathways. Small mixed ligand cationic gold clusters were synthesized using ligand exchange reactions between pre-formed triphenylphosphine ligated (PPh3) gold clusters and monodentate Me- and Cy-substituted ligands in solution and characterized using electrospray ionization mass spectrometry (ESI-MS) and collision-induced dissociation (CID) experiments. Under the same experimental conditions, larger gold-PPh3 clusters undergo efficient exchange of unsubstituted PPh3 ligands for singly Me- and Cy-substituted PPh2Me and PPh2Cymore » ligands. The efficiency of ligand exchange decreases with an increasing number of Me or Cy groups in the substituted phosphine ligands. CID experiments performed for a series of ligand-exchanged gold clusters indicate that loss of a neutral Me-substituted ligand is preferred over loss of a neutral PPh¬3 ligand while the opposite trend is observed for Cy-substituted ligands. The branching ratio of the competing ligand loss channels is strongly correlated with the electron donating ability of the phosphorous lone pair as determined by the relative proton affinity of the ligand. The results indicate that the relative ligand binding energies increase in the order PMe3 < PPhMe2 < PPh2Me < PPh3< PPh2Cy < PPhCy2< PCy3. Furthermore, the difference in relative ligand binding energies increases with the number of substituted PPh3-mMem or PPh3-mCym ligands (L) exchanged onto each cluster. This study provides the first experimental determination of the relative binding energies of ligated gold clusters containing differently substituted monophosphine ligands, which are important to controlling their synthesis and reactivity in solution. The results also indicate that ligand substitution is an important parameter that must be considered in theoretical modeling of these complex systems« less

Remediation of lead-contaminated soil with non-toxic biodegradable natural ligands extracted from soybean.

PubMed

Lee, Yong-Woo; Kim, Chulsung

2012-01-01

Bench-scale soil washing studies were performed to evaluate the potential application of non-toxic, biodegradable extracted soybean-complexing ligands for the remediation of lead-contaminated soils. Results showed that, with extracted soybean-complexing ligands, lead solubility extensively increased when pH of the solution was higher than 6, and approximately 10% (500 mg/kg) of lead was removed from a rifle range soil. Two potential primary factors controlling the effectiveness of lead extraction from lead-contaminated soils with natural ligands are adsorption of extracted aqueous lead ions onto the ground soybean and the pH of the extraction solution. More complexing ligands were extracted from the ground soybean as the reaction pH increased. As a result, significantly higher lead extraction efficiency was observed under basic environments. In addition, less adsorption onto soybean was observed when the pH of the solution was higher than 7. Among two available Lewis base functional groups in the extracted soybean-complexing ligands such as carboxylate and the alpha-amino functional groups, the non-protonated alpha-amino functional groups may play an important role for the dissolution of lead from lead-contaminated soil through the formation of soluble lead--ligand complexes.

Modelling of trace metal uptake by roots taking into account complexation by exogenous organic ligands

NASA Astrophysics Data System (ADS)

Jean-Marc, Custos; Christian, Moyne; Sterckeman, Thibault

2010-05-01

The context of this study is phytoextraction of soil trace metals such as Cd, Pb or Zn. Trace metal transfer from soil to plant depends on physical and chemical processes such as minerals alteration, transport, adsorption/desorption, reactions in solution and biological processes including the action of plant roots and of associated micro-flora. Complexation of metal ions by organic ligands is considered to play a role on the availability of trace metals for roots in particular in the event that synthetic ligands (EDTA, NTA, etc.) are added to the soil to increase the solubility of the contaminants. As this role is not clearly understood, we wanted to simulate it in order to quantify the effect of organic ligands on root uptake of trace metals and produce a tool which could help in optimizing the conditions of phytoextraction.We studied the effect of an aminocarboxilate ligand on the absorption of the metal ion by roots, both in hydroponic solution and in soil solution, for which we had to formalize the buffer power for the metal. We assumed that the hydrated metal ion is the only form which can be absorbed by the plants. Transport and reaction processes were modelled for a system made up of the metal M, a ligand L and the metal complex ML. The Tinker-Nye-Barber model was adapted to describe the transport of solutes M, L and ML in the soil and absorption of M by the roots. This allowed to represent the interactions between transport, chelating reactions, absorption of the solutes at the root surface, root growth with time, in order to simulate metal uptake by a whole root system.Several assumptions were tested such as i) absorption of the metal by an infinite sink and according to a Michaelis-Menten kinetics, solutes transport by diffusion with and without ii) mass flow and iii) soil buffer power for the ligand L. In hydroponic solution (without soil buffer power), ligands decreased the trace metal flux towards roots, as they reduced the concentration of hydrated metal ion. In soil, depending on the L/M ratio, the presence of metal complexes could increase the metal flux taken up by roots since the ligand desorbed the metal on soil solid phase while the complex dissociated and provided metal ions to the solution in the vicinity of the root.The model enabled to surround the conditions in which phytoextraction is thus optimized. In addition of complexation by organic ligands added to the soil, we expect to integrate complexation by roots organic exudates and by soil organic matter, as well as the competition of the metal ions with Ca2+ et H+.

Condensed, solution and gas phase behaviour of mono- and dinuclear 2,6-diacetylpyridine (dap) hydrazone copper complexes probed by X-ray, mass spectrometry and theoretical calculations.

PubMed

Neto, Brenno A D; Viana, Barbara F L; Rodrigues, Thyago S; Lalli, Priscila M; Eberlin, Marcos N; da Silva, Wender A; de Oliveira, Heibbe C B; Gatto, Claudia C

2013-08-28

We describe the synthesis of novel mononuclear and dinuclear copper complexes and an investigation of their behaviour in solution using mass spectrometry (ESI-MS and ESI-MS/MS) and in the solid state using X-ray crystallography. The complexes were synthesized from two widely used diacetylpryridine (dap) ligands, i.e. 2,6-diacetylpyridinebis(benzoic acid hydrazone) and 2,6-diacetylpyridinebis(2-aminobenzoic acid hydrazone). Theoretical calculations (DFT) were used to predict the complex geometries of these new structures, their equilibrium in solution and energies associated with the transformations.

Phosphorescent heterobimetallic complexes involving platinum(iv) and rhenium(vii) centers connected by an unsupported μ-oxido bridge.

PubMed

Molaee, Hajar; Nabavizadeh, S Masoud; Jamshidi, Mahboubeh; Vilsmeier, Max; Pfitzner, Arno; Samandar Sangari, Mozhgan

2017-11-28

Heterobimetallic compounds [(C^N)LMe 2 Pt(μ-O)ReO 3 ] (C^N = ppy, L = PPh 3 , 2a; C^N = ppy, L = PMePh 2 , 2b; C^N = bhq, L = PPh 3 , 2c; C^N = bhq, L = PMePh 2 , 2d) containing a discrete unsupported Pt(iv)-O-Re(vii) bridge have been synthesized through a targeted synthesis route. The compounds have been prepared by a single-pot synthesis in which the Pt(iv) precursor [PtMe 2 I(C^N)L] complexes are allowed to react easily with AgReO 4 in which the iodide ligand of the starting Pt(iv) complex is replaced by an ReO 4 - anion. In these Pt-O-Re complexes, the Pt(iv) centers have an octahedral geometry, completed by a cyclometalated bidentate ligand (C^N), two methyl groups and a phosphine ligand, while the Re(vii) centers have a tetrahedral geometry. Elemental analysis, single crystal X-ray diffraction analysis and multinuclear NMR spectroscopy are used to establish their identities. The new complexes exhibit phosphorescence emission in the solid and solution states at 298 and 77 K, which is an uncommon property of platinum complexes with an oxidation state of +4. According to DFT calculations, we found that this emission behavior in the new complexes originates from ligand centered 3 LC (C^N) character with a slight amount of metal to ligand charge transfer ( 3 MLCT). The solid-state emission data of the corresponding cycloplatinated(iv) precursor complexes [PtMe 2 I(C^N)L], 1a-1d, pointed out that the replacement of I - by an ReO 4 - anion helps enhancing the emission efficiency besides shifting the emission wavelengths.

Bioinspired Orientation of β-Substituents on Porphyrin Antenna Ligands Switches Ytterbium(III) NIR Emission with Thermosensitivity.

PubMed

Ning, Yingying; Ke, Xian-Sheng; Hu, Ji-Yun; Liu, Yi-Wei; Ma, Fang; Sun, Hao-Ling; Zhang, Jun-Long

2017-02-20

"Configurational isomerism" is an important approach found in naturally occurring chlorophylls to modulate light harvesting function without significant structural changes; however, this feature has been seldom applied in design of antenna ligands for lanthanide (Ln) sensitization. In this work, we introduced a bioinspired approach by orientation of β-dilactone moieties on porphyrinates, namely cis-/trans-porphodilactones, to modulate the energy transfer process from the lowest triplet excited state of the ligand (T 1 ) to the emitting level of ytterbium(III) ( 2 F 5/2 , Yb*). Interestingly, near-infrared (NIR) emission of Yb(III) could be switched "on" by the cis-porphodilactone ligand, while the trans-isomer renders Yb(III) emission "off" and the ratio of quantum yields is ∼8. Analysis of the structure-photophysical properties relationship suggests that the significant emission difference is correlated to the energy gaps between T 1 and Yb* (1152 cm -1 in the cis- vs -25 cm -1 in the trans-isomer). More interestingly, due to back energy transfer (BEnT), the Yb(III) complex of cis-porphodilactone exhibits NIR emission with high thermosensitivity (4.0%°C -1 in solution and 4.9%°C -1 in solid state), comparable to previously reported terbium (Tb) and europium (Eu) visible emitters, in contrast to the trivial emission changes of the trans-isomer and porphyrin and porpholactone analogues. This work opens up new access to design NIR emissive Ln complexes by bioinspired modification of antenna ligands.

Sulfate Separation by Selective Crystallization with a Bis-iminoguanidinium Ligand.

PubMed

Seipp, Charles A; Williams, Neil J; Custelcean, Radu

2016-09-08

A simple and effective method for selective sulfate separation from aqueous solutions by crystallization with a bis-guanidinium ligand, 1,4-benzene-bis(iminoguanidinium) (BBIG), is demonstrated. The ligand is synthesized as the chloride salt (BBIG-Cl) by in situ imine condensation of terephthalaldehyde with aminoguanidinium chloride in water, followed by crystallization as the sulfate salt (BBIG-SO4). Alternatively, BBIG-Cl is synthesized ex situ in larger scale from ethanol. The sulfate separation ability of the BBIG ligand is demonstrated by selective and quantitative crystallization of sulfate from seawater. The ligand can be recycled by neutralization of BBIG-SO4 with aqueous NaOH and crystallization of the neutral bis-iminoguanidine, which can be converted back into BBIG-Cl with aqueous HCl and reused in another separation cycle. Finally, (35)S-labeled sulfate and β liquid scintillation counting are employed for monitoring the sulfate concentration in solution. Overall, this protocol will instruct the user in the necessary skills to synthesize a ligand, employ it in the selective crystallization of sulfate from aqueous solutions, and quantify the separation efficiency.

Sulfate Separation by Selective Crystallization with a Bis-iminoguanidinium Ligand

DOE PAGES

Seipp, Charles A.; Williams, Neil J.; Custelcean, Radu

2016-01-01

One simple and effective method for selective sulfate separation from aqueous solutions by crystallization with a bis-guanidinium ligand, 1,4-benzene-bis(iminoguanidinium) (BBIG), is demonstrated. The ligand is synthesized as the chloride salt (BBIG-Cl) by in situ imine condensation of terephthalaldehyde with aminoguanidinium chloride in water, followed by crystallization as the sulfate salt (BBIG-SO4). Alternatively, BBIG-Cl is synthesized ex situ in larger scale from ethanol. Furthermore, the sulfate separation ability of the BBIG ligand is demonstrated by selective and quantitative crystallization of sulfate from seawater. These ligands can then be recycled by neutralization of BBIG-SO4 with aqueous NaOH and crystallization of the neutralmore » bis-iminoguanidine, which can be converted back into BBIG-Cl with aqueous HCl and reused in another separation cycle. Finally, 35S-labeled sulfate and β liquid scintillation counting are employed for monitoring the sulfate concentration in solution. Overall, this protocol will instruct the user in the necessary skills to synthesize a ligand, employ it in the selective crystallization of sulfate from aqueous solutions, and quantify the separation efficiency.« less

Effect of stochastic gating on channel-facilitated transport of non-interacting and strongly repelling solutes.

PubMed

Berezhkovskii, Alexander M; Bezrukov, Sergey M

2017-08-28

Ligand- or voltage-driven stochastic gating-the structural rearrangements by which the channel switches between its open and closed states-is a fundamental property of biological membrane channels. Gating underlies the channel's ability to respond to different stimuli and, therefore, to be functionally regulated by the changing environment. The accepted understanding of the gating effect on the solute flux through the channel is that the mean flux is the product of the flux through the open channel and the probability of finding the channel in the open state. Here, using a diffusion model of channel-facilitated transport, we show that this is true only when the gating is much slower than the dynamics of solute translocation through the channel. If this condition breaks, the mean flux could differ from this simple estimate by orders of magnitude.

Online size-exclusion high-performance liquid chromatography light scattering and differential refractometry methods to determine degree of polymer conjugation to proteins and protein-protein or protein-ligand association states.

PubMed

Kendrick, B S; Kerwin, B A; Chang, B S; Philo, J S

2001-12-15

Characterizing the solution structure of protein-polymer conjugates and protein-ligand interactions is important in fields such as biotechnology and biochemistry. Size-exclusion high-performance liquid chromatography with online classical light scattering (LS), refractive index (RI), and UV detection offers a powerful tool in such characterization. Novel methods are presented utilizing LS, RI, and UV signals to rapidly determine the degree of conjugation and the molecular mass of the protein conjugate. Baseline resolution of the chromatographic peaks is not required; peaks need only be sufficiently separated to represent relatively pure fractions. An improved technique for determining the polypeptide-only mass of protein conjugates is also described. These techniques are applied to determining the degree of erythropoietin glycosylation, the degree of polyethylene glycol conjugation to RNase A and brain-derived neurotrophic factor, and the solution association states of these molecules. Calibration methods for the RI, UV, and LS detectors will also be addressed, as well as online methods to determine protein extinction coefficients and dn/dc values both unconjugated and conjugated protein molecules. (c)2001 Elsevier Science.

fac-Re(CO)3 complexes of 2,6-bis(4-substituted-1,2,3-triazol-1-ylmethyl)pyridine "click" ligands: synthesis, characterisation and photophysical properties.

PubMed

Anderson, Christopher B; Elliott, Anastasia B S; Lewis, James E M; McAdam, C John; Gordon, Keith C; Crowley, James D

2012-12-28

The syntheses of the 4-n-propyl and 4-phenyl substituted fac-Re(CO)(3) complexes of the tridentate "click" ligand (2,6-bis(4-substituted-1,2,3-triazol-1-ylmethyl)pyridine) are described. The complexes were obtained by refluxing methanol solutions of [Re(CO)(5)Cl], AgPF(6) and either the 4-propyl or 4-phenyl substituted ligand for 16 h. The ligands and the two rhenium(I) complexes were characterised by elemental analysis, HR-ESMS, ATR-IR, (1)H and (13)C NMR spectroscopy and the molecular structures of both complexes were confirmed by X-ray crystallography. The electronic structure of the fac-Re(CO)(3) "click" complexes was probed using UV-Vis, Raman and emission spectroscopy, cyclic voltammetry and DFT calculations. Altering the electronic nature of the ligand's substituent, from aromatic to alkyl, had little effect on the absorption/emission maxima and electrochemical properties of the complexes indicating that the 1,2,3-triazole unit may insulate the metal centre from the electronic modification at the ligands' periphery. Both Re(I) complexes were found to be weakly emitting with short excited state lifetimes. The electrochemistry of the complexes is defined by quasi-reversible Re oxidation and irreversible triazole-based ligand reduction processes.

Separation of actinides from lanthanides

DOEpatents

Smith, B.F.; Jarvinen, G.D.; Ryan, R.R.

1988-03-31

An organic extracting solution and an extraction method useful for separating elements of the actinide series of the periodic table from elements of the lanthanide series, where both are in trivalent form is described. The extracting solution consists of a primary ligand and a secondary ligand, preferably in an organic solvent. The primary ligand is a substituted monothio-1,3-dicarbonyl, which includes a substituted 4-acyl-2-pyrazolin-5-thione, such as 4-benzoyl-2,4- dihydro-5-methyl-2-phenyl-3H-pyrazol-3-thione (BMPPT). The secondary ligand is a substituted phosphine oxide, such as trioctylphosphine oxide (TOPO).

Separation of actinides from lanthanides

DOEpatents

Smith, Barbara F.; Jarvinen, Gordon D.; Ryan, Robert R.

1989-01-01

An organic extracting solution and an extraction method useful for separating elements of the actinide series of the periodic table from elements of the lanthanide series, where both are in trivalent form. The extracting solution consists of a primary ligand and a secondary ligand, preferably in an organic solvent. The primary ligand is a substituted monothio-1,3-dicarbonyl, which includes a substituted 4-acyl-2-pyrazolin-5-thione, such as 4-benzoyl-2,4-dihydro-5-methyl-2-phenyl-3H-pyrazol-3-thione (BMPPT). The secondary ligand is a substituted phosphine oxide, such as trioctylphosphine oxide (TOPO).

Exploring the potential energy surface for the interaction of sterically hindered trichloro(diethylenetriamine)gold(III) complexes with water.

PubMed

Dos Santos, Hélio F; Paschoal, Diego; Burda, Jaroslav V

2012-11-15

The reactivity of gold(III) complexes is analyzed for a series of derivatives of 3-azapentane-1,5-diamine (dien) tridentate ligand that can contain some bulky substituents. Two distinct series of compounds are considered where the dien ligand is either deprotonated (R-dien-H) or protonated (R-dien) at the secondary amine where R = ethyl (Et) or methyl (Me). While the deprotonated species will occur in neutral and basic solutions, the protonated forms are likely to be present in acidic environment. Hydration reaction (water/Cl(-) ligand exchange) of 14 complexes is modeled with quantum chemical calculations. Our calculations predict that the reactivity decreases with the increase in the molecular volume of the substituted dien ligand, and the calculated rate constants are in satisfactory agreement with experimental results. In addition, quantitative structure/reactivity models are proposed where the angle between the entering and leaving groups in the transition state structure (the reactivity angle) is used as a molecular descriptor. These models explain the trend of the relative reactivity of these complexes and can be used to design new ligands for gold(III) complexes aiming to adjust the reactivity of the complex.

WAXS studies of the structural diversity of hemoglobin in solution.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Makowski, L.; Bardhan, J.; Gore, D.

2011-01-01

Specific ligation states of hemoglobin are, when crystallized, capable of taking on multiple quaternary structures. The relationship between these structures, captured in crystal lattices, and hemoglobin structure in solution remains uncertain. Wide-angle X-ray solution scattering (WAXS) is a sensitive probe of protein structure in solution that can distinguish among similar structures and has the potential to contribute to these issues. We used WAXS to assess the relationships among the structures of human and bovine hemoglobins in different liganded forms in solution. WAXS data readily distinguished among the various forms of hemoglobins. WAXS patterns confirm some of the relationships among hemoglobinmore » structures that have been defined through crystallography and NMR and extend others. For instance, methemoglobin A in solution is, as expected, nearly indistinguishable from HbCO A. Interestingly, for bovine hemoglobin, the differences between deoxy-Hb, methemoglobin and HbCO are smaller than the corresponding differences in human hemoglobin. WAXS data were also used to assess the spatial extent of structural fluctuations of various hemoglobins in solution. Dynamics has been implicated in allosteric control of hemoglobin, and increased dynamics has been associated with lowered oxygen affinity. Consistent with that notion, WAXS patterns indicate that deoxy-Hb A exhibits substantially larger structural fluctuations than HbCO A. Comparisons between the observed WAXS patterns and those predicted on the basis of atomic coordinate sets suggest that the structures of Hb in different liganded forms exhibit clear differences from known crystal structure.« less

Femtosecond time-resolved optical and Raman spectroscopy of photoinduced spin crossover: temporal resolution of low-to-high spin optical switching.

PubMed

Smeigh, Amanda L; Creelman, Mark; Mathies, Richard A; McCusker, James K

2008-10-29

A combination of femtosecond electronic absorption and stimulated Raman spectroscopies has been employed to determine the kinetics associated with low-spin to high-spin conversion following charge-transfer excitation of a FeII spin-crossover system in solution. A time constant of tau = 190 +/- 50 fs for the formation of the 5T2 ligand-field state was assigned based on the establishment of two isosbestic points in the ultraviolet in conjunction with changes in ligand stretching frequencies and Raman scattering amplitudes; additional dynamics observed in both the electronic and vibrational spectra further indicate that vibrational relaxation in the high-spin state occurs with a time constant of ca. 10 ps. The results set an important precedent for extremely rapid, formally forbidden (DeltaS = 2) nonradiative relaxation as well as defining the time scale for intramolecular optical switching between two electronic states possessing vastly different spectroscopic, geometric, and magnetic properties.

Solution equilibrium behind the room-temperature synthesis of nanocrystalline titanium dioxide

NASA Astrophysics Data System (ADS)

Seisenbaeva, Gulaim A.; Daniel, Geoffrey; Nedelec, Jean-Marie; Kessler, Vadim G.

2013-03-01

Formation of nanocrystalline and monodisperse TiO2 from a water soluble and stable precursor, ammonium oxo-lactato-titanate, (NH4)8Ti4O4(Lactate)8.4H2O, often referred to as TiBALDH or TALH, is demonstrated to be due to a coordination equilibrium. This compound, individual in the solid state, exists in solution in equilibrium with ammonium tris-lactato-titanate, (NH4)2Ti(Lactate)3 and uniform crystalline TiO2 nanoparticles (anatase) stabilized by surface-capping with lactate ligands. This equilibrium can be shifted towards nano-TiO2via application of a less polar solvent like methanol or ethanol, dilution of the solution, introduction of salts or raising the temperature, and reverted on addition of polar and strongly solvating media such as dimethyl sulfoxide, according to NMR. Aggregation and precipitation of the particles were followed by DLS and could be achieved by a decrease in their surface charge by adsorption of strongly hydrogen-bonding cations, e.g. in solutions of ammonia, ethanolamine or amino acid arginine or by addition of ethanol. The observed equilibrium may be involved in formation of nano-titania on the surface of plant roots exerting chelating organic carboxylate ligands and thus potentially influencing plant interactions.Formation of nanocrystalline and monodisperse TiO2 from a water soluble and stable precursor, ammonium oxo-lactato-titanate, (NH4)8Ti4O4(Lactate)8.4H2O, often referred to as TiBALDH or TALH, is demonstrated to be due to a coordination equilibrium. This compound, individual in the solid state, exists in solution in equilibrium with ammonium tris-lactato-titanate, (NH4)2Ti(Lactate)3 and uniform crystalline TiO2 nanoparticles (anatase) stabilized by surface-capping with lactate ligands. This equilibrium can be shifted towards nano-TiO2via application of a less polar solvent like methanol or ethanol, dilution of the solution, introduction of salts or raising the temperature, and reverted on addition of polar and strongly solvating media such as dimethyl sulfoxide, according to NMR. Aggregation and precipitation of the particles were followed by DLS and could be achieved by a decrease in their surface charge by adsorption of strongly hydrogen-bonding cations, e.g. in solutions of ammonia, ethanolamine or amino acid arginine or by addition of ethanol. The observed equilibrium may be involved in formation of nano-titania on the surface of plant roots exerting chelating organic carboxylate ligands and thus potentially influencing plant interactions. Electronic supplementary information (ESI) available: Crystallographic data in cif and table format, detailed description of hydrogen bonding in (NH4)2[Ti(l-Lactate)3].3H2O, additional TEM images, DLS data on particle size in solutions and NanoSight data on particle size distribution, photos of produced TiO2 colloids, details of NMR experiments and a real-time movie demonstrating the equilibrium leading to TiO2 formation and re-dissolution in pH-neutral ammonium lactate solutions. CCDC 915222. For ESI and crystallographic data in CIF or other electronic format. see DOI: 10.1039/c3nr34068f

Controlling the size of hot injection made nanocrystals by manipulating the diffusion coefficient of the solute.

PubMed

De Nolf, Kim; Capek, Richard K; Abe, Sofie; Sluydts, Michael; Jang, Youngjin; Martins, José C; Cottenier, Stefaan; Lifshitz, Efrat; Hens, Zeger

2015-02-25

We investigate the relation between the chain length of ligands used and the size of the nanocrystals formed in the hot injection synthesis. With two different CdSe nanocrystal syntheses, we consistently find that longer chain carboxylic acids result in smaller nanocrystals with improved size dispersions. By combining a more in-depth experimental investigation with kinetic reaction simulations, we come to the conclusion that this size tuning is due to a change in the diffusion coefficient and the solubility of the solute. The relation between size tuning by the ligand chain length and the coordination of the solute by the ligands is further explored by expanding the study to amines and phosphine oxides. In line with the weak coordination of CdSe nanocrystals by amines, no influence of the chain length on the nanocrystals is found, whereas the size tuning brought about by phosphine oxides can be attributed to a solubility change. We conclude that the ligand chain length provides a practical handle to optimize the outcome of a hot injection synthesis in terms of size and size dispersion and can be used to probe the interaction between ligands and the actual solute.

Molecular simulations of multimodal ligand-protein binding: elucidation of binding sites and correlation with experiments.

PubMed

Freed, Alexander S; Garde, Shekhar; Cramer, Steven M

2011-11-17

Multimodal chromatography, which employs more than one mode of interaction between ligands and proteins, has been shown to have unique selectivity and high efficacy for protein purification. To test the ability of free solution molecular dynamics (MD) simulations in explicit water to identify binding regions on the protein surface and to shed light on the "pseudo affinity" nature of multimodal interactions, we performed MD simulations of a model protein ubiquitin in aqueous solution of free ligands. Comparisons of MD with NMR spectroscopy of ubiquitin mutants in solutions of free ligands show a good agreement between the two with regard to the preferred binding region on the surface of the protein and several binding sites. MD simulations also identify additional binding sites that were not observed in the NMR experiments. "Bound" ligands were found to be sufficiently flexible and to access a number of favorable conformations, suggesting only a moderate loss of ligand entropy in the "pseudo affinity" binding of these multimodal ligands. Analysis of locations of chemical subunits of the ligand on the protein surface indicated that electrostatic interaction units were located on the periphery of the preferred binding region on the protein. The analysis of the electrostatic potential, the hydrophobicity maps, and the binding of both acetate and benzene probes were used to further study the localization of individual ligand moieties. These results suggest that water-mediated electrostatic interactions help the localization and orientation of the MM ligand to the binding region with additional stability provided by nonspecific hydrophobic interactions.

Effects of electrostatic interactions on ligand dissociation kinetics

NASA Astrophysics Data System (ADS)

Erbaş, Aykut; de la Cruz, Monica Olvera; Marko, John F.

2018-02-01

We study unbinding of multivalent cationic ligands from oppositely charged polymeric binding sites sparsely grafted on a flat neutral substrate. Our molecular dynamics simulations are suggested by single-molecule studies of protein-DNA interactions. We consider univalent salt concentrations spanning roughly a 1000-fold range, together with various concentrations of excess ligands in solution. To reveal the ionic effects on unbinding kinetics of spontaneous and facilitated dissociation mechanisms, we treat electrostatic interactions both at a Debye-Hückel (DH) (or implicit ions, i.e., use of an electrostatic potential with a prescribed decay length) level and by the more precise approach of considering all ionic species explicitly in the simulations. We find that the DH approach systematically overestimates unbinding rates, relative to the calculations where all ion pairs are present explicitly in solution, although many aspects of the two types of calculation are qualitatively similar. For facilitated dissociation (FD) (acceleration of unbinding by free ligands in solution) explicit-ion simulations lead to unbinding at lower free-ligand concentrations. Our simulations predict a variety of FD regimes as a function of free-ligand and ion concentrations; a particularly interesting regime is at intermediate concentrations of ligands where nonelectrostatic binding strength controls FD. We conclude that explicit-ion electrostatic modeling is an essential component to quantitatively tackle problems in molecular ligand dissociation, including nucleic-acid-binding proteins.

Revisiting HgCl 2: A solution- and solid-state 199Hg NMR and ZORA-DFT computational study

NASA Astrophysics Data System (ADS)

Taylor, R. E.; Carver, Colin T.; Larsen, Ross E.; Dmitrenko, Olga; Bai, Shi; Dybowski, C.

2009-07-01

The 199Hg chemical-shift tensor of solid HgCl 2 was determined from spectra of polycrystalline materials, using static and magic-angle spinning (MAS) techniques at multiple spinning frequencies and field strengths. The chemical-shift tensor of solid HgCl 2 is axially symmetric ( η = 0) within experimental error. The 199Hg chemical-shift anisotropy (CSA) of HgCl 2 in a frozen solution in dimethylsulfoxide (DMSO) is significantly smaller than that of the solid, implying that the local electronic structure in the solid is different from that of the material in solution. The experimental chemical-shift results (solution and solid state) are compared with those predicted by density functional theory (DFT) calculations using the zeroth-order regular approximation (ZORA) to account for relativistic effects. 199Hg spin-lattice relaxation of HgCl 2 dissolved in DMSO is dominated by a CSA mechanism, but a second contribution to relaxation arises from ligand exchange. Relaxation in the solid state is independent of temperature, suggesting relaxation by paramagnetic impurities or defects.

Active Brownian agents with concentration-dependent chemotactic sensitivity.

PubMed

Meyer, Marcel; Schimansky-Geier, Lutz; Romanczuk, Pawel

2014-02-01

We study a biologically motivated model of overdamped, autochemotactic Brownian agents with concentration-dependent chemotactic sensitivity. The agents in our model move stochastically and produce a chemical ligand at their current position. The ligand concentration obeys a reaction-diffusion equation and acts as a chemoattractant for the agents, which bias their motion towards higher concentrations of the dynamically altered chemical field. We explore the impact of concentration-dependent response to chemoattractant gradients on large-scale pattern formation, by deriving a coarse-grained macroscopic description of the individual-based model, and compare the conditions for emergence of inhomogeneous solutions for different variants of the chemotactic sensitivity. We focus primarily on the so-called receptor-law sensitivity, which models a nonlinear decrease of chemotactic sensitivity with increasing ligand concentration. Our results reveal qualitative differences between the receptor law, the constant chemotactic response, and the so-called log law, with respect to stability of the homogeneous solution, as well as the emergence of different patterns (labyrinthine structures, clusters, and bubbles) via spinodal decomposition or nucleation. We discuss two limiting cases, where the model can be reduced to the dynamics of single species: (I) the agent density governed by a density-dependent effective diffusion coefficient and (II) the ligand field with an effective bistable, time-dependent reaction rate. In the end, we turn to single clusters of agents, studying domain growth and determining mean characteristics of the stationary inhomogeneous state. Analytical results are confirmed and extended by large-scale GPU simulations of the individual based model.

Homoleptic Ce(III) and Ce(IV) Nitroxide Complexes: Significant Stabilization of the 4+ Oxidation State

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bogart, Justin A.; Lewis, Andrew J.; Medling, Scott A.

2014-06-25

Electrochemical experiments performed on the complex Ce-IV[2-((BuNO)-Bu-t)py](4), where [2-((BuNO)-Bu-t)py](-) = N-tert-butyl-N-2-pyridylnitroxide, indicate a 2.51 V stabilization of the 4+ oxidation state of Ce compared to [(Bu4N)-Bu-n](2)[Ce(NO3)(6)] in acetonitrile and a 2.95 V stabilization compared to the standard potential for the ion under aqueous conditions. Density functional theory calculations suggest that this preference for the higher oxidation state is a result of the tetrakis(nitroxide) ligand framework at the Ce cation, which allows for effective electron donation into, and partial covalent overlap with, vacant 4f orbitals with delta symmetry. The results speak to the behavior of CeO2 and related solid solutions inmore » oxygen uptake and transport applications, in particular an inherent local character of bonding that stabilizes the 4+ oxidation state. The results indicate a cerium(IV) complex that has been stabilized to an unprecedented degree through tuning of its ligand-field environment.« less

Mechanisms of neptunium redox reactions in nitric acid solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chatterjee, Sayandev; Bryan, Samuel A.; Casella, Amanda J.

First transuranium element neptunium (Np) exhibits complicated behavior in acidic solutions because it can adopt wide range of oxidation states typically from +3 to +6 and coordinate large variety of ligands. In particular, accurate determination of Np redox potentials in nitric acid solutions is challenging due to overlapping chemical and electrochemical reactions leading to significant experimental uncertainties. Furthermore, over past decades spectrophotometry has been extensively applied to identify and characterize Np solution species in different oxidation states. However, relevant spectral database of Np in nitric acid solutions that can serve for the reference purposes has yet to be established duemore » to the experimental difficulty to isolate and stabilize Np species in pure oxidation states without compromising solution optical properties. This work demonstrates that combination of voltammetry and controlled-potential in situ thin-layer spectropotentiometry overcomes these challenges so that Np species in pure +3, +4, +5, or +6 oxidation states were electrochemically generated in the systematically varied 0.1 – 5 M nitric acid solutions, and corresponding vis-NIR spectral signatures were obtained. In situ optical monitoring of the interconversion between adjacent Np oxidation states resulted in elucidation of the mechanisms of the involved redox reactions, in-depth understanding of the relative stability of the Np oxidation states, and allowed benchmarking of the redox potentials of the NpO22+/NpO2+, NpO2+/Np4+ and Np4+/Np3+ couples. Notably, the NpO2+/Np4+ couple was distinguished from the proximal Np4+/Np3+ process overcoming previous concerns and challenges encountered in accurate determination of the respective potentials.« less

Solution equilibrium behind the room-temperature synthesis of nanocrystalline titanium dioxide.

PubMed

Seisenbaeva, Gulaim A; Daniel, Geoffrey; Nedelec, Jean-Marie; Kessler, Vadim G

2013-04-21

Formation of nanocrystalline and monodisperse TiO2 from a water soluble and stable precursor, ammonium oxo-lactato-titanate, (NH4)8Ti4O4(Lactate)8·4H2O, often referred to as TiBALDH or TALH, is demonstrated to be due to a coordination equilibrium. This compound, individual in the solid state, exists in solution in equilibrium with ammonium tris-lactato-titanate, (NH4)2Ti(Lactate)3 and uniform crystalline TiO2 nanoparticles (anatase) stabilized by surface-capping with lactate ligands. This equilibrium can be shifted towards nano-TiO2via application of a less polar solvent like methanol or ethanol, dilution of the solution, introduction of salts or raising the temperature, and reverted on addition of polar and strongly solvating media such as dimethyl sulfoxide, according to NMR. Aggregation and precipitation of the particles were followed by DLS and could be achieved by a decrease in their surface charge by adsorption of strongly hydrogen-bonding cations, e.g. in solutions of ammonia, ethanolamine or amino acid arginine or by addition of ethanol. The observed equilibrium may be involved in formation of nano-titania on the surface of plant roots exerting chelating organic carboxylate ligands and thus potentially influencing plant interactions.

A new family of Ln₇ clusters with an ideal D(3h) metal-centered trigonal prismatic geometry, and SMM and photoluminescence behaviors.

PubMed

Mazarakioti, Eleni C; Poole, Katye M; Cunha-Silva, Luis; Christou, George; Stamatatos, Theocharis C

2014-08-14

The first use of the flexible Schiff base ligand N-salicylidene-2-aminocyclohexanol in metal cluster chemistry has afforded a new family of Ln7 clusters with ideal D(3h) point group symmetry and metal-centered trigonal prismatic topology; solid-state and solution studies revealed SMM and photoluminescence behaviors.

Methods for preparing colloidal nanocrystal-based thin films

DOEpatents

Kagan, Cherie R.; Fafarman, Aaron T.; Choi, Ji-Hyuk; Koh, Weon-kyu; Kim, David K.; Oh, Soong Ju; Lai, Yuming; Hong, Sung-Hoon; Saudari, Sangameshwar Rao; Murray, Christopher B.

2016-05-10

Methods of exchanging ligands to form colloidal nanocrystals (NCs) with chalcogenocyanate (xCN)-based ligands and apparatuses using the same are disclosed. The ligands may be exchanged by assembling NCs into a thin film and immersing the thin film in a solution containing xCN-based ligands. The ligands may also be exchanged by mixing a xCN-based solution with a dispersion of NCs, flocculating the mixture, centrifuging the mixture, discarding the supernatant, adding a solvent to the pellet, and dispersing the solvent and pellet to form dispersed NCs with exchanged xCN-ligands. The NCs with xCN-based ligands may be used to form thin film devices and/or other electronic, optoelectronic, and photonic devices. Devices comprising nanocrystal-based thin films and methods for forming such devices are also disclosed. These devices may be constructed by depositing NCs on to a substrate to form an NC thin film and then doping the thin film by evaporation and thermal diffusion.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnston, Ryne C.; Zhou, Jing; Smith, Jeremy C.

In redox processes in complex transition metal-containing species are often intimately associated with changes in ligand protonation states and metal coordination number. Moreover, a major challenge is therefore to develop consistent computational approaches for computing pH-dependent redox and ligand dissociation properties of organometallic species. Reduction of the Co center in the vitamin B12 derivative aquacobalamin can be accompanied by ligand dissociation, protonation, or both, making these properties difficult to compute accurately. We examine this challenge here by using density functional theory and continuum solvation to compute Co ligand binding equilibrium constants (Kon/off), pKas and reduction potentials for models of aquacobalaminmore » in aqueous solution. We consider two models for cobalamin ligand coordination: the first follows the hexa, penta, tetra coordination scheme for Co III, Co II, and Co I species, respectively, and the second model features saturation of each vacant axial coordination site on Co II and Co I species with a single, explicit water molecule to maintain six directly interacting ligands or water molecules in each oxidation state. Comparing these two coordination schemes in combination with five dispersion-corrected density functionals, we find that the accuracy of the computed properties is largely independent of the scheme used, but including only a continuum representation of the solvent yields marginally better results than saturating the first solvation shell around Co throughout. PBE performs best, displaying balanced accuracy and superior performance overall, with RMS errors of 80 mV for seven reduction potentials, 2.0 log units for five pK as and 2.3 log units for two log K on/off values for the aquacobalamin system. Furthermore, we find that the BP86 functional commonly used in corrinoid studies suffers from erratic behavior and inaccurate descriptions of Co axial ligand binding, leading to substantial errors in predicted pK as and K on/off values. Finally, these findings demonstrate the effectiveness of the present approach for computing electrochemical and thermodynamic properties of a complex transition metal-containing cofactor.« less

Zinc complexes of the biomimetic N,N,O ligand family of substituted 3,3-bis(1-alkylimidazol-2-yl)propionates: the formation of oxalate from pyruvate

PubMed Central

Bruijnincx, Pieter C. A.; Lutz, Martin; den Breejen, Johan P.; van Koten, Gerard

2007-01-01

The coordination chemistry of the 2-His-1-carboxylate facial triad mimics 3,3-bis(1-methylimidazol-2-yl)propionate (MIm2Pr) and 3,3-bis(1-ethyl-4-isopropylimidazol-2-yl) propionate (iPrEtIm2Pr) towards ZnCl2 was studied both in solution and in the solid state. Different coordination modes were found depending both on the stoichiometry and on the ligand that was employed. In the 2:1 ligand-to-metal complex [Zn(MIm2Pr)2], the ligand coordinates in a tridentate, tripodal N,N,O fashion similar to the 2-His-1-carboxylate facial triad. However, the 1:1 ligand-to-metal complexes [Zn(MIm2Pr)Cl(H2O)] and [Zn(iPrEtIm2Pr)Cl] were crystallographically characterized and found to be polymeric in nature. A new, bridging coordination mode of the ligands was observed in both structures comprising N,N-bidentate coordination of the ligand to one zinc atom and O-monodentate coordination to a zinc second atom. A rather unique transformation of pyruvate into oxalate was found with [Zn(MIm2Pr)Cl], which resulted in the isolation of the new, oxalato bridged zinc coordination polymer [Zn2(MIm2Pr)2(ox)]·6H2O, the structure of which was established by X-ray crystal structure determination. PMID:17828423

Copper(II) ion catalytic oxidation of o-phenylenediamine and characterization, X-ray crystal structure and solution studies of the final product [DAPH][H3O][Cu(dipic)2]·3H2O

NASA Astrophysics Data System (ADS)

Ghasemi, Khaled; Rezvani, Ali Reza; Shokrollahi, Ardeshir; Abdul Razak, Ibrahim; Refahi, Masoud; Moghimi, Abolghasem; Rosli, Mohd Mustaqim

2015-09-01

The complex [DAPH][H3O][Cu(dipic)2]·3H2O, (1) (dipicH2 = 2,6-pyridinedicarboxylic acid and DAP = 2,3-diaminophenazine) was prepared from the reaction of Cu(NO3)2·2H2O with mixture of o-phenylenediamine (OPD) and 2,6-pyridinedicarboxylic acid in water. The complex was characterized by FTIR, elemental analysis, UV-Vis and the single-crystal X-ray diffraction. The crystal system is monoclinic with the space group P21/c. This complex is stabilized in the solid state by an extensive network of hydrogen bonds between crystallized water, anionic and cationic fragments, which form a three-dimensional network. Furthermore, hydrogen bonds, π⋯π and Csbnd O⋯π stacking interactions seem to be effective in stabilizing the crystal structures. The protonation constants of dipic (L) and DAP (Q), the equilibrium constants for the dipic-DAP proton transfer system and the stoichiometry and stability constants of binary complexes including each of ligands (dipic, DAP) in presence Cu2+ ion, ternary complexes including, both of ligands (dipic-DAP) in presence of metal ion were calculated in aqueous solutions by potentiometric pH titration method using the Hyperquad2008 program. The stoichiometry of the most complexes species in solution was found to be very similar to the solid-state of cited metal ion complex.

The Solution Structure, Binding Properties, and Dynamics of the Bacterial Siderophore-binding Protein FepB*

PubMed Central

Chu, Byron C. H.; Otten, Renee; Krewulak, Karla D.; Mulder, Frans A. A.; Vogel, Hans J.

2014-01-01

The periplasmic binding protein (PBP) FepB plays a key role in transporting the catecholate siderophore ferric enterobactin from the outer to the inner membrane in Gram-negative bacteria. The solution structures of the 34-kDa apo- and holo-FepB from Escherichia coli, solved by NMR, represent the first solution structures determined for the type III class of PBPs. Unlike type I and II PBPs, which undergo large “Venus flytrap” conformational changes upon ligand binding, both forms of FepB maintain similar overall folds; however, binding of the ligand is accompanied by significant loop movements. Reverse methyl cross-saturation experiments corroborated chemical shift perturbation results and uniquely defined the binding pocket for gallium enterobactin (GaEnt). NMR relaxation experiments indicated that a flexible loop (residues 225–250) adopted a more rigid and extended conformation upon ligand binding, which positioned residues for optimal interactions with the ligand and the cytoplasmic membrane ABC transporter (FepCD), respectively. In conclusion, this work highlights the pivotal role that structural dynamics plays in ligand binding and transporter interactions in type III PBPs. PMID:25173704

How to Compute Labile Metal-Ligand Equilibria

ERIC Educational Resources Information Center

de Levie, Robert

2007-01-01

The different methods used for computing labile metal-ligand complexes, which are suitable for an iterative computer solution, are illustrated. The ligand function has allowed students to relegate otherwise tedious iterations to a computer, while retaining complete control over what is calculated.

MATHEMATICAL ANALYSIS OF STEADY-STATE SOLUTIONS IN COMPARTMENT AND CONTINUUM MODELS OF CELL POLARIZATION

PubMed Central

ZHENG, ZHENZHEN; CHOU, CHING-SHAN; YI, TAU-MU; NIE, QING

2013-01-01

Cell polarization, in which substances previously uniformly distributed become asymmetric due to external or/and internal stimulation, is a fundamental process underlying cell mobility, cell division, and other polarized functions. The yeast cell S. cerevisiae has been a model system to study cell polarization. During mating, yeast cells sense shallow external spatial gradients and respond by creating steeper internal gradients of protein aligned with the external cue. The complex spatial dynamics during yeast mating polarization consists of positive feedback, degradation, global negative feedback control, and cooperative effects in protein synthesis. Understanding such complex regulations and interactions is critical to studying many important characteristics in cell polarization including signal amplification, tracking dynamic signals, and potential trade-off between achieving both objectives in a robust fashion. In this paper, we study some of these questions by analyzing several models with different spatial complexity: two compartments, three compartments, and continuum in space. The step-wise approach allows detailed characterization of properties of the steady state of the system, providing more insights for biological regulations during cell polarization. For cases without membrane diffusion, our study reveals that increasing the number of spatial compartments results in an increase in the number of steady-state solutions, in particular, the number of stable steady-state solutions, with the continuum models possessing infinitely many steady-state solutions. Through both analysis and simulations, we find that stronger positive feedback, reduced diffusion, and a shallower ligand gradient all result in more steady-state solutions, although most of these are not optimally aligned with the gradient. We explore in the different settings the relationship between the number of steady-state solutions and the extent and accuracy of the polarization. Taken together these results furnish a detailed description of the factors that influence the tradeoff between a single correctly aligned but poorly polarized stable steady-state solution versus multiple more highly polarized stable steady-state solutions that may be incorrectly aligned with the external gradient. PMID:21936604

Heteroleptic copper(I) complexes prepared from phenanthroline and bis-phosphine ligands.

PubMed

Kaeser, Adrien; Mohankumar, Meera; Mohanraj, John; Monti, Filippo; Holler, Michel; Cid, Juan-José; Moudam, Omar; Nierengarten, Iwona; Karmazin-Brelot, Lydia; Duhayon, Carine; Delavaux-Nicot, Béatrice; Armaroli, Nicola; Nierengarten, Jean-François

2013-10-21

Preparation of [Cu(NN)(PP)](+) derivatives has been systematically investigated starting from two libraries of phenanthroline (NN) derivatives and bis-phosphine (PP) ligands, namely, (A) 1,10-phenanthroline (phen), neocuproine (2,9-dimethyl-1,10-phenanthroline, dmp), bathophenanthroline (4,7-diphenyl-1,10-phenanthroline, Bphen), 2,9-diphenethyl-1,10-phenanthroline (dpep), and 2,9-diphenyl-1,10-phenanthroline (dpp); (B) bis(diphenylphosphino)methane (dppm), 1,2-bis(diphenylphosphino)ethane (dppe), 1,3-bis(diphenylphosphino)propane (dppp), 1,2-bis(diphenylphosphino)benzene (dppb), 1,1'-bis(diphenylphosphino)ferrocene (dppFc), and bis[(2-diphenylphosphino)phenyl] ether (POP). Whatever the bis-phosphine ligand, stable heteroleptic [Cu(NN)(PP)](+) complexes are obtained from the 2,9-unsubstituted-1,10-phenanthroline ligands (phen and Bphen). By contrast, heteroleptic complexes obtained from dmp and dpep are stable in the solid state, but a dynamic ligand exchange reaction is systematically observed in solution, and the homoleptic/heteroleptic ratio is highly dependent on the bis-phosphine ligand. Detailed analysis revealed that the dynamic equilibrium resulting from ligand exchange reactions is mainly influenced by the relative thermodynamic stability of the different possible complexes. Finally, in the case of dpp, only homoleptic complexes were obtained whatever the bis-phosphine ligand. Obviously, steric effects resulting from the presence of the bulky phenyl rings on the dpp ligand destabilize the heteroleptic [Cu(NN)(PP)](+) complexes. In addition to the remarkable thermodynamic stability of [Cu(dpp)2]BF4, this negative steric effect drives the dynamic complexation scenario toward almost exclusive formation of homoleptic [Cu(NN)2](+) and [Cu(PP)2](+) complexes. This work provides the definitive rationalization of the stability of [Cu(NN)(PP)](+) complexes, marking the way for future developments in this field.

Rapid and Efficient Collection of Platinum from Karstedt's Catalyst Solution via Ligands-Exchange-Induced Assembly.

PubMed

Yang, Gonghua; Wei, Yanlong; Huang, Zhenzhu; Hu, Jiwen; Liu, Guojun; Ou, Ming; Lin, Shudong; Tu, Yuanyuan

2018-02-21

Reported herein is a novel strategy for the rapid and efficient collection of platinum from Karstedt's catalyst solution. By taking advantage of a ligand-exchange reaction between alkynols and the 1,3-divinyltetramethyldisiloxane ligand (M Vi M Vi ) that coordinated with platinum (Pt(0)), the Karstedt's catalyst particles with a size of approximately 2.5 ± 0.7 nm could be reconstructed and assembled into larger particles with a size of 150 ± 35 nm due to the hydrogen bonding between the hydroxyl groups of the alkynol. In addition, because the silicone-soluble M Vi M Vi ligand of the Karstedt's catalyst was replaced by water-soluble alkynol ligands, the resultant large particles were readily dispersed in water, resulting in rapid, efficient, and complete collection of platinum from the Karstedt's catalyst solutions with platinum concentrations in the range from ∼20 000 to 0.05 ppm. Our current strategy not only was used for the rapid and efficient collection of platinum from the Karstedt's catalyst solutions, but it also enabled the precise evaluation of the platinum content in the Karstedt's catalysts, even if this platinum content was extremely low (i.e., 0.05 ppm). Moreover, these platinum specimens that were efficiently collected from the Karstedt's catalyst solutions could be directly used for the evaluation of platinum without the need for pretreatment processes, such as calcination and digestion with hydrofluoric acid, that were traditionally used prior to testing via inductively coupled plasma mass spectrometry in conventional methods.

Coumarin Derivative Directly Coordinated to Lanthanides Acts as an Excellent Antenna for UV-Vis and Near-IR Emission.

PubMed

Guzmán-Méndez, Óscar; González, Federico; Bernès, Sylvain; Flores-Álamo, Marcos; Ordóñez-Hernández, Javier; García-Ortega, Héctor; Guerrero, Joselin; Qian, Wenjie; Aliaga-Alcalde, Nuria; Gasque, Laura

2018-02-05

A chelating coumarin-derived ligand sensitizes all emitting lanthanide ions in the solid state and gives high absolute quantum yields for ethanol solutions of complexes of Sm, Eu, Tb, and Dy, above 20% for the last two. Crystal structures of these four complexes are [Ln(Cum) 3 (H 2 O)(X)]·X where X = MeOH or EtOH.

The luminescence properties of the heteroleptic [Re(CO)3(N∩N)Cl] and [Re(CO)3(N∩N)(CH3CN)](+) complexes in view of the combined Marcus-Jortner and Mulliken-Hush formalism.

PubMed

Woźna, Agnieszka; Kapturkiewicz, Andrzej

2015-11-11

The luminescence properties of the heteroleptic fac-Re(CO)3(+) complexes with α-diimine N∩N ligands, neutral [Re(CO)3(N∩N)Cl] and cationic [Re(CO)3(N∩N)(CH3CN)](+) species, have been studied in acetonitrile solutions at room temperature. The investigated complexes exhibit the metal to ligand charge-transfer (MLCT) phosphorescence with the emission characteristics strongly affected by the nature of coordinated α-diimine N∩N ligands. The observed trends can be quantitatively described by invoking the electronic interactions between (3)*LC and (3)*MLCT states as well as the spin-orbit interactions between (3)*MLCT and (1)*MLCT states, respectively. All quantities necessary for the description can be straightforwardly accounted from analysis of the radiative (1)*MLCT ← S0 and (3)*MLCT → S0 charge transfer processes. It is also demonstrated that the radiative kr and non-radiative knr decay rate constants of the excited (3)*MLCT states can be interpreted within the same set of parameters. As expected from the Mulliken-Hush formalism the both processes are strictly related that allows prediction of the non-radiative knr rate constants using the parameters available from analysis of the radiative (1)*MLCT ← S0 and (3)*MLCT → S0 charge transfer processes.

Transport capabilities of environmental Pseudomonads for sulfur compounds

DOE PAGES

Zerbs, Sarah; Korajczyk, Peter J.; Noirot, Philippe H.; ...

2017-01-27

Sulfur is an essential element in plant rhizospheres and microbial activity plays a key role in increasing the biological availability of sulfur in soil environments. To better understand the mechanisms facilitating the exchange of sulfur-containing molecules in soil, we profiled the binding specificities of eight previously uncharacterized ABC transporter solute-binding proteins from plant-associated Pseudomonads. A high-throughput screening procedure indicated eighteen significant organosulfur binding ligands, with at least one high-quality screening hit for each protein target. Calorimetric and spectroscopic methods were used to validate the best ligand assignments and catalog the thermodynamic properties of the protein-ligand interactions. Two novel high-affinity ligandmore » binding activities were identified and quantified in this set of solute binding proteins. Bacteria were cultured in minimal media with screening library components supplied as the sole sulfur sources, demonstrating that these organosulfur compounds can be metabolized and confirming the relevance of ligand assignments. These results expand the set of experimentally validated ligands amenable to transport by this ABC transporter family and demonstrate the complex range of protein-ligand interactions that can be accomplished by solute-binding proteins. As a result, characterizing new nutrient import pathways provides insight into Pseudomonad metabolic capabilities which can be used to further interrogate bacterial survival and participation in soil and rhizosphere communities.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zerbs, Sarah; Korajczyk, Peter J.; Noirot, Philippe H.

Sulfur is an essential element in plant rhizospheres and microbial activity plays a key role in increasing the biological availability of sulfur in soil environments. To better understand the mechanisms facilitating the exchange of sulfur-containing molecules in soil, we profiled the binding specificities of eight previously uncharacterized ABC transporter solute-binding proteins from plant-associated Pseudomonads. A high-throughput screening procedure indicated eighteen significant organosulfur binding ligands, with at least one high-quality screening hit for each protein target. Calorimetric and spectroscopic methods were used to validate the best ligand assignments and catalog the thermodynamic properties of the protein-ligand interactions. Two novel high-affinity ligandmore » binding activities were identified and quantified in this set of solute binding proteins. Bacteria were cultured in minimal media with screening library components supplied as the sole sulfur sources, demonstrating that these organosulfur compounds can be metabolized and confirming the relevance of ligand assignments. These results expand the set of experimentally validated ligands amenable to transport by this ABC transporter family and demonstrate the complex range of protein-ligand interactions that can be accomplished by solute-binding proteins. As a result, characterizing new nutrient import pathways provides insight into Pseudomonad metabolic capabilities which can be used to further interrogate bacterial survival and participation in soil and rhizosphere communities.« less

Molecular mechanism of acetylcholine receptor-controlled ion translocation across cell membranes

PubMed Central

Cash, Derek J.; Hess, George P.

1980-01-01

Two molecular processes, the binding of acetylcholine to the membrane-bound acetylcholine receptor protein and the receptor-controlled flux rates of specific inorganic ions, are essential in determining the electrical membrane potential of nerve and muscle cells. The measurements reported establish the relationship between the two processes: the acetylcholine receptor-controlled transmembrane ion flux of 86Rb+ and the concentration of carbamoylcholine, a stable analog of acetylcholine. A 200-fold concentration range of carbamoylcholine was used. The flux was measured in the millisecond-to-minute time region by using a quench flow technique with membrane vesicles prepared from the electric organ of Electrophorus electricus in eel Ringer's solution at pH 7.0 and 1°C. The technique makes possible the study of the transmembrane transport of specific ions, with variable known internal and external ion concentrations, in a system in which a determinable number of receptors is exposed to a known concentration of ligand. The response curve of ion flux to ligand was sigmoidal with an average maximum rate of 84 sec-1. Carbamoylcholine induced inactivation of the receptor with a maximum rate of 2.7 sec-1 and a different ligand dependence so that it was fast relative to ion flux at low ligand concentration but slow relative to ion flux at high ligand concentration. The simplest model that fits the data consists of receptor in the active and inactive states in ligand-controlled equilibria. Receptor inactivation occurs with one or two ligand molecules bound. For channel opening, two ligand molecules bound to the active state are required, and cooperativity results from the channel opening process itself. With carbamoylcholine, apparently, the equilibrium position for the channel opening step is only one-fourth open. The integrated rate equation, based on the model, predicts the time dependence of receptor-controlled ion flux over the concentration range of carbamoylcholine investigated. The values of the constants in the rate equation form the basis for predicting receptor-controlled changes in the transmembrane potential of cells and the conditions leading to transmission of signals between cells. PMID:6928684

Toward Quantitatively Accurate Calculation of the Redox-Associated Acid–Base and Ligand Binding Equilibria of Aquacobalamin

DOE PAGES

Johnston, Ryne C.; Zhou, Jing; Smith, Jeremy C.; ...

2016-07-08

In redox processes in complex transition metal-containing species are often intimately associated with changes in ligand protonation states and metal coordination number. Moreover, a major challenge is therefore to develop consistent computational approaches for computing pH-dependent redox and ligand dissociation properties of organometallic species. Reduction of the Co center in the vitamin B12 derivative aquacobalamin can be accompanied by ligand dissociation, protonation, or both, making these properties difficult to compute accurately. We examine this challenge here by using density functional theory and continuum solvation to compute Co ligand binding equilibrium constants (Kon/off), pKas and reduction potentials for models of aquacobalaminmore » in aqueous solution. We consider two models for cobalamin ligand coordination: the first follows the hexa, penta, tetra coordination scheme for Co III, Co II, and Co I species, respectively, and the second model features saturation of each vacant axial coordination site on Co II and Co I species with a single, explicit water molecule to maintain six directly interacting ligands or water molecules in each oxidation state. Comparing these two coordination schemes in combination with five dispersion-corrected density functionals, we find that the accuracy of the computed properties is largely independent of the scheme used, but including only a continuum representation of the solvent yields marginally better results than saturating the first solvation shell around Co throughout. PBE performs best, displaying balanced accuracy and superior performance overall, with RMS errors of 80 mV for seven reduction potentials, 2.0 log units for five pK as and 2.3 log units for two log K on/off values for the aquacobalamin system. Furthermore, we find that the BP86 functional commonly used in corrinoid studies suffers from erratic behavior and inaccurate descriptions of Co axial ligand binding, leading to substantial errors in predicted pK as and K on/off values. Finally, these findings demonstrate the effectiveness of the present approach for computing electrochemical and thermodynamic properties of a complex transition metal-containing cofactor.« less

Tuning colloidal quantum dot band edge positions through solution-phase surface chemistry modification

DOE PAGES

Kroupa, Daniel M.; Vörös, Márton; Brawand, Nicholas P.; ...

2017-05-16

Band edge positions of semiconductors determine their functionality in many optoelectronic applications such as photovoltaics, photoelectrochemical cells and light emitting diodes. Here we show that band edge positions of lead sulfide (PbS) colloidal semiconductor nanocrystals, specifically quantum dots (QDs), can be tuned over 2.0 eV through surface chemistry modification. We achieved this remarkable control through the development of simple, robust and scalable solution-phase ligand exchange methods, which completely replace native ligands with functionalized cinnamate ligands, allowing for well-defined, highly tunable chemical systems. By combining experiments and ab initio simulations, we establish clear relationships between QD surface chemistry and the bandmore » edge positions of ligand/QD hybrid systems. We find that in addition to ligand dipole, inter-QD ligand shell inter-digitization contributes to the band edge shifts. As a result, we expect that our established relationships and principles can help guide future optimization of functional organic/inorganic hybrid nanostructures for diverse optoelectronic applications.« less

Tuning colloidal quantum dot band edge positions through solution-phase surface chemistry modification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kroupa, Daniel M.; Vörös, Márton; Brawand, Nicholas P.

Band edge positions of semiconductors determine their functionality in many optoelectronic applications such as photovoltaics, photoelectrochemical cells and light emitting diodes. Here we show that band edge positions of lead sulfide (PbS) colloidal semiconductor nanocrystals, specifically quantum dots (QDs), can be tuned over 2.0 eV through surface chemistry modification. We achieved this remarkable control through the development of simple, robust and scalable solution-phase ligand exchange methods, which completely replace native ligands with functionalized cinnamate ligands, allowing for well-defined, highly tunable chemical systems. By combining experiments and ab initio simulations, we establish clear relationships between QD surface chemistry and the bandmore » edge positions of ligand/QD hybrid systems. We find that in addition to ligand dipole, inter-QD ligand shell inter-digitization contributes to the band edge shifts. As a result, we expect that our established relationships and principles can help guide future optimization of functional organic/inorganic hybrid nanostructures for diverse optoelectronic applications.« less

Tuning colloidal quantum dot band edge positions through solution-phase surface chemistry modification

PubMed Central

Kroupa, Daniel M.; Vörös, Márton; Brawand, Nicholas P.; McNichols, Brett W.; Miller, Elisa M.; Gu, Jing; Nozik, Arthur J.; Sellinger, Alan; Galli, Giulia; Beard, Matthew C.

2017-01-01

Band edge positions of semiconductors determine their functionality in many optoelectronic applications such as photovoltaics, photoelectrochemical cells and light emitting diodes. Here we show that band edge positions of lead sulfide (PbS) colloidal semiconductor nanocrystals, specifically quantum dots (QDs), can be tuned over 2.0 eV through surface chemistry modification. We achieved this remarkable control through the development of simple, robust and scalable solution-phase ligand exchange methods, which completely replace native ligands with functionalized cinnamate ligands, allowing for well-defined, highly tunable chemical systems. By combining experiments and ab initio simulations, we establish clear relationships between QD surface chemistry and the band edge positions of ligand/QD hybrid systems. We find that in addition to ligand dipole, inter-QD ligand shell inter-digitization contributes to the band edge shifts. We expect that our established relationships and principles can help guide future optimization of functional organic/inorganic hybrid nanostructures for diverse optoelectronic applications. PMID:28508866

Tuning colloidal quantum dot band edge positions through solution-phase surface chemistry modification

NASA Astrophysics Data System (ADS)

Kroupa, Daniel M.; Vörös, Márton; Brawand, Nicholas P.; McNichols, Brett W.; Miller, Elisa M.; Gu, Jing; Nozik, Arthur J.; Sellinger, Alan; Galli, Giulia; Beard, Matthew C.

2017-05-01

Band edge positions of semiconductors determine their functionality in many optoelectronic applications such as photovoltaics, photoelectrochemical cells and light emitting diodes. Here we show that band edge positions of lead sulfide (PbS) colloidal semiconductor nanocrystals, specifically quantum dots (QDs), can be tuned over 2.0 eV through surface chemistry modification. We achieved this remarkable control through the development of simple, robust and scalable solution-phase ligand exchange methods, which completely replace native ligands with functionalized cinnamate ligands, allowing for well-defined, highly tunable chemical systems. By combining experiments and ab initio simulations, we establish clear relationships between QD surface chemistry and the band edge positions of ligand/QD hybrid systems. We find that in addition to ligand dipole, inter-QD ligand shell inter-digitization contributes to the band edge shifts. We expect that our established relationships and principles can help guide future optimization of functional organic/inorganic hybrid nanostructures for diverse optoelectronic applications.

Bio-layer interferometry for measuring kinetics of protein-protein interactions and allosteric ligand effects.

PubMed

Shah, Naman B; Duncan, Thomas M

2014-02-18

We describe the use of Bio-layer Interferometry to study inhibitory interactions of subunit ε with the catalytic complex of Escherichia coli ATP synthase. Bacterial F-type ATP synthase is the target of a new, FDA-approved antibiotic to combat drug-resistant tuberculosis. Understanding bacteria-specific auto-inhibition of ATP synthase by the C-terminal domain of subunit ε could provide a new means to target the enzyme for discovery of antibacterial drugs. The C-terminal domain of ε undergoes a dramatic conformational change when the enzyme transitions between the active and inactive states, and catalytic-site ligands can influence which of ε's conformations is predominant. The assay measures kinetics of ε's binding/dissociation with the catalytic complex, and indirectly measures the shift of enzyme-bound ε to and from the apparently nondissociable inhibitory conformation. The Bio-layer Interferometry signal is not overly sensitive to solution composition, so it can also be used to monitor allosteric effects of catalytic-site ligands on ε's conformational changes.

Synthesis and binding studies of Alzheimer ligands on solid support.

PubMed

Rzepecki, Petra; Geib, Nina; Peifer, Manuel; Biesemeier, Frank; Schrader, Thomas

2007-05-11

Aminopyrazole derivatives constitute the first class of nonpeptidic rationally designed beta-sheet ligands. Here we describe a double solid-phase protocol for both synthesis and affinity testing. The presented solid-phase synthesis of four types of hybrid compounds relies on the Fmoc strategy and circumvents subsequent HPLC purification by precipitating the final product from organic solution in pure form. Hexa- and octapeptide pendants with internal di- and tetrapeptide bridges are now amenable in high yields to combinatorial synthesis of compound libraries for high-throughput screening purposes. Solid-phase peptide synthesis (SPPS) on an acid-resistant PAM allows us, after PMB deprotection, to subject the free aminopyrazole binding sites in an immobilized state to on-bead assays with fluorescence-labeled peptides. From the fluorescence emission intensity decrease, individual binding constants can be calculated via reference curves by simple application of the law of mass action. Gratifyingly, host/guest complexation can be monitored quantitatively even for those ligands, which are almost insoluble in water.

Single-Molecule Patch-Clamp FRET Anisotropy Microscopy Studies of NMDA Receptor Ion Channel Activation and Deactivation under Agonist Ligand Binding in Living Cells.

PubMed

Sasmal, Dibyendu Kumar; Yadav, Rajeev; Lu, H Peter

2016-07-20

N-methyl-d-aspartate (NMDA) receptor ion channel is activated by the binding of two pairs of glycine and glutamate along with the application of action potential. Binding and unbinding of ligands changes its conformation that plays a critical role in the open-close activities of NMDA receptor. Conformation states and their dynamics due to ligand binding are extremely difficult to characterize either by conventional ensemble experiments or single-channel electrophysiology method. Here we report the development of a new correlated technical approach, single-molecule patch-clamp FRET anisotropy imaging and demonstrate by probing the dynamics of NMDA receptor ion channel and kinetics of glycine binding with its ligand binding domain. Experimentally determined kinetics of ligand binding with receptor is further verified by computational modeling. Single-channel patch-clamp and four-channel fluorescence measurement are recorded simultaneously to get correlation among electrical on and off states, optically determined conformational open and closed states by FRET, and binding-unbinding states of the glycine ligand by anisotropy measurement at the ligand binding domain of GluN1 subunit. This method has the ability to detect the intermediate states in addition to electrical on and off states. Based on our experimental results, we have proposed that NMDA receptor gating goes through at least one electrically intermediate off state, a desensitized state, when ligands remain bound at the ligand binding domain with the conformation similar to the fully open state.

Investigating Protein-Ligand Interactions by Solution Nuclear Magnetic Resonance Spectroscopy.

PubMed

Becker, Walter; Bhattiprolu, Krishna Chaitanya; Gubensäk, Nina; Zangger, Klaus

2018-04-17

Protein-ligand interactions are of fundamental importance in almost all processes in living organisms. The ligands comprise small molecules, drugs or biological macromolecules and their interaction strength varies over several orders of magnitude. Solution NMR spectroscopy offers a large repertoire of techniques to study such complexes. Here, we give an overview of the different NMR approaches available. The information they provide ranges from the simple information about the presence of binding or epitope mapping to the complete 3 D structure of the complex. NMR spectroscopy is particularly useful for the study of weak interactions and for the screening of binding ligands with atomic resolution. © 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Spectroscopic and DFT Study of RhIII Chloro Complex Transformation in Alkaline Solutions.

PubMed

Vasilchenko, Danila B; Berdyugin, Semen N; Korenev, Sergey V; O'Kennedy, Sean; Gerber, Wilhelmus J

2017-09-05

The hydrolysis of [RhCl 6 ] 3- in NaOH-water solutions was studied by spectrophotometric methods. The reaction proceeds via successive substitution of chloride with hydroxide to quantitatively form [Rh(OH) 6 ] 3- . Ligand substitution kinetics was studied in an aqueous 0.434-1.085 M NaOH matrix in the temperature range 5.5-15.3 °C. Transformation of [RhCl 6 ] 3- into [RhCl 5 (OH)] 3- was found to be the rate-determining step with activation parameters of ΔH † = 105 ± 4 kJ mol -1 and ΔS † = 59 ± 10 J K -1 mol -1 . The coordinated hydroxo ligand(s) induces rapid ligand substitution to form [Rh(OH) 6 ] 3- . By simulating ligand substitution as a dissociative mechanism, using density functional theory (DFT), we can now explain the relatively fast and slow kinetics of chloride substitution in basic and acidic matrices, respectively. Moreover, the DFT calculated activation energies corroborated experimental data that the kinetic stereochemical sequence of [RhCl 6 ] 3- hydrolysis in an acidic solution proceeds as [RhCl 6 ] 3- → [RhCl 5 (H 2 O)] 2- → cis-[RhCl 4 (H 2 O) 2 ] - . However, DFT calculations predict in a basic solution the trans route of substitution [RhCl 6 ] 3- → [RhCl 5 (OH)] 3- → trans-[RhCl 4 (OH) 2 ] 3- is kinetically favored.

Luminescent low-valent rhenium complexes with 1,2-bis(dialkylphosphino)ethane ligands. synthesis and X-ray crystallographic, electrochemical, and spectroscopic characterization.

PubMed

Messersmith, Stephania J; Kirschbaum, Kristin; Kirchhoff, Jon R

2010-04-19

A series of low-valent rhenium phosphine complexes with the general formula [Re(dmpe)(3-x)(depe)(x)](2+/+) (x = 0-3), where dmpe is 1,2-bis(dimethylphosphino)ethane and depe is 1,2-bis(diethylphosphino)ethane, were synthesized and characterized. The reaction of [Re(benzil)(PPh(3))Cl(3)] with the appropriate phosphine yielded the homoleptic tris complexes [Re(dmpe)(3)](+) and [Re(depe)(3)](2+), while the mixed-ligand complexes [Re(dmpe)(2)(depe)](+) and [Re(dmpe)(depe)(2)](2+) were prepared from [Re(dmpe)(2)Cl(2)](+) and [Re(depe)(2)Cl(2)](+), respectively. The oxidation state of the final product strongly depends on the donating properties of the ligand. Each complex, however, exhibits a diffusion-controlled, reversible one-electron transfer between Re(I) and Re(II) with formal reduction potentials, E degrees ', ranging from -0.09 to -0.28 V versus a ferrocene external standard. Subsequent oxidation to Re(III) was found to be chemically irreversible. UV-vis and luminescence spectroelectrochemical techniques were used to study the spectral properties of the Re(I) and Re(II) forms. The Re(II) complexes are red in color and exhibit absorption features from 350 to 600 nm; the lowest-energy transition was assigned as a sigma(P) to dpi(Re) ligand-to-metal charge-transfer (LMCT) transition. Excitation into the lowest-energy absorption band revealed rare examples of luminescent (Phi approximately 0.07) LMCT excited states from d(5) transition-metal complexes in a room temperature solution. Structural characterization of salts of both oxidation states of [Re(dmpe)(2)(depe)](2+/+) was also performed.

Surface ligands affect photoinduced modulation of the quantum dots optical performance

NASA Astrophysics Data System (ADS)

Krivenkov, Victor A.; Samokhvalov, Pavel S.; Linkov, Pavel A.; Solovyeva, Daria O.; Kotkovskii, Gennadii E.; Chistyakov, Alexander A.; Nabiev, Igor

2014-05-01

Changes of optical properties of the solutions of CdSe/ZnS quantum dots (QDs) covered with the trioctylphosphine oxide (TOPO) ligands under the pulsed ultraviolet (UV) laser irradiation are observed. The fluorescence quantum yield (QY) of QDs decreases by more than an order of magnitude when the radiation dose approaches 2 × 10-15 J per particle. This process is accompanied by a blue shift of both fluorescence and the first excitonic absorption peaks. The fluorescence quenching becomes less pronounced when the overall TOPO content in the solution is increased. When ТОРО ligands are replaced with n-hexadecylamine (HDA), QY and spectral properties are not changed at the same irradiation conditions. We assume that the above changes of the optical properties are associated with photooxidation of TOPO ligands by excited QD. Such process is less probable for the HDA ligand due to its different energy structure.

Mitochondrial Hsp90 is a ligand-activated molecular chaperone coupling ATP binding to dimer closure through a coiled-coil intermediate

PubMed Central

Sung, Nuri; Lee, Jungsoon; Kim, Ji-Hyun; Chang, Changsoo; Joachimiak, Andrzej; Lee, Sukyeong; Tsai, Francis T. F.

2016-01-01

Heat-shock protein of 90 kDa (Hsp90) is an essential molecular chaperone that adopts different 3D structures associated with distinct nucleotide states: a wide-open, V-shaped dimer in the apo state and a twisted, N-terminally closed dimer with ATP. Although the N domain is known to mediate ATP binding, how Hsp90 senses the bound nucleotide and facilitates dimer closure remains unclear. Here we present atomic structures of human mitochondrial Hsp90N (TRAP1N) and a composite model of intact TRAP1 revealing a previously unobserved coiled-coil dimer conformation that may precede dimer closure and is conserved in intact TRAP1 in solution. Our structure suggests that TRAP1 normally exists in an autoinhibited state with the ATP lid bound to the nucleotide-binding pocket. ATP binding displaces the ATP lid that signals the cis-bound ATP status to the neighboring subunit in a highly cooperative manner compatible with the coiled-coil intermediate state. We propose that TRAP1 is a ligand-activated molecular chaperone, which couples ATP binding to dramatic changes in local structure required for protein folding. PMID:26929380

Metal-organic complexes in geochemical processes: temperature dependence of the standard thermodynamic properties of aqueous complexes between metal cations and dicarboxylate ligands

NASA Astrophysics Data System (ADS)

Prapaipong, Panjai; Shock, Everett L.; Koretsky, Carla M.

1999-10-01

By combining results from regression and correlation methods, standard state thermodynamic properties for aqueous complexes between metal cations and divalent organic acid ligands (oxalate, malonate, succinate, glutarate, and adipate) are evaluated and applied to geochemical processes. Regression of experimental standard-state equilibrium constants with the revised Helgeson-Kirkham-Flowers (HKF) equation of state yields standard partial molal entropies (S¯°) of aqueous metal-organic complexes, which allow determination of thermodynamic properties of the complexes at elevated temperatures. In cases where S¯° is not available from either regression or calorimetric measurement, the values of S¯° can be estimated from a linear correlation between standard partial molal entropies of association (ΔS¯°r) and standard partial molal entropies of aqueous cations (S¯°M). The correlation is independent of cation charge, which makes it possible to predict S¯° for complexes between divalent organic acids and numerous metal cations. Similarly, correlations between standard Gibbs free energies of association of metal-organic complexes (ΔḠ°r) and Gibbs free energies of formation (ΔḠ°f) for divalent metal cations allow estimates of standard-state equilibrium constants where experimental data are not available. These correlations are found to be a function of ligand structure and cation charge. Predicted equilibrium constants for dicarboxylate complexes of numerous cations were included with those for inorganic and other organic complexes to study the effects of dicarboxylate complexes on the speciation of metals and organic acids in oil-field brines. Relatively low concentrations of oxalic and malonic acids affect the speciation of cations more than similar concentrations of succinic, glutaric, and adipic acids. However, the extent to which metal-dicarboxylate complexes contribute to the speciation of dissolved metals depends on the type of dicarboxylic acid ligand; relative concentration of inorganic, mono-, and dicarboxylate ligands; and the type of metal cation. As an example, in the same solution, dicarboxylic acids have a greater influence on the speciation of Fe+2 and Mg+2 than on the speciation of Zn+2 and Mn+2.

Iodide Ion Pairing with Highly Charged Ruthenium Polypyridyl Cations in CH3CN.

PubMed

Swords, Wesley B; Li, Guocan; Meyer, Gerald J

2015-05-04

A series of three highly charged cationic ruthenium(II) polypyridyl complexes of the general formula [Ru(deeb)3-x(tmam)x](PF6)2x+2, where deeb is 4,4'-diethyl ester-2,2'-bipyridine and tmam is 4,4'-bis[(trimethylamino)methyl]-2,2'-bipyridine, were synthesized and characterized and are referred to as 1, 2, or 3 based on the number of tmam ligands. Crystals suitable for X-ray crystallography were obtained for the homoleptic complex 3, which was found to possess D3 symmetry over the entire ruthenium complex. The complexes displayed visible absorption spectra typical of metal-to-ligand charge-transfer (MLCT) transitions. In acetonitrile, quasi-reversible waves were assigned to Ru(III/II) electron transfer, with formal reduction potentials that shifted negative as the number of tmam ligands was increased. Room temperature photoluminescence was observed in acetonitrile with quantum yields of ϕ ∼ 0.1 and lifetimes of τ ∼ 2 μs. The spectroscopic and electrochemical data were most consistent with excited-state localization on the deeb ligand for 1 and 2 and on the tmam ligand for 3. The addition of tetrabutylammonium iodide to the complexes dissolved in a CH3CN solution led to changes in the UV-vis absorption spectra consistent with ion pairing. A Benesi-Hildebrand-type analysis of these data revealed equilibrium constants that increased with the cationic charge 1 < 2 < 3 with K = 4000, 4400, and 7000 M(-1). (1)H NMR studies in CD3CN also revealed evidence for iodide ion pairs and indicated that they occur predominantly with iodide localization near the tmam ligand(s). The diastereotopic H atoms on the methylene carbon that link the amine to the bipyridine ring were uniquely sensitive to the presence of iodide; analysis revealed that an iodide "binding pocket" exists wherein iodide forms an adduct with the 3 and 3' bipyridyl H atoms and the quaternized amine. The MLCT excited states were efficiently quenched by iodide. Time-resolved photoluminescence measurements of 1 revealed a static component consistent with rapid electron transfer from iodide in the "binding pocket" to the Ru metal center in the excited state, ket > 10(8) s(-1). The possible relevance of this work to solar energy conversion and dye-sensitized solar cells is discussed.

Complications in complexation kinetics for lanthanides with DTPA using dye probe molecules in aqueous solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Larsson, K.; Cullen, T. D.; Mezyk, S. P.

The complexation kinetics for the polyaminopolycarboxylic ligand DTPA to lanthanides in acidic aqueous solution were investigated using the dye ligand displacement technique and stopped-flow spectroscopy. Significant rate differences were obtained for different dye probes used, indicating that the kinetics of the dissociation of the dye molecule significantly impacts the overall measured kinetics when using this common methodology. The conditions of the solution also influenced the dye-lanthanide-DTPA interactions, which reconciled previously disparate data in the literature.

Complications in complexation kinetics for lanthanides with DTPA using dye probe molecules in aqueous solution

DOE PAGES

Larsson, K.; Cullen, T. D.; Mezyk, S. P.; ...

2017-05-17

The complexation kinetics for the polyaminopolycarboxylic ligand DTPA to lanthanides in acidic aqueous solution were investigated using the dye ligand displacement technique and stopped-flow spectroscopy. Significant rate differences were obtained for different dye probes used, indicating that the kinetics of the dissociation of the dye molecule significantly impacts the overall measured kinetics when using this common methodology. The conditions of the solution also influenced the dye-lanthanide-DTPA interactions, which reconciled previously disparate data in the literature.

Template-Free Mesoporous Electrochromic Films on Flexible Substrates from Tungsten Oxide Nanorods

DOE PAGES

Heo, Sungyeon; Kim, Jongwook; Ong, Gary K.; ...

2017-08-08

Low-temperature processed mesoporous nanocrystal thin films are platforms for fabricating functional composite thin films on flexible substrates. Using a random arrangement of anisotropic nanocrystals can be a facile solution to generate pores without templates. However, the tendency for anisotropic particles to spontaneously assemble into a compact structure must be overcome. Here in this paper, we present a method to achieve random networking of nanorods during solution phase deposition by switching their ligand-stabilized colloidal nature into a charge-stabilized nature by a ligand-stripping chemistry. Ligand-stripped tungsten suboxide (WO 2.72) nanorods result in uniform mesoporous thin films owing to repulsive electrostatic forces preventingmore » nanorods from densely packing. Porosity and pore size distribution of thin films are controlled by changing the aspect ratio of the nanorods. This template-free mesoporous structure, achieved without annealing, provides a framework for introducing guest components, therefore enabling our fabrication of inorganic nanocomposite electrochromic films on flexible substrates. Following infilling of niobium polyoxometalate clusters into pores and successive chemical condensation, a WO x–NbO x composite film is produced that selectively controls visible and near-infrared light transmittance without any annealing required. The composite shows rapid switching kinetics and can be stably cycled between optical states over 2000 times. This simple strategy of using anisotropic nanocrystals gives insight into mesoporous thin film fabrication with broader applications for flexible devices.« less

Template-Free Mesoporous Electrochromic Films on Flexible Substrates from Tungsten Oxide Nanorods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heo, Sungyeon; Kim, Jongwook; Ong, Gary K.

Low-temperature processed mesoporous nanocrystal thin films are platforms for fabricating functional composite thin films on flexible substrates. Using a random arrangement of anisotropic nanocrystals can be a facile solution to generate pores without templates. However, the tendency for anisotropic particles to spontaneously assemble into a compact structure must be overcome. Here in this paper, we present a method to achieve random networking of nanorods during solution phase deposition by switching their ligand-stabilized colloidal nature into a charge-stabilized nature by a ligand-stripping chemistry. Ligand-stripped tungsten suboxide (WO 2.72) nanorods result in uniform mesoporous thin films owing to repulsive electrostatic forces preventingmore » nanorods from densely packing. Porosity and pore size distribution of thin films are controlled by changing the aspect ratio of the nanorods. This template-free mesoporous structure, achieved without annealing, provides a framework for introducing guest components, therefore enabling our fabrication of inorganic nanocomposite electrochromic films on flexible substrates. Following infilling of niobium polyoxometalate clusters into pores and successive chemical condensation, a WO x–NbO x composite film is produced that selectively controls visible and near-infrared light transmittance without any annealing required. The composite shows rapid switching kinetics and can be stably cycled between optical states over 2000 times. This simple strategy of using anisotropic nanocrystals gives insight into mesoporous thin film fabrication with broader applications for flexible devices.« less

Vanadate complexes bearing an imidazolidine-bridged bis(aryloxido) ligand: synthesis and solid state and solution structure.

PubMed

Kober, Ewa; Nerkowski, Tomasz; Janas, Zofia; Jerzykiewicz, Lucjan B

2012-05-07

A new imidazolidine-bridged bis(aryloxido) ligand precursor (H(2)L) [H(2)L = 2,2'-(imidazolidine-1,3-diylbis(methylene))bis(4-(1,1,3,3-tetramethylbutyl-2-yl)phenol)] was prepared in a relatively high yield (∼60%) via a single-step Mannich condensation of 4-(1,1,3,3-tetramethylbutyl)phenol, ethylenediamine and paraformaldehyde at 2:1:3 molar ratio and characterized by chemical and physical techniques including X-ray crystallography. Reactions of H(2)L with [VO(OEt)(3)] at 1:1 and 1:2 molar ratios in toluene afforded [V(L-κ(3)O,N,N,O)(O)(OEt)] (1) and [V(2)(μ-L-κ(4)O,N,N,O)(μ-OEt)(2)(O)(2)(OEt)(2)] (2), respectively. Alcoholysis of 1 with EtOH enables elimination of one molecule of H(2)L and the formation of 2. Compounds 1 and 2 were characterized by IR and NMR spectroscopy as well as ES-MS experiments. The definitive molecular structure of 2 was provided by a single-crystal analysis and revealed its dinuclear nature, featuring two octahedral vanadium centres bridged by both OEt groups and the L ligand. The (51)V, (1)H and (13)C NMR spectra as well as ES-MS showed that 2 does not stay intact in solution and undergoes dissociation to give 1 and [VO(OEt)(3)].

Surface chemical modification of nanocrystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Helms, Brett Anthony; Milliron, Delia Jane; Rosen, Evelyn Louise

Nanocrystals comprising organic ligands at surfaces of the plurality of nanocrystals are provided. The organic ligands are removed from the surfaces of the nanocrystals using a solution comprising a trialkyloxonium salt in a polar aprotic solvent. The removal of the organic ligands causes the nanocrystals to become naked nanocrystals with cationic surfaces.

Chemical composition of an aqueous oxalato-/citrato-VO(2+) solution as determinant for vanadium oxide phase formation.

PubMed

Peys, Nick; Maurelli, Sara; Reekmans, Gunter; Adriaensens, Peter; De Gendt, Stefan; Hardy, An; Van Doorslaer, Sabine; Van Bael, Marlies K

2015-01-05

Aqueous solutions of oxalato- and citrato-VO(2+) complexes are prepared, and their ligand exchange reaction is investigated as a function of the amount of citrate present in the aqueous solution via continuous-wave electron paramagnetic resonance (CW EPR) and hyperfine sublevel correlation (HYSCORE) spectroscopy. With a low amount of citrate, monomeric cis-oxalato-VO(2+) complexes occur with a distorted square-pyramidal geometry. As the amount of citrate increases, oxalate is gradually exchanged for citrate. This leads to (i) an intermediate situation of monomeric VO(2+) complexes with a mix of oxalate/citrate ligands and (ii) a final situation of both monomeric and dimeric complexes with exclusively citrato ligands. The monomeric citrato-VO(2+) complexes dominate (abundance > 80%) and are characterized by a 6-fold chelation of the vanadium(IV) ion by 4 RCO2(-) ligands at the equatorial positions and a H2O/R-OH ligand at the axial position. The different redox stabilities of these complexes, relative to that of dissolved O2 in the aqueous solution, is analyzed via (51)V NMR. It is shown that the oxidation rate is the highest for the oxalato-VO(2+) complexes. In addition, the stability of the VO(2+) complexes can be drastically improved by evacuation of the dissolved O2 from the solution and subsequent storage in a N2 ambient atmosphere. The vanadium oxide phase formation process, starting with the chemical solution deposition of the aqueous solutions and continuing with subsequent processing in an ambient 0.1% O2 atmosphere, differs for the two complexes. The oxalato-VO(2+) complexes turn into the oxygen-deficient crystalline VO2 B at 400 °C, which then turns into crystalline V6O13 at 500 °C. In contrast, the citrato-VO(2+) complexes form an amorphous film at 400 °C that crystallizes into VO2 M1 and V6O13 at 500 °C.

Synthesis, structural characterization, reactivity, and catalytic properties of copper(I) complexes with a series of tetradentate tripodal tris(pyrazolylmethyl)amine ligands.

PubMed

Haldón, Estela; Delgado-Rebollo, Manuela; Prieto, Auxiliadora; Alvarez, Eleuterio; Maya, Celia; Nicasio, M Carmen; Pérez, Pedro J

2014-04-21

Novel tris(pyrazolylmethyl)amine ligands Tpa(Me3), Tpa*(,Br), and Tpa(Br3) have been synthesized and structurally characterized. The coordination chemistries of these three new tetradentate tripodal ligands and the already known Tpa and Tpa* have been explored using different copper(I) salts as starting materials. Cationic copper(I) complexes [Tpa(x)Cu]PF6 (1-4) have been isolated from the reaction of [Cu(NCMe)4]PF6 and 1 equiv of the ligand. Complexes 2 (Tpa(x) = Tpa*) and 3 (Tpa(x) = Tpa(Me3)) have been characterized by X-ray studies. The former is a 1D helical coordination polymer, and the latter is a tetranuclear helicate. In both structures, the Tpa(x) ligand adopts a μ(2):κ(2):κ(1)-coordination mode. However, in solution, all of the four complexes form fluxional species. When CuI is used as the copper(I) source, neutral compounds 5-8 have been obtained. Complexes 6-8 exhibit a 1:1 metal-to-ligand ratio, whereas 5 presents 2:1 stoichiometry. Its solid-state structure has been determined by X-ray diffraction, revealing its 3D polymeric nature. The polymer is composed by the assembly of [Tpa2Cu4I4] units, in which Cu4I4 presents a step-stair structure. The Tpa ligands bridge the Cu4I4 clusters, adopting also a μ(2):κ(2):κ(1)-coordination mode. As observed for the cationic derivatives, the NMR spectra of 5-8 show the equivalence of the three pyrazolyl arms of the ligands in these complexes. The reactivities of cationic copper(I) derivatives 1-4 with PPh3 and CO have been explored. In all cases, 1:1 adducts [Tpa(x)CuL]PF6 [L = PPh3 (9-11), CO (12-15)] have been isolated. The crystal structure of [Tpa*Cu(PPh3)]PF6 (9) has been obtained, showing that the coordination geometry around copper(I) is trigonal-pyramidal with the apical position occupied by the tertiary amine N atom. The Tpa* ligand binds the Cu center to three of its four N atoms, with one pyrazolyl arm remaining uncoordinated. In solution, the carbonyl adducts 13-15 exist as a mixture of two isomers; the four- and five-coordinate species can be distinguished by means of their IR νCO stretching bands. Finally, the catalytic activities of complexes 1-4 have been demonstrated in carbene- and nitrene-transfer reactions.

Concerted Dynamic Motions of an FABP4 Model and Its Ligands Revealed by Microsecond Molecular Dynamics Simulations

PubMed Central

2015-01-01

In this work, we investigate the dynamic motions of fatty acid binding protein 4 (FABP4) in the absence and presence of a ligand by explicitly solvated all-atom molecular dynamics simulations. The dynamics of one ligand-free FABP4 and four ligand-bound FABP4s is compared via multiple 1.2 μs simulations. In our simulations, the protein interconverts between the open and closed states. Ligand-free FABP4 prefers the closed state, whereas ligand binding induces a conformational transition to the open state. Coupled with opening and closing of FABP4, the ligand adopts distinct binding modes, which are identified and compared with crystal structures. The concerted dynamics of protein and ligand suggests that there may exist multiple FABP4–ligand binding conformations. Thus, this work provides details about how ligand binding affects the conformational preference of FABP4 and how ligand binding is coupled with a conformational change of FABP4 at an atomic level. PMID:25231537

Concerted dynamic motions of an FABP4 model and its ligands revealed by microsecond molecular dynamics simulations.

PubMed

Li, Yan; Li, Xiang; Dong, Zigang

2014-10-14

In this work, we investigate the dynamic motions of fatty acid binding protein 4 (FABP4) in the absence and presence of a ligand by explicitly solvated all-atom molecular dynamics simulations. The dynamics of one ligand-free FABP4 and four ligand-bound FABP4s is compared via multiple 1.2 μs simulations. In our simulations, the protein interconverts between the open and closed states. Ligand-free FABP4 prefers the closed state, whereas ligand binding induces a conformational transition to the open state. Coupled with opening and closing of FABP4, the ligand adopts distinct binding modes, which are identified and compared with crystal structures. The concerted dynamics of protein and ligand suggests that there may exist multiple FABP4-ligand binding conformations. Thus, this work provides details about how ligand binding affects the conformational preference of FABP4 and how ligand binding is coupled with a conformational change of FABP4 at an atomic level.

Luminescence Studies of the Ligand Exchange Between Two Phenanthroline Complexes and Bovine Serum Albumin

NASA Astrophysics Data System (ADS)

Lin, H.-B.; Shen, Q.-H.

2017-03-01

The interactions between bovine serum albumin (BSA) and two Cu(II) phenanthroline complexes were studied by fluorescence and UV-visible absorption spectroscopy. The obtained results confirm that the phen ligand (phen = 1,10-phenanthroline) is dissociated from the two complexes and moves into the hydrophobic cavity of BSA and that the M-L complexes (M = Co2+, Cu2+; L = Hlact, imda; Hlact = lactic acid, H2imda = iminodiacetic acid) coordinate with the amino acids on the surface of the peptide in the solution. This mode of action significantly inhibits the denaturation of BSA. The calculated distance between the BSA and the two complexes suggests that the energy transfer from the excited state of BSA to a complex occurs with high efficiency.

1,2-Hydroxypyridonates as Contrast Agents for Magnetic ResonanceImaging: TREN-1,2-HOPO

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jocher, Christoph J.; Moore, Evan G.; Xu, Jide

2007-05-08

1,2-Hydroxypyridinones (1,2-HOPO) form very stable lanthanide complexes that may be useful as contrast agents for Magnetic Resonance Imaging (MRI). X-ray diffraction of single crystals established that the solid state structures of the Eu(III) and the previously reported [Inorg. Chem. 2004, 43, 5452] Gd(III) complex are identical. The recently discovered sensitizing properties of 1,2-HOPO chelates for Eu(III) luminescence allow direct measurement of the number if water molecules in the metal complex. Fluorescence measurements of the Eu(III) complex corroborate that in solution two water molecules coordinate the lanthanide (q = 2) as proposed from the analysis of NMRD profiles. In addition, fluorescencemore » measurements have verified the anion binding interactions of lanthanide TREN-1,2-HOPO complexes in solution, studied by relaxivity, revealing only very weak oxalate binding (K{sub A} = 82.7 {+-} 6.5 M{sup -1}). Solution thermodynamic studies of the metal complex and free ligand have been carried out using potentiometry, spectrophotometry and fluorescence spectroscopy. The metal ion selectivity of TREN-1,2-HOPO supports the feasibility of using 1,2-HOPO ligands for selective lanthanide binding [pGd = 19.3 (2); pZn = 15.2 (2), pCa = 8.8 (3)].« less

Characterization of Non-Innocent Metal Complexes Using Solid-State NMR Spectroscopy: o-Dioxolene Vanadium Complexes

PubMed Central

Chatterjee, Pabitra B.; Goncharov-Zapata, Olga; Quinn, Laurence L.; Hou, Guangjin; Hamaed, Hiyam; Schurko, Robert W.; Polenova, Tatyana; Crans, Debbie C.

2012-01-01

51V solid-state NMR (SSNMR) studies of a series of non-innocent vanadium(V) catechol complexes have been conducted to evaluate the possibility that 51V NMR observables, quadrupolar and chemical shift anisotropies, and electronic structures of such compounds can be used to characterize these compounds. The vanadium(V) catechol complexes described in these studies have relatively small quadrupolar coupling constants, which cover a surprisingly small range from 3.4 to 4.2 MHz. On the other hand, isotropic 51V NMR chemical shifts cover a wide range from −200 ppm to 400 ppm in solution and from −219 to 530 ppm in the solid state. A linear correlation of 51V NMR isotropic solution and solid-state chemical shifts of complexes containing non-innocent ligands is observed. These experimental results provide the information needed for the application of 51V SSNMR spectroscopy in characterizing the electronic properties of a wide variety of vanadium-containing systems, and in particular those containing non-innocent ligands and that have chemical shifts outside the populated range of −300 ppm to −700 ppm. The studies presented in this report demonstrate that the small quadrupolar couplings covering a narrow range of values reflect the symmetric electronic charge distribution, which is also similar across these complexes. These quadrupolar interaction parameters alone are not sufficient to capture the rich electronic structure of these complexes. In contrast, the chemical shift anisotropy tensor elements accessible from 51V SSNMR experiments are a highly sensitive probe of subtle differences in electronic distribution and orbital occupancy in these compounds. Quantum chemical (DFT) calculations of NMR parameters for [VO(hshed)(Cat)] yield 51V CSA tensor in reasonable agreement with the experimental results, but surprisingly, the calculated quadrupolar coupling constant is significantly greater than the experimental value. The studies demonstrate that substitution of the catechol ligand with electron donating groups results in an increase in the HOMO-LUMO gap and can be directly followed by an upfield shift for the vanadium catechol complex. In contrast, substitution of the catechol ligand with electron withdrawing groups results in a decrease in the HOMO-LUMO gap and can directly be followed by a downfield shift for the complex. The vanadium catechol complexes were used in this work because the 51V is a half-integer quadrupolar nucleus whose NMR observables are highly sensitive to the local environment. However, the results are general and could be extended to other redox active complexes that exhibit similar coordination chemistry as the vanadium catechol complexes. PMID:21842875

Complexes of oxovanadium(IV), dioxovanadium(V) and dioxouranium(VI) with aminoacids in aqueous solution

NASA Astrophysics Data System (ADS)

Lagrange, P.; Schneider, M.; Lagrange, J.

1998-11-01

The equilibria between three oxocations (VO2+, VO2+ and UO22+) and several ?- aminoacids (glycine, serine, asparagine, lysine, aspartic acid and glutamic acid) are studied in aqueous solution. Stoichiometry and stability of the complexes formed are determined from a combination of potentiometric and spectroscopic measurements. Solution structures of the different complexes are proposed based on the thermodynamic results. The oxovanadium(IV) complexes appear less stable than the corresponding dioxouranium(VI) and dioxovanadium(V) complexes. VO2+ can be bound to only one ligand to form monodentate or chelate complexes. UO22+ and VO2+ cations may be chelated by one or two ligands. Les équilibres entre trois oxocations, VO2+, VO2+ et UO22+ et plusieurs α-aminoacides, glycine, sérine, asparagine, lysine et acides aspartique et glutamique, sont étudiés en solution aqueuse par potentiométrie couplée à la spectrophotométrie. Les complexes de VO2+ sont moins stables que les complexes de VO2+ et UO22+ de même stoechiométrie. VO2+ ne peut se lier qu'à un seul ligand pour former soit des complexes monodentés, soit des chélates. UO22+ et VO2+ peuvent être chélatés par un ou deux ligands. Des structures hypothétiques en solution sont proposées.

A spectroscopic study on the coordination and solution structures of the interaction systems between biperoxidovanadate complexes and the pyrazolylpyridine-like ligands.

PubMed

Yu, Xian-Yong; Deng, Lin; Zheng, Baishu; Zeng, Bi-Rong; Yi, Pinggui; Xu, Xin

2014-01-28

In order to understand the substitution effects of pyrazolylpyridine (pzpy) on the coordination reaction equilibria, the interactions between a series of pzpy-like ligands and biperoxidovanadate ([OV(O2)2(D2O)](-)/[OV(O2)2(HOD)](-), abbrv. bpV) have been explored using a combination of multinuclear ((1)H, (13)C, and (51)V) magnetic resonance, heteronuclear single quantum coherence (HSQC), and variable temperature NMR in a 0.15 mol L(-1) NaCl D2O solution that mimics the physiological conditions. Both the direct NMR data and the equilibrium constants are reported for the first time. A series of new hepta-coordinated peroxidovanadate species [OV(O2)2L](-) (L = pzpy-like chelating ligands) are formed due to several competitive coordination interactions. According to the equilibrium constants for products between bpV and the pzpy-like ligands, the relative affinity of the ligands is found to be pzpy > 2-Ester-pzpy ≈ 2-Me-pzpy ≈ 2-Amide-pzpy > 2-Et-pzpy. In the interaction system between bpV and pzpy, a pair of isomers (Isomers A and B) are observed in aqueous solution, which are attributed to different types of coordination modes between the metal center and the ligands, while the crystal structure of NH4[OV(O2)2(pzpy)]·6H2O (CCDC 898554) has the same coordination structure as Isomer A (the main product for pzpy). For the N-substituted ligands, however, Isomer A or B type complexes can also be observed in solution but the molar ratios of the isomer are reversed (i.e., Isomer B type is the main product). These results demonstrate that when the N atom in the pyrazole ring has a substitution group, hydrogen bonding (from the H atom in the pyrazole ring), the steric effect (from alkyl) and the solvation effect (from the ester or amide group) can jointly affect the coordination reaction equilibrium.

Deciphering ligands' interaction with Cu and Cu2O nanocrystal surfaces by NMR solution tools.

PubMed

Glaria, Arnaud; Cure, Jérémy; Piettre, Kilian; Coppel, Yannick; Turrin, Cédric-Olivier; Chaudret, Bruno; Fau, Pierre

2015-01-12

The hydrogenolysis of [Cu2{(iPrN)2(CCH3)}2] in the presence of hexadecylamine (HDA) or tetradecylphosphonic acid (TDPA) in toluene leads to 6-9 nm copper nanocrystals. Solution NMR spectroscopy has been used to describe the nanoparticle surface chemistry during the dynamic phenomenon of air oxidation. The ligands are organized as multilayered shells around the nanoparticles. The shell of ligands is controlled by both their intermolecular interactions and their bonding strength on the nanocrystals. Under ambient atmosphere, the oxidation rate of colloidal copper nanocrystals closely relies on the chemical nature of the employed ligands (base or acid). Primary amine molecules behave as soft ligands for Cu atoms, but are even more strongly coordinated on surface Cu(I) sites, thus allowing a very efficient corrosion protection of the copper core. On the contrary, the TDPA ligands lead to a rapid oxidation rate of Cu nanoparticles and eventually to the re-dissolution of Cu(II) species at the expense of the nanocrystals. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Experimental considerations in metal mobilization from soil by chelating ligands: The influence of soil-solution ratio and pre-equilibration - A case study on Fe acquisition by phytosiderophores.

PubMed

Schenkeveld, W D C; Kimber, R L; Walter, M; Oburger, E; Puschenreiter, M; Kraemer, S M

2017-02-01

The efficiency of chelating ligands in mobilizing metals from soils and sediments is generally examined under conditions remote from those under which they are exuded or applied in the field. This may lead to incorrect estimations of the mobilizing efficiency. The aim of this study was to establish the influence of the soil solution ratio (SSR) and pre-equilibration with electrolyte solution on metal mobilization and metal displacement. For this purpose a series of interaction experiments with a calcareous clay soil and a biogenic chelating agent, the phytosiderophore 2'-deoxymugineic acid (DMA) were carried out. For a fixed ligand concentration, the SSR had a strong influence on metal mobilization and displacement. Metal complexation was faster at higher SSR. Reactive pools of metals that were predominantly mobilized at SSR 6 (in this case Cu), became depleted at SSR 0.1, whereas metals that were marginally mobilized at SSR 6, were dominantly mobilized at SSR 0.1 (in this case Fe), because of large soil reactive pools. For a fixed "amount of ligand"-to-"amount of soil"-ratio, metal complexation scaled linearly with the SSR. The efficiency of ligands in mobilizing metals under field conditions can be predicted with batch experiments, as long as the ligand-to-soil-ratio is matched. In most previously reported studies this criterion was not met. Equivalent metal-complex concentrations under field conditions can be back-calculated using adsorption isotherms for the respective metal-complexes. Drying and dry storage created labile pools of Fe, Cu and Zn, which were rapidly mobilized upon addition of DMA solution to dry soil. Pre-equilibration decreased these labile pools, leading to smaller concentrations of these metals during initial mobilization, but did not reduce the lag time between ligand addition and onset of microbial degradation of the metal-complexes. Hence SSR and pre-equilibration should be carefully considered when testing the metal mobilizing efficiency of chelating ligands. Copyright © 2016. Published by Elsevier B.V.

Guest-tuned spin crossover in flexible supramolecular assemblies templated by a halide (Cl -, Br - or I - )

DOE Office of Scientific and Technical Information (OSTI.GOV)

Darawsheh, M. D.; Barrios, L. A.; Roubeau, O.

Ligand 1,3-bis(3-(pyridin-2-yl)-1H-pyrazol-5-yl)benzene, L, forms mononuclear spin crossover complexes [FeL 3] 2+ with pendant arms that cause them to dimerize through numerous intermolecular interactions forming supramolecular (X@[FeL 3] 2) 3+ cations. Finally, hey have the flexibility to encapsulate Cl -, Br - or I -, which allow tuning the magnetic properties, in the solid state and in solution.

Guest-tuned spin crossover in flexible supramolecular assemblies templated by a halide (Cl -, Br - or I - )

DOE PAGES

Darawsheh, M. D.; Barrios, L. A.; Roubeau, O.; ...

2016-12-05

Ligand 1,3-bis(3-(pyridin-2-yl)-1H-pyrazol-5-yl)benzene, L, forms mononuclear spin crossover complexes [FeL 3] 2+ with pendant arms that cause them to dimerize through numerous intermolecular interactions forming supramolecular (X@[FeL 3] 2) 3+ cations. Finally, hey have the flexibility to encapsulate Cl -, Br - or I -, which allow tuning the magnetic properties, in the solid state and in solution.

Molybdenum-oxide based unique polyprotic nanoacids showing different deprotonations and related assembly processes in solution.

PubMed

Kistler, Melissa L; Liu, Tianbo; Gouzerh, Pierre; Todea, Ana Maria; Müller, Achim

2009-07-14

We report the self-assembly processes in solution of three Keplerate-type molybdenum-oxide based clusters {Mo72V30}, {Mo72Cr30} and {Mo72Fe30} (all with diameters of approximately 2.5 nm). These clusters behave as unique weak polyprotic acids owing to the external water ligands attached to the non-Mo metal centers. Whereas the Cr and Fe clusters have 30 water ligands attached at the 30 M3+ centers pointing outside, {Mo72V30} has 20 water ligands coordinated to vanadium atoms, of which only 10 are pointing outside. The self-assembly processes of the Keplerates leading to supramolecular blackberry-type structures are influenced by the effective charge densities on the cluster surfaces, which can be tuned by the pH values and solvent properties. As expected, {Mo72Cr30} and {Mo72Fe30} behave similarly in aqueous solution due to their analogous structures and in both cases the self-assembly follows the partial deprotonation of the external water ligands attached to the non-Mo metal centers. However, the M-OH2 functionalities differ not only in acidity but also lability, i.e. in different residence times of the H2O ligands. In contrast to {Mo72Cr30} and {Mo72Fe30}, the {Mo72V30} clusters carry a rather large number of negative charges so that their solution properties are different. They exist as discrete macroions in dilute aqueous solution, and form only in mixed water/organic solvent (like acetone) blackberry-type structures whose size increases with acetone content. The comparison of the properties of the clusters allows more general information about the interesting self-assembly phenomenon to be unveiled.

Outer-sphere interaction of aluminum and gallium solvates with competitive anions in 1,2-propanediol solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petrosyants, S.P.; Buslaeva, E.R.

1986-04-01

The interaction of aluminum and gallium solvates with ..pi..-acid ligand in 1,2-propanediol solutions has been investigated. The formation of associates of hexacoordinate aluminum solvates depends on the solvation of the anions in the bulk of the solution or on the faces of the solvento complexes. In the case of gallium the association of the solvates with the anions is determined by two factors: the existence of a configurational equilibrium for the solvento complexes and the preferential solvation of the competitive ..pi..-acid ligands.

An Integrated approach (thermodynamic, structural, and computational) to the study of complexation of alkali-metal cations by a lower-rim calix[4]arene amide derivative in acetonitrile.

PubMed

Horvat, Gordan; Stilinović, Vladimir; Hrenar, Tomica; Kaitner, Branko; Frkanec, Leo; Tomišić, Vladislav

2012-06-04

The calix[4]arene secondary-amide derivative L was synthesized, and its complexation with alkali-metal cations in acetonitrile (MeCN) was studied by means of spectrophotometric, NMR, conductometric, and microcalorimetric titrations at 25 °C. The stability constants of the 1:1 (metal/ligand) complexes determined by different methods were in excellent agreement. For the complexation of M(+) (M = Li, Na, K) with L, both enthalpic and entropic contributions were favorable, with their values and mutual relations being quite strongly dependent on the cation. The enthalpic and overall stability was the largest in the case of the sodium complex. Molecular and crystal structures of free L, its methanol and MeCN solvates, the sodium complex, and its MeCN solvate were determined by single-crystal X-ray diffraction. The inclusion of a MeCN molecule in the calixarene hydrophobic cavity was observed both in solution and in the solid state. This specific interaction was found to be stronger in the case of metal complexes compared to the free ligand because of the better preorganization of the hydrophobic cone to accept the solvent molecule. Density functional theory calculations showed that the flattened cone conformation (C(2) point group) of L was generally more favorable than the square cone conformation (C(4) point group). In the complex with Na(+), L was in square cone conformation, whereas in its adduct with MeCN, the conformation was slightly distorted from the full symmetry. These conformations were in agreement with those observed in the solid state. The classical molecular dynamics simulations indicated that the MeCN molecule enters the L hydrophobic cavity of both the free ligand and its alkali-metal complexes. The inclusion of MeCN in the cone of free L was accompanied by the conformational change from C(2) to C(4) symmetry. As in solution studies, in the case of ML(+) complexes, an allosteric effect was observed: the ligand was already in the appropriate square cone conformation to bind the solvent molecule, allowing it to more easily and faster enter the calixarene cavity.

The impact of mixed solvents on the complexation thermodynamics of Eu(III) by simple carboxylate and amino carboxylate ligands

DOE PAGES

Felmy, Heather M.; Bennett, Kevin T.; Clark, Sue B.

2017-05-12

To gain insight on the role of mixed solvents on the thermodynamic driving forces for the complexation between trivalent f-elements and organic ligands, solution phase thermodynamic parameters were determined for Eu(III) complexation with 2-hydroxyisobutyric acid (HIBA) and 2-aminoisobutyric acid (AIBA) in mixed methanol (MeOH)-water and N,N-dimethylformamide (DMF)-water solvents. Included in this study were the determination of mixed solvent autoprotolysis constants (pK α) as well as the thermodynamic formation constants: log β, ΔG, ΔH, and ΔS, for ligand protonation and Eu(III)-ligand complexation utilizing potentiometry and calorimetry techniques. The results presented are conditional thermodynamic values determined at an ionic strength of 1.0more » M NaClO 4 and a temperature of 298 K. It was found that moving from an aqueous solution to a binary aqueous-organic solvent affected all solution equilibria to some degree and that the extent of change depended on both the type of mixed solvent and the ligand in each study. Here, the ability to understand and predict these changes in thermodynamic values as a function of solvent composition provides important information about the chemistry of the trivalent f-elements.« less

The impact of mixed solvents on the complexation thermodynamics of Eu(III) by simple carboxylate and amino carboxylate ligands

DOE Office of Scientific and Technical Information (OSTI.GOV)

Felmy, Heather M.; Bennett, Kevin T.; Clark, Sue B.

To gain insight on the role of mixed solvents on the thermodynamic driving forces for the complexation between trivalent f-elements and organic ligands, solution phase thermodynamic parameters were determined for Eu(III) complexation with 2-hydroxyisobutyric acid (HIBA) and 2-aminoisobutyric acid (AIBA) in mixed methanol (MeOH)-water and N,N-dimethylformamide (DMF)-water solvents. Included in this study were the determination of mixed solvent autoprotolysis constants (pK α) as well as the thermodynamic formation constants: log β, ΔG, ΔH, and ΔS, for ligand protonation and Eu(III)-ligand complexation utilizing potentiometry and calorimetry techniques. The results presented are conditional thermodynamic values determined at an ionic strength of 1.0more » M NaClO 4 and a temperature of 298 K. It was found that moving from an aqueous solution to a binary aqueous-organic solvent affected all solution equilibria to some degree and that the extent of change depended on both the type of mixed solvent and the ligand in each study. Here, the ability to understand and predict these changes in thermodynamic values as a function of solvent composition provides important information about the chemistry of the trivalent f-elements.« less

Microfluidic free-flow electrophoresis for the discovery and characterisation of calmodulin binding partners

NASA Astrophysics Data System (ADS)

Herling, Therese; Linse, Sara; Knowles, Tuomas

2015-03-01

Non-covalent and transient protein-ligand interactions are integral to cellular function and malfunction. Key steps in signalling and regulatory pathways rely on reversible non-covalent protein-protein binding or ion chelation. Here we present a microfluidic free-flow electrophoresis method for detecting and characterising protein-ligand interactions in solution. We apply this method to probe the binding equilibria of calmodulin, a central protein to calcium signalling pathways. In this study we characterise the specific binding of calmodulin to phosphorylase kinase, a known target, and creatine kinase, which we identify as a putative binding partner through a protein array screen and surface plasmon resonance experiments. We verify the interaction between calmodulin and creatine kinase in solution using free-flow electrophoresis and investigate the effect of calcium and sodium chloride on the calmodulin-ligand binding affinity in free solution without the presence of a potentially interfering surface. Our results demonstrate the general applicability of quantitative microfluidic electrophoresis to characterise binding equilibria between biomolecules in solution.

Heterometallic molecular precursors for a lithium-iron oxide material: synthesis, solid state structure, solution and gas-phase behaviour, and thermal decomposition.

PubMed

Han, Haixiang; Wei, Zheng; Barry, Matthew C; Filatov, Alexander S; Dikarev, Evgeny V

2017-05-02

Three heterometallic single-source precursors with a Li : Fe = 1 : 1 ratio for a LiFeO 2 oxide material are reported. Heterometallic compounds LiFeL 3 (L = tbaoac (1), ptac (2), and acac(3)) have been obtained on a large scale, in nearly quantitative yields by one-step reactions that employ readily available reagents. The heterometallic precursor LiFe(acac) 3 (3) with small, symmetric substituents on the ligand (acac = pentane-2,4-dionate), maintains a 1D polymeric structure in the solid state that limits its volatility and prevents solubility in non-coordinating solvents. The application of the unsymmetrical ligands, tbaoac (tert-butyl acetoacetate) and ptac (1,1,1-trifluoro-5,5-dimethyl-2,4-hexanedionate), that exhibit different bridging properties at the two ends of the ligand, allowed us to change the connectivity pattern within the heterometallic assembly. The latter was demonstrated by structural characterization of heterometallic complexes LiFe(tbaoac) 3 (1) and LiFe(ptac) 3 (2) that consist of discrete heterocyclic tetranuclear molecules Li 2 Fe 2 L 6 . The compounds are highly volatile and exhibit a congruent sublimation character. DART mass spectrometric investigation revealed the presence of heterometallic molecules in the gas phase. The positive mode spectra are dominated by the presence of [M - L] + peaks (M = Li 2 Fe 2 L 6 ). In accord with their discrete molecular structure, complexes 1 and 2 are highly soluble in nearly all common solvents. In order to test the retention of the heterometallic structure in solution, the diamagnetic analog of 1, LiMg(tbaoac) 3 (4), has been isolated. Its tetranuclear molecular structure was found to be isomorphous to that of the iron counterpart. 1 H and 7 Li NMR spectroscopy unambiguously confirmed the presence of heterometallic molecules in solutions of non-coordinating solvents. The heterometallic precursor 1 was shown to exhibit clean thermal decomposition in air that results in phase-pure α-modification of layered oxide LiFeO 2 , the prospective cathode material for lithium ion batteries.

STARD6 on steroids: solution structure, multiple timescale backbone dynamics and ligand binding mechanism

NASA Astrophysics Data System (ADS)

Létourneau, Danny; Bédard, Mikaël; Cabana, Jérôme; Lefebvre, Andrée; Lehoux, Jean-Guy; Lavigne, Pierre

2016-06-01

START domain proteins are conserved α/β helix-grip fold that play a role in the non-vesicular and intracellular transport of lipids and sterols. The mechanism and conformational changes permitting the entry of the ligand into their buried binding sites is not well understood. Moreover, their functions and the identification of cognate ligands is still an active area of research. Here, we report the solution structure of STARD6 and the characterization of its backbone dynamics on multiple time-scales through 15N spin-relaxation and amide exchange studies. We reveal for the first time the presence of concerted fluctuations in the Ω1 loop and the C-terminal helix on the microsecond-millisecond time-scale that allows for the opening of the binding site and ligand entry. We also report that STARD6 binds specifically testosterone. Our work represents a milestone for the study of ligand binding mechanism by other START domains and the elucidation of the biological function of STARD6.

Excitation energy transfer in europium chelate with doxycycline in the presence of a second ligand in micellar solutions of nonionic surfactants

NASA Astrophysics Data System (ADS)

Smirnova, T. D.; Shtykov, S. N.; Kochubei, V. I.; Khryachkova, E. S.

2011-01-01

The complexation of Eu3+ with doxycycline (DC) antibiotic in the presence of several second ligands and surfactant micelles of different types is studied by the spectrophotometric and luminescence methods. It is found that the efficiency of excitation energy transfer in Eu3+-DC chelate depends on the nature of the second ligand and surfactant micelles. Using thenoyltrifluoroacetone (TTA) as an example, it is shown that the second ligand additionally sensitizes the europium fluorescence, and the possibility of intermediate sensitization of DC and then of europium is shown by the example of 1,10-phenanthroline. In all cases, the excitation energy transfer efficiency was increased due to the so-called antenna effect. The decay kinetics of the sensitized fluorescence of the binary and mixed-ligand chelates in aqueous and micellar solutions of nonionic surfactants is studied and the relative quantum yields and lifetimes of fluorescence are determined.

Solution NMR Spectroscopy in Target-Based Drug Discovery.

PubMed

Li, Yan; Kang, Congbao

2017-08-23

Solution NMR spectroscopy is a powerful tool to study protein structures and dynamics under physiological conditions. This technique is particularly useful in target-based drug discovery projects as it provides protein-ligand binding information in solution. Accumulated studies have shown that NMR will play more and more important roles in multiple steps of the drug discovery process. In a fragment-based drug discovery process, ligand-observed and protein-observed NMR spectroscopy can be applied to screen fragments with low binding affinities. The screened fragments can be further optimized into drug-like molecules. In combination with other biophysical techniques, NMR will guide structure-based drug discovery. In this review, we describe the possible roles of NMR spectroscopy in drug discovery. We also illustrate the challenges encountered in the drug discovery process. We include several examples demonstrating the roles of NMR in target-based drug discoveries such as hit identification, ranking ligand binding affinities, and mapping the ligand binding site. We also speculate the possible roles of NMR in target engagement based on recent processes in in-cell NMR spectroscopy.

Multi-stimuli responsive luminescent azepane-substituted β-diketones and difluoroboron complexes.

PubMed

Wang, Fang; DeRosa, Christopher A; Daly, Margaret L; Song, Daniel; Fraser, Cassandra L

2017-09-01

Difluoroboron β-diketonate (BF 2 bdk) compounds show environment-sensitive optical properties in solution, aggregation-induced emission (AIE) and multi-stimuli responsive fluorescence switching in the solid state. Here, a series of 4-azepane-substituted β-diketone (bdk) ligands ( L-H , L-OMe , L-Br ) and their corresponding difluoroboron dyes ( D-H , D-OMe , D-Br ) were synthesized, and various responsive fluorescence properties of the compounds were studied, including solvatochromism, viscochromism, AIE, mechanochromic luminescence (ML) and halochromism. Compared to the β-diketones, the boron complexes exhibited higher extinction coefficients but lower quantum yields, and red-shifted absorption and emission in CH 2 Cl 2 . Computational studies showed that intramolecular charge transfer (ICT) dominated rather than π-π* transitions in all the compounds regardless of boron coordination. In solution, all the bdk ligands and boron dyes showed red-shifted emission in more polar solvents and increased fluorescence intensity in more viscous media. Upon aggregation, the emission of the β-diketones was quenched, however, the boronated dyes showed increased emission, indicative of AIE. Solid-state emission properties, ML and halochromism, were investigated on spin cast films. For ML, smearing caused a bathochromic emission shift for L-Br , and powder X-ray diffraction (XRD) patterns showed that the "as spun" and thermally annealed states were more crystalline and the smeared state was amorphous. No obvious ML emission shift was observed for L-H or L-OMe , and the boronated dyes were not mechano-active. Trifluoroacetic acid (TFA) and triethylamine (TEA) vapors were used to study halochromism. Large hypsochromic emission shifts were observed for all the compounds after TFA vapor was applied, and reversible fluorescence switching was achieved using the acid/base pair.

Orbital-specific mapping of the ligand exchange dynamics of Fe(CO)5 in solution.

PubMed

Wernet, Ph; Kunnus, K; Josefsson, I; Rajkovic, I; Quevedo, W; Beye, M; Schreck, S; Grübel, S; Scholz, M; Nordlund, D; Zhang, W; Hartsock, R W; Schlotter, W F; Turner, J J; Kennedy, B; Hennies, F; de Groot, F M F; Gaffney, K J; Techert, S; Odelius, M; Föhlisch, A

2015-04-02

Transition-metal complexes have long attracted interest for fundamental chemical reactivity studies and possible use in solar energy conversion. Electronic excitation, ligand loss from the metal centre, or a combination of both, creates changes in charge and spin density at the metal site that need to be controlled to optimize complexes for photocatalytic hydrogen production and selective carbon-hydrogen bond activation. An understanding at the molecular level of how transition-metal complexes catalyse reactions, and in particular of the role of the short-lived and reactive intermediate states involved, will be critical for such optimization. However, suitable methods for detailed characterization of electronic excited states have been lacking. Here we show, with the use of X-ray laser-based femtosecond-resolution spectroscopy and advanced quantum chemical theory to probe the reaction dynamics of the benchmark transition-metal complex Fe(CO)5 in solution, that the photo-induced removal of CO generates the 16-electron Fe(CO)4 species, a homogeneous catalyst with an electron deficiency at the Fe centre, in a hitherto unreported excited singlet state that either converts to the triplet ground state or combines with a CO or solvent molecule to regenerate a penta-coordinated Fe species on a sub-picosecond timescale. This finding, which resolves the debate about the relative importance of different spin channels in the photochemistry of Fe(CO)5 (refs 4, 16 - 20), was made possible by the ability of femtosecond X-ray spectroscopy to probe frontier-orbital interactions with atom specificity. We expect the method to be broadly applicable in the chemical sciences, and to complement approaches that probe structural dynamics in ultrafast processes.

Orbital-specific mapping of the ligand exchange dynamics of Fe(CO)5 in solution

NASA Astrophysics Data System (ADS)

Wernet, Ph.; Kunnus, K.; Josefsson, I.; Rajkovic, I.; Quevedo, W.; Beye, M.; Schreck, S.; Grübel, S.; Scholz, M.; Nordlund, D.; Zhang, W.; Hartsock, R. W.; Schlotter, W. F.; Turner, J. J.; Kennedy, B.; Hennies, F.; de Groot, F. M. F.; Gaffney, K. J.; Techert, S.; Odelius, M.; Föhlisch, A.

2015-04-01

Transition-metal complexes have long attracted interest for fundamental chemical reactivity studies and possible use in solar energy conversion. Electronic excitation, ligand loss from the metal centre, or a combination of both, creates changes in charge and spin density at the metal site that need to be controlled to optimize complexes for photocatalytic hydrogen production and selective carbon-hydrogen bond activation. An understanding at the molecular level of how transition-metal complexes catalyse reactions, and in particular of the role of the short-lived and reactive intermediate states involved, will be critical for such optimization. However, suitable methods for detailed characterization of electronic excited states have been lacking. Here we show, with the use of X-ray laser-based femtosecond-resolution spectroscopy and advanced quantum chemical theory to probe the reaction dynamics of the benchmark transition-metal complex Fe(CO)5 in solution, that the photo-induced removal of CO generates the 16-electron Fe(CO)4 species, a homogeneous catalyst with an electron deficiency at the Fe centre, in a hitherto unreported excited singlet state that either converts to the triplet ground state or combines with a CO or solvent molecule to regenerate a penta-coordinated Fe species on a sub-picosecond timescale. This finding, which resolves the debate about the relative importance of different spin channels in the photochemistry of Fe(CO)5 (refs 4, 16,17,18,19 and 20), was made possible by the ability of femtosecond X-ray spectroscopy to probe frontier-orbital interactions with atom specificity. We expect the method to be broadly applicable in the chemical sciences, and to complement approaches that probe structural dynamics in ultrafast processes.

Molecular dynamics simulations of apocupredoxins: insights into the formation and stabilization of copper sites under entatic control.

PubMed

Abriata, Luciano A; Vila, Alejandro J; Dal Peraro, Matteo

2014-06-01

Cupredoxins perform copper-mediated long-range electron transfer (ET) in biological systems. Their copper-binding sites have evolved to force copper ions into ET-competent systems with decreased reorganization energy, increased reduction potential, and a distinct electronic structure compared with those of non-ET-competent copper complexes. The entatic or rack-induced state hypothesis explains these special properties in terms of the strain that the protein matrix exerts on the metal ions. This idea is supported by X-ray structures of apocupredoxins displaying "closed" arrangements of the copper ligands like those observed in the holoproteins; however, it implies completely buried copper-binding atoms, conflicting with the notion that they must be exposed for copper loading. On the other hand, a recent work based on NMR showed that the copper-binding regions of apocupredoxins are flexible in solution. We have explored five cupredoxins in their "closed" apo forms through molecular dynamics simulations. We observed that prearranged ligand conformations are not stable as the X-ray data suggest, although they do form part of the dynamic landscape of the apoproteins. This translates into variable flexibility of the copper-binding regions within a rigid fold, accompanied by fluctuations of the hydrogen bonds around the copper ligands. Major conformations with solvent-exposed copper-binding atoms could allow initial binding of the copper ions. An eventual subsequent incursion to the closed state would result in binding of the remaining ligands, trapping the closed conformation thanks to the additional binding energy and the fastening of noncovalent interactions that make up the rack.

Selective oxoanion separation using a tripodal ligand

DOEpatents

Custelcean, Radu; Moyer, Bruce A.; Rajbanshi, Arbin

2016-02-16

The present invention relates to urea-functionalized crystalline capsules self-assembled by sodium or potassium cation coordination and by hydrogen-bonding water bridges to selectively encapsulate tetrahedral divalent oxoanions from highly competitive aqueous alkaline solutions and methods using this system for selective anion separations from industrial solutions. The method involves competitive crystallizations using a tripodal tris(urea) functionalized ligand and, in particular, provides a viable approach to sulfate separation from nuclear wastes.

An X-ray study of the effect of the bite angle of chelating ligands on the geometry of palladium(allyl) complexes: implications for the regioselectivity in the allylic alkylation.

PubMed

van Haaren, R J; Goubitz, K; Fraanje, J; van Strijdonck, G P; Oevering, H; Coussens, B; Reek, J N; Kamer, P C; van Leeuwen, P W

2001-07-02

X-ray crystal structures of a series of cationic (P-P)palladium(1,1-(CH(3))(2)C(3)H(3)) complexes (P-P = dppe (1,2-bis(diphenylphosphino)ethane), dppf (1,1'-bis(diphenylphosphino)ferrocene), and DPEphos (2,2'-bis(diphenylphosphino)diphenyl ether)) and the (Xantphos)Pd(C(3)H(5))BF(4) (Xantphos = 4,5-bis(diphenylphosphino)-9,9-dimethylxanthene) complex have been determined. In the solid state structure, the phenyl rings of the ligand are oriented in the direction of the nonsymmetrically bound [1,1-(CH(3))(2)C(3)H(3)] moiety. An increase of the bite angle of the chelating ligand results in an increase of the cone angle. In complexes containing ligands having a large cone angle, the distances between the phenyl rings and the allyl moiety become small, resulting in a distortion of the symmetry of the palladium-allyl bond. In solution, two types of dynamic exchange have been observed, the pi-sigma rearrangement and the apparent rotation of the allyl moiety. At the same time, the folded structure of the ligand changes from an endo to an exo orientation or vice versa. The regioselectivity in the palladium-catalyzed allylic alkylation of 3-methyl-but-2-enyl acetate is determined by the cone angle of the bidentate phosphine ligand. Nucleophilic attack by a malonate anion takes place preferentially at the allylic carbon atom having the largest distance to palladium. Ligands with a larger cone angle direct the regioselectivity to the formation of the branched product, from 8% for dppe (1) to 61% found for Xantphos (6). The influence of the cone angle on the regioselectivity has been assigned to a sterically induced electronic effect.

C-H functionalization: thoroughly tuning ligands at a metal ion, a chemist can greatly enhance catalyst's activity and selectivity.

PubMed

Shul'pin, Georgiy B

2013-09-28

This brief essay consists of a few "exciting stories" devoted to relations within a metal-complex catalyst between a metal ion and a coordinated ligand. When, as in the case of a human couple, the rapport of the partners is cordial and a love cements these relations, a chemist finds an ideal married couple, in other words he obtains a catalyst of choice which allows him to functionalize C-H bonds very efficiently and selectively. Examples of such lucky marriages in the catalytic world of ions and ligands are discussed here. Activity of the catalyst is characterized by turnover number (TON) or turnover frequency (TOF) as well as by yield of a target product. Introducing a chelating N,N- or N,O-ligand to the catalyst molecule (this can be an iron or manganese derivative) sharply enhances its activity. However, the activity of vanadium derivatives (with additionally added to the solution pyrazinecarboxylic acid, PCA) as well as of various osmium complexes does not dramatically depend on the nature of ligands surrounding metal ions. Complexes of these metals are very efficient catalysts in oxidations with H2O2. Osmium derivatives are record-holders exhibiting extremely high TONs whereas vanadium complexes are on the second position. Finally, elegant examples of alkane functionalization on the ions of non-transition metals (aluminium, gallium etc.) are described when one ligand within the metal complex (namely, hydroperoxyl ligand HOO(-)) helps other ligand of this complex (H2O2 molecule coordinated to the metal) to disintegrate into two species, generating very reactive hydroxyl radical. Hydrogen peroxide molecule, even ligated to the metal ion, is perfectly stable without the assistance of the neighboring HOO(-) ligand. This ligand can be easily oxidized donating an electron to its partner ligand (H2O2). In an analogous case, when the central ion in the catalyst is a transition metal, this ion changing its oxidation state can donate an electron to the coordinated H2O2 fragment. This provokes the O-O bond rupture in the hydrogen peroxide molecule as is assumed for the role of Fe(2+) ions in the Fenton system.

Thermodynamic and kinetic study of scandium(III) complexes of DTPA and DOTA: a step toward scandium radiopharmaceuticals.

PubMed

Pniok, Miroslav; Kubíček, Vojtěch; Havlíčková, Jana; Kotek, Jan; Sabatie-Gogová, Andrea; Plutnar, Jan; Huclier-Markai, Sandrine; Hermann, Petr

2014-06-23

Diethylenetriamine-N,N,N',N'',N''-pentaacetic acid (DTPA) and 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) scandium(III) complexes were investigated in the solution and solid state. Three (45)Sc NMR spectroscopic references suitable for aqueous solutions were suggested: 0.1 M Sc(ClO4)3 in 1 M aq. HClO4 (δSc =0.0 ppm), 0.1 M ScCl3 in 1 M aq. HCl (δSc =1.75 ppm) and 0.01 M [Sc(ox)4](5-) (ox(2-) = oxalato) in 1 M aq. K2C2O4 (δSc =8.31 ppm). In solution, [Sc(dtpa)](2-) complex (δSc = 83 ppm, Δν = 770 Hz) has a rather symmetric ligand field unlike highly unsymmetrical donor atom arrangement in [Sc(dota)](-) anion (δSc = 100 ppm, Δν = 4300 Hz). The solid-state structure of K8[Sc2(ox)7]⋅13 H2O contains two [Sc(ox)3](3-) units bridged by twice "side-on" coordinated oxalate anion with Sc(3+) ion in a dodecahedral O8 arrangement. Structures of [Sc(dtpa)](2-) and [Sc(dota)](-) in [(Hguanidine)]2[Sc(dtpa)]⋅3 H2O and K[Sc(dota)][H6 dota]Cl2⋅4 H2O, respectively, are analogous to those of trivalent lanthanide complexes with the same ligands. The [Sc(dota)](-) unit exhibits twisted square-antiprismatic arrangement without an axial ligand (TSA' isomer) and [Sc(dota)](-) and (H6 dota)(2+) units are bridged by a K(+) cation. A surprisingly high value of the last DOTA dissociation constant (pKa =12.9) was determined by potentiometry and confirmed by using NMR spectroscopy. Stability constants of scandium(III) complexes (log KScL 27.43 and 30.79 for DTPA and DOTA, respectively) were determined from potentiometric and (45)Sc NMR spectroscopic data. Both complexes are fully formed even below pH 2. Complexation of DOTA with the Sc(3+) ion is much faster than with trivalent lanthanides. Proton-assisted decomplexation of the [Sc(dota)](-) complex (τ1/2 =45 h; 1 M aq. HCl, 25 °C) is much slower than that for [Ln(dota)](-) complexes. Therefore, DOTA and its derivatives seem to be very suitable ligands for scandium radioisotopes. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tetra- and Heptametallic Ru(II),Rh(III) Supramolecular Hydrogen Production Photocatalysts

DOE PAGES

Manbeck, Gerald F.; Fujita, Etsuko; Brewer, Karen J.

2017-06-01

Supramolecular mixed metal complexes combining the trimetallic chromophore [{(bpy) 2Ru(dpp)} 2Ru(dpp)] 6+ (Ru 3) with [Rh(bpy)Cl 2] + or [RhCl 2] + catalytic fragments to form [{(bpy) 2Ru(dpp)} 2Ru(dpp)RhCl 2(bpy)](PF 6) 7 (Ru 3Rh) or [{(bpy) 2Ru(dpp)} 2Ru(dpp)] 2RhCl 2(PF 6) 13 (Ru 3RhRu 3) (bpy = 2,2'-bipyridine and dpp = 2,3-bis(2-pyridyl)pyrazine) catalyze the photochemical reduction of protons to H 2. This first example of a heptametallic Ru,Rh photocatalyst produces over 300 turnovers of H 2 upon photolysis of a solution of acetonitrile, water, triflic acid, and N,N-dimethylaniline as an electron donor. Conversely, the tetrametallic Ru 3Rh produces only 40more » turnovers of H 2 due to differences in the excited state properties and nature of the catalysts upon reduction as ascertained from electrochemical data, transient absorption spectroscopy, and flash-quench experiments. And while the lowest unoccupied molecular orbital of Ru 3Rh is localized on a bridging ligand, it is Rh-centered in Ru 3RhRu 3 facilitating electron collection at Rh in the excited state and reductively quenched state. The Ru → Rh charge separated state of Ru 3RhRu 3 is endergonic with respect to the emissive Ru → dpp 3MLCT excited and cannot be formed by static electron transfer quenching of the 3MLCT state. Instead, a mechanism of subnanosecond charge separation from high lying states is proposed. Multiple reductions of Ru 3 and Ru 3Rh using sodium amalgam were carried out to compare UV–vis absorption spectra of reduced species and to evaluate the stability of highly reduced complexes. Furthermore, the Ru 3 and Ru 3Rh can be reduced by 10 and 13 electrons, respectively, to final states with all bridging ligands doubly reduced and all bpy ligands singly reduced.« less

Standard state thermodynamic properties of Ba2+(aq), Co2+(aq), and Cu2+(aq) up to 598.15 K, and temperature effect on ligand field.

PubMed

Djamali, Essmaiil; Chen, Keith; Murray, Richard C; Turner, Peter J; Cobble, James W

2009-02-26

Integral heat of solution measurements of barium chloride to 619.81 K, copper oxide in an excess of perrhenic acid to 585 K, and cobalt perrhenate in perrhenic acid to 573 K were measured in a high dilution calorimeter (< or =10(-3) m) at psat, from which the high temperature thermodynamic properties of aqueous barium chloride, copper perrhenate, and cobalt perrhenate were obtained. From the known differences between the corresponding properties for aqueous perrhenate and chloride ions, the thermodynamic properties of completely ionized aqueous copper and cobalt chloride were obtained from ionic additivity. The enthalpy and derived heat capacity data at higher temperatures (T > 473.15 K) suggest that the ligand field stabilization energy of Co2+(aq) may be disappearing.

Aqueous vanadium ion dynamics relevant to bioinorganic chemistry: A review.

PubMed

Kustin, Kenneth

2015-06-01

Aqueous solutions of the four highest vanadium oxidation states exhibit four diverse colors, which only hint at the diverse reactions that these ions can undergo. Cationic vanadium ions form complexes with ligands; anionic vanadium ions form complexes with ligands and self-react to form isopolyanions. All vanadium species undergo oxidation-reduction reactions. With a few exceptions, elucidation of the dynamics of these reactions awaited the development of fast reaction techniques before the kinetics of elementary ligation, condensation, reduction, and oxidation of the aqueous vanadium ions could be investigated. As the biological roles played by endogenous and therapeutic vanadium expand, it is appropriate to bring the results of the diverse kinetics studies under one umbrella. To achieve this goal this review presents a systematic examination of elementary aqueous vanadium ion dynamics. Copyright © 2014 Elsevier Inc. All rights reserved.

Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM

PubMed Central

Gagnon, Jessica K.; Law, Sean M.; Brooks, Charles L.

2016-01-01

Protein-ligand docking is a commonly used method for lead identification and refinement. While traditional structure-based docking methods represent the receptor as a rigid body, recent developments have been moving toward the inclusion of protein flexibility. Proteins exist in an inter-converting ensemble of conformational states, but effectively and efficiently searching the conformational space available to both the receptor and ligand remains a well-appreciated computational challenge. To this end, we have developed the Flexible CDOCKER method as an extension of the family of complete docking solutions available within CHARMM. This method integrates atomically detailed side chain flexibility with grid-based docking methods, maintaining efficiency while allowing the protein and ligand configurations to explore their conformational space simultaneously. This is in contrast to existing approaches that use induced-fit like sampling, such as Glide or Autodock, where the protein or the ligand space is sampled independently in an iterative fashion. Presented here are developments to the CHARMM docking methodology to incorporate receptor flexibility and improvements to the sampling protocol as demonstrated with re-docking trials on a subset of the CCDC/Astex set. These developments within CDOCKER achieve docking accuracy competitive with or exceeding the performance of other widely utilized docking programs. PMID:26691274

Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM.

PubMed

Gagnon, Jessica K; Law, Sean M; Brooks, Charles L

2016-03-30

Protein-ligand docking is a commonly used method for lead identification and refinement. While traditional structure-based docking methods represent the receptor as a rigid body, recent developments have been moving toward the inclusion of protein flexibility. Proteins exist in an interconverting ensemble of conformational states, but effectively and efficiently searching the conformational space available to both the receptor and ligand remains a well-appreciated computational challenge. To this end, we have developed the Flexible CDOCKER method as an extension of the family of complete docking solutions available within CHARMM. This method integrates atomically detailed side chain flexibility with grid-based docking methods, maintaining efficiency while allowing the protein and ligand configurations to explore their conformational space simultaneously. This is in contrast to existing approaches that use induced-fit like sampling, such as Glide or Autodock, where the protein or the ligand space is sampled independently in an iterative fashion. Presented here are developments to the CHARMM docking methodology to incorporate receptor flexibility and improvements to the sampling protocol as demonstrated with re-docking trials on a subset of the CCDC/Astex set. These developments within CDOCKER achieve docking accuracy competitive with or exceeding the performance of other widely utilized docking programs. © 2015 Wiley Periodicals, Inc.

Effects of ancillary ligands on selectivity of protein labeling with platinum(II) chloro complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Xia-Ying.

1990-02-01

Potassium (2,6-pyridinedicarboxylato)chloroplatinate(II) was synthesized. The molecular structure of the complex in (n-Bu){sub 4}N(Pt(dipic)Cl){center dot}0.5H{sub 2}O was determined by x-ray crystallography. The (Pt(dipic)Cl){sup {minus}} is essentially planar and contains a Pt(II) atom, a tridentate dipicolinate dianion ligand, and a unidentate Cl{sup {minus}} ligand. The bis(bidentate) complex trans-(Pt(dipic){sub 2}){sup 2{minus}} was also observed by {sup 1}H NMR. A red gel-like substance was observed when the yellow aqueous solution of K(Pt(dipic)Cl) was cooled or concentrated. The K(Pt(dipic)Cl) molecules form stacks in the solid state and gel-like substance but remain monomeric over a wide range of concentrations and temperatures. The reactivity and selectivity of(Pt(dipic)Cl){supmore » {minus}} toward cytochromes c from horse and tuna were studied. The new transition-metal reagent is specific for methionine residues. Di(2-pyridyl-{beta}-ethyl)sulfidochloroplatinum(II) chloride dihydrate was also synthesized. This complex labels histidine and methionine residues in cytochrome c. The ancillary ligands in these platinum(II) complexes clearly determine the selectivity of protein labeling. 106 refs., 10 figs., 11 tabs.« less

Effects of the Hydroxyl Group on Phenyl Based Ligand/ERRγ Protein Binding

PubMed Central

2015-01-01

Bisphenol-A (4,4′-dihydroxy-2,2-diphenylpropane, BPA, or BPA-A) and its derivatives, when exposed to humans, may affect functions of multiple organs by specific binding to the human estrogen-related receptor γ (ERRγ). We carried out atomistic molecular dynamics (MD) simulations of three ligand compounds including BPA-A, 4-α-cumylphenol (BPA-C), and 2,2-diphenylpropane (BPA-D) binding to the ligand binding domain (LBD) of a human ERRγ to study the structures and energies associated with the binding. We used the implicit Molecular Mechanics/Poisson–Boltzmann Surface Area (MM/PBSA) method to estimate the free energies of binding for the phenyl based compound/ERRγ systems. The addition of hydroxyl groups to the aromatic ring had only a minor effect on binding structures and a significant effect on ligand/protein binding energy in an aqueous solution. Free binding energies of BPA-D to the ERRγ were found to be considerably less than those of BPA-A and BPA-C to the ERRγ. These results are well correlated with those from experiments where no binding affinities were determined in the BPA-D/ERRγ complex. No conformational change was observed for the helix 12 (H-12) of ERRγ upon binding of these compounds preserving an active transcriptional conformation state. PMID:25098505

Benchmarking of HPCC: A novel 3D molecular representation combining shape and pharmacophoric descriptors for efficient molecular similarity assessments.

PubMed

Karaboga, Arnaud S; Petronin, Florent; Marchetti, Gino; Souchet, Michel; Maigret, Bernard

2013-04-01

Since 3D molecular shape is an important determinant of biological activity, designing accurate 3D molecular representations is still of high interest. Several chemoinformatic approaches have been developed to try to describe accurate molecular shapes. Here, we present a novel 3D molecular description, namely harmonic pharma chemistry coefficient (HPCC), combining a ligand-centric pharmacophoric description projected onto a spherical harmonic based shape of a ligand. The performance of HPCC was evaluated by comparison to the standard ROCS software in a ligand-based virtual screening (VS) approach using the publicly available directory of useful decoys (DUD) data set comprising over 100,000 compounds distributed across 40 protein targets. Our results were analyzed using commonly reported statistics such as the area under the curve (AUC) and normalized sum of logarithms of ranks (NSLR) metrics. Overall, our HPCC 3D method is globally as efficient as the state-of-the-art ROCS software in terms of enrichment and slightly better for more than half of the DUD targets. Since it is largely admitted that VS results depend strongly on the nature of the protein families, we believe that the present HPCC solution is of interest over the current ligand-based VS methods. Copyright © 2013 Elsevier Inc. All rights reserved.

Fingerprinting redox and ligand states in haemprotein crystal structures using resonance Raman spectroscopy.

PubMed

Kekilli, Demet; Dworkowski, Florian S N; Pompidor, Guillaume; Fuchs, Martin R; Andrew, Colin R; Antonyuk, Svetlana; Strange, Richard W; Eady, Robert R; Hasnain, S Samar; Hough, Michael A

2014-05-01

It is crucial to assign the correct redox and ligand states to crystal structures of proteins with an active redox centre to gain valid functional information and prevent the misinterpretation of structures. Single-crystal spectroscopies, particularly when applied in situ at macromolecular crystallography beamlines, allow spectroscopic investigations of redox and ligand states and the identification of reaction intermediates in protein crystals during the collection of structural data. Single-crystal resonance Raman spectroscopy was carried out in combination with macromolecular crystallography on Swiss Light Source beamline X10SA using cytochrome c' from Alcaligenes xylosoxidans. This allowed the fingerprinting and validation of different redox and ligand states, identification of vibrational modes and identification of intermediates together with monitoring of radiation-induced changes. This combined approach provides a powerful tool to obtain complementary data and correctly assign the true oxidation and ligand state(s) in redox-protein crystals.

Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling

NASA Astrophysics Data System (ADS)

Rosenfeld, Robin J.; Goodsell, David S.; Musah, Rabi A.; Morris, Garrett M.; Goodin, David B.; Olson, Arthur J.

2003-08-01

The W191G cavity of cytochrome c peroxidase is useful as a model system for introducing small molecule oxidation in an artificially created cavity. A set of small, cyclic, organic cations was previously shown to bind in the buried, solvent-filled pocket created by the W191G mutation. We docked these ligands and a set of non-binders in the W191G cavity using AutoDock 3.0. For the ligands, we compared docking predictions with experimentally determined binding energies and X-ray crystal structure complexes. For the ligands, predicted binding energies differed from measured values by ± 0.8 kcal/mol. For most ligands, the docking simulation clearly predicted a single binding mode that matched the crystallographic binding mode within 1.0 Å RMSD. For 2 ligands, where the docking procedure yielded an ambiguous result, solutions matching the crystallographic result could be obtained by including an additional crystallographically observed water molecule in the protein model. For the remaining 2 ligands, docking indicated multiple binding modes, consistent with the original electron density, suggesting disordered binding of these ligands. Visual inspection of the atomic affinity grid maps used in docking calculations revealed two patches of high affinity for hydrogen bond donating groups. Multiple solutions are predicted as these two sites compete for polar hydrogens in the ligand during the docking simulation. Ligands could be distinguished, to some extent, from non-binders using a combination of two trends: predicted binding energy and level of clustering. In summary, AutoDock 3.0 appears to be useful in predicting key structural and energetic features of ligand binding in the W191G cavity.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Agnew, Douglas W.; Gembicky, Milan; Moore, Curtis E.

Here, the preparation of 3D and 2D Cu(I) coordination networks using ditopic m-terphenyl isocyanides is described. The incorporation of sterically encumbering substituents enables the controlled, solid-state preparation of Cu(I) tris-isocyanide nodes with a labile solvent ligand in a manner mirroring solution-phase chemistry of monomeric complexes. The protection afforded by the m-terphenyl groups is also shown to engender significant stability towards heat as well as acidic or basic conditions, resulting in robust single-metal-node networks that can transition from 3D to 2D extended structures.

ITC-derived binding affinity may be biased due to titrant (nano)-aggregation. Binding of halogenated benzotriazoles to the catalytic domain of human protein kinase CK2

PubMed Central

Winiewska, Maria; Bugajska, Ewa

2017-01-01

The binding of four bromobenzotriazoles to the catalytic subunit of human protein kinase CK2 was assessed by two complementary methods: Microscale Thermophoresis (MST) and Isothermal Titration Calorimetry (ITC). New algorithm proposed for the global analysis of MST pseudo-titration data enabled reliable determination of binding affinities for two distinct sites, a relatively strong one with the Kd of the order of 100 nM and a substantially weaker one (Kd > 1 μM). The affinities for the strong binding site determined for the same protein-ligand systems using ITC were in most cases approximately 10-fold underestimated. The discrepancy was assigned directly to the kinetics of ligand nano-aggregates decay occurring upon injection of the concentrated ligand solution to the protein sample. The binding affinities determined in the reverse ITC experiment, in which ligands were titrated with a concentrated protein solution, agreed with the MST-derived data. Our analysis suggests that some ITC-derived Kd values, routinely reported together with PDB structures of protein-ligand complexes, may be biased due to the uncontrolled ligand (nano)-aggregation, which may occur even substantially below the solubility limit. PMID:28273138

Radiolytic degradation of a new diglycol-diamide ligand for actinide and lanthanide co-extraction from spent nuclear fuel

NASA Astrophysics Data System (ADS)

Ossola, Annalisa; Macerata, Elena; Tinonin, Dario A.; Faroldi, Federica; Giola, Marco; Mariani, Mario; Casnati, Alessandro

2016-07-01

Within the Partitioning and Transmutation strategies, great efforts have been devoted in the last decades to the development of lipophilic ligands able to co-extract trivalent Lanthanides (Ln) and Actinides (An) from spent nuclear fuel. Because of the harsh working conditions these ligands undergo, it is important to prove their chemical and radiolytic stability during the counter-current multi-stage extraction process. In the present work the hydrolytic and radiolytic resistance of the freshly prepared and aged organic solutions containing the new ligand (2,6-bis[(N-methyl-N-dodecyl)carboxamide]-4-methoxy-tetrahydro-pyran) were investigated in order to evaluate the impact on the safety and efficiency of the process. Liquid-liquid extraction tests with spiked solutions showed that the ligand extracting performances are strongly impaired by storing the samples at room temperature and in the light. Moreover, the extracting efficiency of the irradiated samples resulted to be influenced by gamma irradiation, while selectivity remains unchanged. Preliminary mass spectrometric data showed that degradation is mainly due to the acid-catalysed reaction of the ligand carboxamide and ether groups with the 1-octanol present in the diluent.

Investigating the Vanadium Environments in Hydroxylamido V(V) Dipicolinate Complexes Using 51V NMR Spectroscopy and Density Functional Theory

PubMed Central

Ooms, Kristopher J.; Bolte, Stephanie E.; Smee, Jason J.; Baruah, Bharat; Crans, Debbie C.; Polenova, Tatyana

2014-01-01

Using 51V magic angle spinning solid-state NMR, SSNMR, spectroscopy and quantum chemical DFT calculations we have characterized the chemical shift and quadrupolar coupling parameters of a series of 8 hydroxylamido vanadium(V) dipicolinate complexes of the general formula VO(dipic)(ONR1R2)(H2O) where R1 and R2 can be H, CH3, or CH2CH3. This class of vanadium compounds was chosen for investigation because of their seven coordinate vanadium atom, a geometry for which there is limited 51V SSNMR data. Furthermore, a systematic series of compounds with different electronic properties are available and allows for the effects of ligand substitution on the NMR parameters to be studied. The quadrupolar coupling constants, CQ, are small, 3.0 to 3.9 MHz, but exhibit variations as a function of the ligand substitution. The chemical shift tensors in the solid state are sensitive to changes in both the hydroxylamide substituent and the dipic ligand, a sensitivity which is not observed for isotropic chemical shifts in solution. The chemical shift tensors span approximately 1000 ppm, and are nearly axially symmetric. Based on DFT calculations of the chemical shift tensors, one of the largest contributors to the magnetic shielding anisotropy is an occupied molecular orbital with significant vanadium dz2 character along the V=O bond. PMID:17902653

Nanostructured layers of thermoelectric materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Urban, Jeffrey J.; Lynch, Jared; Coates, Nelson

This disclosure provides systems, methods, and apparatus related to thermoelectric materials. In one aspect, a method includes providing a plurality of nanostructures. The plurality of nanostructures comprise a thermoelectric material, with each nanostructure of the plurality of nanostructures having first ligands disposed on a surface of the nanostructure. The plurality of nanostructures is mixed with a solution containing second ligands and a ligand exchange process occurs in which the first ligands disposed on the plurality of nanostructures are replaced with the second ligands. The plurality of nanostructures is deposited on a substrate to form a layer. The layer is thermallymore » annealed.« less

Studies on the retention mechanism of solutes in hydrophilic interaction chromatography using stoichiometric displacement theory I. The linear relationship of lgk' vs. lg[H2O].

PubMed

Wang, Fei; Yang, Fan; Tian, Yang; Liu, Jiawei; Shen, Jiwei; Bai, Quan

2018-01-01

A stoichiometric displacement model for retention (SDM-R) of small solutes and proteins based on hydrophilic interaction chromatography (HILIC) was presented. A linear equation that related the logarithm of the capacity factor of the solute to the logarithm of the concentration of water in the mobile phase was derived. The stoichiometric displacement parameters, Z (the number of water molecules required to displace a solute from ligands) and lgI (containing a number of constants that relate to the affinity of solute to the ligands) could be obtained from the slope and the intercept of the linear plots of lgk' vs. lg[H 2 O]. The retention behaviors and retention mechanism of 15 kinds of small solutes and 6 kinds of proteins on 5 kinds HILIC columns with different ligands were investigated with SDM-R in typical range of water concentration in mobile phase. A good linear relationship between lgk' and lg[H 2 O] demonstrated that the most rational retention mechanism of solute in HILIC was a stoichiometric displacement process between solute and solvent molecules with water as displacing agents, which was not only valid for small solutes, but also could be used to explain the retention mechanism of biopolymers in HILIC. Comparing with the partition and adsorption models in HILIC, SDM-R was superior to them. Copyright © 2017 Elsevier B.V. All rights reserved.

Eco-friendly luminescent solar concentrators with low reabsorption losses and resistance to concentration quenching based on aqueous-solution-processed thiolate-gold nanoclusters

NASA Astrophysics Data System (ADS)

Huang, H. Y.; Cai, K. B.; Chang, L. Y.; Chen, P. W.; Lin, T. N.; Lin, C. A. J.; Shen, J. L.; Talite, M. J.; Chou, W. C.; Yuan, C. T.

2017-09-01

Heavy-metal-containing quantum dots (QDs) with engineered electronic states have been served as luminophores in luminescent solar concentrators (LSCs) with impressive optical efficiency. Unfortunately, those QDs involve toxic elements and need to be synthesized in a hazardous solvent. Recently, biocompatible, eco-friendly gold nanoclusters (AuNCs), which can be directly synthesized in an aqueous solution, have gained much attention for promising applications in ‘green photonics’. Here, we explored the solid-state photophysical properties of aqueous-solution-processed, glutathione-stabilized gold nanoclusters (GSH-AuNCs) with a ligand-to-metal charge-transfer (LMCT) state for developing ‘green’ LSCs. We found that such GSH-AuNCs exhibit a large Stokes shift with almost no spectral overlap between the optical absorption and PL emission due to the LMCT states, thus, suppressing reabsorption losses. Compared with GSH-AuNCs in solution, the photoluminescence quantum yields (PL-QYs) of the LSCs can be enhanced, accompanied with a lengthened PL lifetime owing to the suppression of non-radiative recombination rates. In addition, the LSCs do not suffer from severe concentration-induced PL quenching, which is a common weakness for conventional luminophores. As a result, a common trade-off between light-harvesting efficiency and solid-state PL-QYs can be bypassed due to nearly-zero spectral overlap integral between the optical absorption and PL emission. We expect that GSH-AuNCs hold great promise for serving as luminophores for ‘green’ LSCs by further enhancing solid-state PL-QYs.

Eco-friendly luminescent solar concentrators with low reabsorption losses and resistance to concentration quenching based on aqueous-solution-processed thiolate-gold nanoclusters.

PubMed

Huang, H Y; Cai, K B; Chang, L Y; Chen, P W; Lin, T N; Lin, C A J; Shen, J L; Talite, M J; Chou, W C; Yuan, C T

2017-09-15

Heavy-metal-containing quantum dots (QDs) with engineered electronic states have been served as luminophores in luminescent solar concentrators (LSCs) with impressive optical efficiency. Unfortunately, those QDs involve toxic elements and need to be synthesized in a hazardous solvent. Recently, biocompatible, eco-friendly gold nanoclusters (AuNCs), which can be directly synthesized in an aqueous solution, have gained much attention for promising applications in 'green photonics'. Here, we explored the solid-state photophysical properties of aqueous-solution-processed, glutathione-stabilized gold nanoclusters (GSH-AuNCs) with a ligand-to-metal charge-transfer (LMCT) state for developing 'green' LSCs. We found that such GSH-AuNCs exhibit a large Stokes shift with almost no spectral overlap between the optical absorption and PL emission due to the LMCT states, thus, suppressing reabsorption losses. Compared with GSH-AuNCs in solution, the photoluminescence quantum yields (PL-QYs) of the LSCs can be enhanced, accompanied with a lengthened PL lifetime owing to the suppression of non-radiative recombination rates. In addition, the LSCs do not suffer from severe concentration-induced PL quenching, which is a common weakness for conventional luminophores. As a result, a common trade-off between light-harvesting efficiency and solid-state PL-QYs can be bypassed due to nearly-zero spectral overlap integral between the optical absorption and PL emission. We expect that GSH-AuNCs hold great promise for serving as luminophores for 'green' LSCs by further enhancing solid-state PL-QYs.

Effect of stochastic gating on channel-facilitated transport of non-interacting and strongly repelling solutes

NASA Astrophysics Data System (ADS)

Berezhkovskii, Alexander M.; Bezrukov, Sergey M.

2017-08-01

Ligand- or voltage-driven stochastic gating—the structural rearrangements by which the channel switches between its open and closed states—is a fundamental property of biological membrane channels. Gating underlies the channel's ability to respond to different stimuli and, therefore, to be functionally regulated by the changing environment. The accepted understanding of the gating effect on the solute flux through the channel is that the mean flux is the product of the flux through the open channel and the probability of finding the channel in the open state. Here, using a diffusion model of channel-facilitated transport, we show that this is true only when the gating is much slower than the dynamics of solute translocation through the channel. If this condition breaks, the mean flux could differ from this simple estimate by orders of magnitude.

Versatile chelating behavior of benzil bis(thiosemicarbazone) in zinc, cadmium, and nickel complexes.

PubMed

López-Torres, Elena; Mendiola, Ma Antonia; Pastor, César J; Pérez, Beatriz Souto

2004-08-23

Reactions of benzil bis(thiosemicarbazone), LH(6), with M(NO(3))(2).nH(2)O (M = Zn, Cd, and Ni), in the presence of LiOH.H(2)O, show the versatile behavior of this molecule. The structure of the ligand, with the thiosemicarbazone moieties on opposite sides of the carbon backbone, changes to form complexes by acting as a chelating molecule. Complexes of these metal ions with empirical formula [MLH(4)] were obtained, although they show different molecular structures depending on their coordinating preferences. The zinc complex is the first example of a crystalline coordination polymer in which a bis(thiosemicarbazone) acts as bridging ligand, through a nitrogen atom, giving a 1D polymeric structure. The coordination sphere is formed by the imine nitrogen and sulfur atoms, and the remaining position, in a square-based pyramid, is occupied by an amine group of another ligand. The cadmium derivative shows the same geometry around the metal ion but consists of a dinuclear structure with sulfur atoms acting as a bridge between the metal ions. However, in the nickel complex LH(6) acts as a N(2)S(2) ligand yielding a planar structure for the nickel atom. The ligand and its complexes have been characterized by X-ray crystallography, microanalysis, mass spectrometry, IR, (1)H, and (13)C NMR spectroscopies and for the cadmium complex by (113)Cd NMR in solution and in the solid state.

Spatial Analysis and Quantification of the Thermodynamic Driving Forces in Protein-Ligand Binding: Binding Site Variability

PubMed Central

Raman, E. Prabhu; MacKerell, Alexander D.

2015-01-01

The thermodynamic driving forces behind small molecule-protein binding are still not well understood, including the variability of those forces associated with different types of ligands in different binding pockets. To better understand these phenomena we calculate spatially resolved thermodynamic contributions of the different molecular degrees of freedom for the binding of propane and methanol to multiple pockets on the proteins Factor Xa and p38 MAP kinase. Binding thermodynamics are computed using a statistical thermodynamics based end-point method applied on a canonical ensemble comprising the protein-ligand complexes and the corresponding free states in an explicit solvent environment. Energetic and entropic contributions of water and ligand degrees of freedom computed from the configurational ensemble provides an unprecedented level of detail into the mechanisms of binding. Direct protein-ligand interaction energies play a significant role in both non-polar and polar binding, which is comparable to water reorganization energy. Loss of interactions with water upon binding strongly compensates these contributions leading to relatively small binding enthalpies. For both solutes, the entropy of water reorganization is found to favor binding in agreement with the classical view of the “hydrophobic effect”. Depending on the specifics of the binding pocket, both energy-entropy compensation and reinforcement mechanisms are observed. Notable is the ability to visualize the spatial distribution of the thermodynamic contributions to binding at atomic resolution showing significant differences in the thermodynamic contributions of water to the binding of propane versus methanol. PMID:25625202

Tris-amidoximate uranyl complexes via η2 binding mode coordinated in aqueous solution shown by X-ray absorption spectroscopy and density functional theory methods.

PubMed

Zhang, Linjuan; Qie, Meiying; Su, Jing; Zhang, Shuo; Zhou, Jing; Li, Jiong; Wang, Yu; Yang, Shitong; Wang, Shuao; Li, Jingye; Wu, Guozhong; Wang, Jian Qiang

2018-03-01

The present study sheds some light on the long-standing debate concerning the coordination properties between uranyl ions and the amidoxime ligand, which is a key ingredient for achieving efficient extraction of uranium. Using X-ray absorption fine structure combined with theoretical simulation methods, the binding mode and bonding nature of a uranyl-amidoxime complex in aqueous solution were determined for the first time. The results show that in a highly concentrated amidoxime solution the preferred binding mode between UO 2 2+ and the amidoxime ligand is η 2 coordination with tris-amidoximate species. In such a uranyl-amidoximate complex with η 2 binding motif, strong covalent interaction and orbital hybridization between U 5f/6d and (N, O) 2p should be responsible for the excellent binding ability of the amidoximate ligand to uranyl. The study was performed directly in aqueous solution to avoid the possible binding mode differences caused by crystallization of a single-crystal sample. This work also is an example of the simultaneous study of local structure and electronic structure in solution systems using combined diagnostic tools.

DFT study of uranyl peroxo complexes with H2O, F-, OH-, CO3(2-), and NO3(-).

PubMed

Odoh, Samuel O; Schreckenbach, Georg

2013-05-06

The structural and electronic properties of monoperoxo and diperoxo uranyl complexes with aquo, fluoride, hydroxo, carbonate, and nitrate ligands have been studied using scalar relativistic density functional theory (DFT). Only the complexes in which the peroxo ligands are coordinated to the uranyl moiety in a bidentate mode were considered. The calculated binding energies confirm that the affinity of the peroxo ligand for the uranyl group far exceeds that of the F(-), OH(-), CO3(2-), NO3(-), and H2O ligands. The formation of the monoperoxo complexes from UO2(H2O)5(2+) and HO2(-) were found to be exothermic in solution. In contrast, the formation of the monouranyl-diperoxo, UO2(O2)2X2(4-) or UO2(O2)2X(4-/3-) (where X is any of F(-), OH(-), CO3(2-), or NO3(-)), complexes were all found to be endothermic in aqueous solution. This suggests that the monoperoxo species are the terminal monouranyl peroxo complexes in solution, in agreement with recent experimental work. Overall, we find that the properties of the uranyl-peroxo complexes conform to well-known trends: the coordination of the peroxo ligand weakens the U-O(yl) bonds, stabilizes the σ(d) orbitals and causes a mixing between the uranyl π- and peroxo σ- and π-orbitals. The weakening of the U-O(yl) bonds upon peroxide coordination results in uranyl stretching vibrational frequencies that are much lower than those obtained after the coordination of carbonato or hydroxo ligands.

pH-specific synthesis and spectroscopic, structural, and magnetic studies of a chromium(III)-citrate species. Aqueous solution speciation of the binary chromium(III)-citrate system.

PubMed

Gabriel, C; Raptopoulou, C P; Terzis, A; Tangoulis, V; Mateescu, C; Salifoglou, A

2007-04-16

In an attempt to understand the aqueous interactions of Cr(III) with the low-molecular-mass physiological ligand citric acid, the pH-specific synthesis in the binary Cr(III)-citrate system was explored, leading to the complex (NH4)4[Cr(C6H4O7)(C6H5O7)].3H2O (1). 1 crystallizes in the monoclinic space group I2/a, with a = 19.260(10) A, b = 10.006(6) A, c = 23.400(10) A, beta = 100.73(2) degrees , V = 4431(4) A3, and Z = 8. 1 was characterized by elemental analysis and spectroscopic, structural, thermal, and magnetic susceptibility studies. Detailed aqueous speciation studies in the Cr(III)-citrate system suggest the presence of a number of species, among which is the mononuclear [Cr(C6H4O7)(C6H5O7)]4- complex, optimally present around pH approximately 5.5. The structure of 1 reveals a mononuclear octahedral complex of Cr(III) with two citrate ligands bound to it. The two citrate ligands have different deprotonation states, thus signifying the importance of the mixed deprotonation state in the coordination sphere of the Cr(III) species in aqueous speciation. The latter reveals the distribution of numerous species, including 1, for which the collective structural, spectroscopic, and magnetic data point out its physicochemical profile in the solid state and in solution. The importance of the synthetic efforts linked to 1 and the potential ramifications of Cr(III) reactivity toward both low- and high-molecular-mass biotargets are discussed in light of (a) the quest for well-characterized soluble Cr(III) species that could be detected and identified in biologically relevant fluids, (b) ongoing efforts to delineate the aqueous speciation of the Cr(III)-citrate system and its link to biotoxic Cr(III) manifestations, and (c) the synthetic utility of convenient Cr(III) precursors in the synthesis of advanced materials.

Ligand protons in a frozen solution of copper histidine relax via a T1e-driven three-spin mechanism

NASA Astrophysics Data System (ADS)

Stoll, S.; Epel, B.; Vega, S.; Goldfarb, D.

2007-10-01

Davies electron-nuclear double resonance spectra can exhibit strong asymmetries for long mixing times, short repetition times, and large thermal polarizations. These asymmetries can be used to determine nuclear relaxation rates in paramagnetic systems. Measurements of frozen solutions of copper(L-histidine)2 reveal a strong field dependence of the relaxation rates of the protons in the histidine ligand, increasing from low (g‖) to high (g⊥) field. It is shown that this can be attributed to a concentration-dependent T1e-driven relaxation process involving strongly mixed states of three spins: the histidine proton, the Cu(II) electron spin of the same complex, and another distant electron spin with a resonance frequency differing from the spectrometer frequency approximately by the proton Larmor frequency. The protons relax more efficiently in the g⊥ region, since the number of distant electrons able to participate in this relaxation mechanism is higher than in the g‖ region. Analytical expressions for the associated nuclear polarization decay rate Teen-1 are developed and Monte Carlo simulations are carried out, reproducing both the field and the concentration dependences of the nuclear relaxation.

Cubes, squares, and books: a simple transition metal/bridging ligand combination can lead to a surprising range of structural types with the same metal/ligand proportions.

PubMed

Najar, Adel M; Tidmarsh, Ian S; Adams, Harry; Ward, Michael D

2009-12-21

Reaction of two structurally related bridging ligands L(26Py) and L(13Ph), in which two bidentate chelating pyrazolyl-pyridine units are connected to either a 2,6-pyridine-diyl or 1,3-benzene-diyl central group via methylene spacers, with first-row transition metal dications, results in a surprising variety of structures. The commonest is that of an octanuclear coordination cage [M(8)L(12)]X(16) [M = Co(II) or Zn(II); X = perchlorate or tetrafluoroborate] in which a metal ion is located at each of the eight vertices of an approximate cube, and one bis-bidentate bridging ligand spans each edge. The arrangement of fac and mer tris-chelate metal centers around the inversion center results in approximate (non-crystallographic) S(6) symmetry. Another structural type observed in the solid state is a hexanuclear complex [Co(6)(L(13Ph))(9)](ClO(4))(12) in which the six metal ions are in a rectangular array (two rows of three), folded about the central Co-Co vector like a partially open book, with each metal-metal edge containing one bridging ligand apart from the two outermost metal-metal edges which are spanned by a pair of bridging ligands in a double helical array. The final structural type we observed is a tetranuclear square [Ni(4)(L(26Py))(6)](BF(4))(8), with the four Ni-Ni edges spanned alternately by one and two bridging ligand such that it effectively consists of two dinuclear double helicates cross-linked by additional bridging ligands. A balance between the "cube" and "book" forms, which varied from compound to compound, was observed in solution in many cases by (1)H NMR and ES mass spectrometry studies.

Synthesis, structure, and excited state kinetics of heteroleptic Cu(i) complexes with a new sterically demanding phenanthroline ligand

DOE PAGES

Kohler, Lars; Hadt, Ryan G.; Hayes, Dugan; ...

2017-09-25

In this paper we describe the synthesis of a new phenanthroline ligand, 2,9-di(2,4,6-tri-isopropyl-phenyl)-1,10-phenanthroline (bL2) and its use as the blocking ligand in the preparation of two new heteroleptic Cu(I)diimine complexes. Analysis of the CuHETPHEN single crystal structures shows a distinct distortion from an ideal tetrahedral geometry around the Cu(I) center, forced by the secondary phenanthroline ligand rotating to accommodate the isopropyl groups of bL2. The increased steric bulk of bL2 as compared to the more commonly used 2,9-dimesityl-1,10-phenanthroline blocking ligand prohibits intramolecular ligand–ligand interaction, which is unique among CuHETPHEN complexes. The ground state optical and redox properties of CuHETPHEN complexesmore » are responsive to the substitution on the blocking ligand even though the differences in structure are far removed from the Cu(I) center. Transient optical spectroscopy was used to understand the excited state kinetics in both coordinating and non-coordinating solvents following visible excitation. Substitution of the blocking phenanthroline ligand has a significant impact on the 3MLCT decay and can be used to increase the excited state lifetime by 50%. Electronic structure calculations established relationships between ground and excited state properties, and general entatic state concepts are discussed for copper photosensitizers. This work contributes to the growing library of CuHETPHEN complexes and broadens the fundamental understanding of their ground and excited state properties.« less

All-inorganic Germanium nanocrystal films by cationic ligand exchange

DOE PAGES

Wheeler, Lance M.; Nichols, Asa W.; Chernomordik, Boris D.; ...

2016-01-21

In this study, we introduce a new paradigm for group IV nanocrystal surface chemistry based on room temperature surface activation that enables ionic ligand exchange. Germanium nanocrystals synthesized in a gas-phase plasma reactor are functionalized with labile, cationic alkylammonium ligands rather than with traditional covalently bound groups. We employ Fourier transform infrared and 1H nuclear magnetic resonance spectroscopies to demonstrate the alkylammonium ligands are freely exchanged on the germanium nanocrystal surface with a variety of cationic ligands, including short inorganic ligands such as ammonium and alkali metal cations. This ionic ligand exchange chemistry is used to demonstrate enhanced transport inmore » germanium nanocrystal films following ligand exchange as well as the first photovoltaic device based on an all-inorganic germanium nanocrystal absorber layer cast from solution. This new ligand chemistry should accelerate progress in utilizing germanium and other group IV nanocrystals for optoelectronic applications.« less

Copper(II) Thiosemicarbazone Complexes and Their Proligands upon UVA Irradiation: An EPR and Spectrophotometric Steady-State Study.

PubMed

Hricovíni, Michal; Mazúr, Milan; Sîrbu, Angela; Palamarciuc, Oleg; Arion, Vladimir B; Brezová, Vlasta

2018-03-21

X- and Q-band electron paramagnetic resonance (EPR) spectroscopy was used to characterize polycrystalline Cu(II) complexes that contained sodium 5-sulfonate salicylaldehyde thiosemicarbazones possessing a hydrogen, methyl, ethyl, or phenyl substituent at the terminal nitrogen. The ability of thiosemicarbazone proligands to generate superoxide radical anions and hydroxyl radicals upon their exposure to UVA irradiation in aerated aqueous solutions was evidenced by the EPR spin trapping technique. The UVA irradiation of proligands in neutral or alkaline solutions and dimethylsulfoxide (DMSO) caused a significant decrease in the absorption bands of aldimine and phenolic chromophores. Mixing of proligand solutions with the equimolar amount of copper(II) ions resulted in the formation of 1:1 Cu(II)-to-ligand complex, with the EPR and UV-Vis spectra fully compatible with those obtained for the dissolved Cu(II) thiosemicarbazone complexes. The formation of the complexes fully inhibited the photoinduced generation of reactive oxygen species, and only subtle changes were found in the electronic absorption spectra of the complexes in aqueous and DMSO solutions upon UVA steady-state irradiation. The dark redox activity of copper(II) complexes and proligand/Cu(II) aqueous solutions towards hydrogen peroxide which resulted in the generation of hydroxyl radicals, was confirmed by spin trapping experiments.

Crystal structure of the solute-binding protein BxlE from Streptomyces thermoviolaceus OPC-520 complexed with xylobiose.

PubMed

Tomoo, Koji; Miki, Yasuhiro; Morioka, Hideaki; Seike, Kiho; Ishida, Toshimasa; Ikenishi, Sadao; Miyamoto, Katsushiro; Hasegawa, Tomokazu; Yamano, Akihito; Hamada, Kensaku; Tsujibo, Hiroshi

2017-06-01

BxlE from Streptomyces thermoviolaceus OPC-520 is a xylo-oligosaccharide (mainly xylobiose)-binding protein that serves as the initial receptor for the bacterial ABC-type xylo-oligosaccharide transport system. To determine the ligand-binding mechanism of BxlE, X-ray structures of ligand-free (open form) and ligand (xylobiose)-bound (closed form) BxlE were determined at 1.85 Å resolution. BxlE consists of two globular domains that are linked by two β-strands, with the cleft at the interface of the two domains creating the ligand-binding pocket. In the ligand-free open form, this pocket consists of a U-shaped and negatively charged groove located between the two domains. In the xylobiose-bound closed form of BxlE, both the N and C domains move to fold the ligand without conformational changes in either domain. Xylobiose is buried in the groove and wrapped by the N-domain mainly via hydrogen bond interactions and by the C-domain primarily via non-polar interactions with Trp side chains. In addition to the concave shape matching the binding of xylobiose, an inter-domain salt bridge between Asp-47 and Lys-294 limits the space in the ligand-binding site. This domain-stabilized mechanism of ligand binding to BxlE is a unique feature that is not observed with other solute-binding proteins. © The Authors 2017. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory.

PubMed

Pritišanac, Iva; Degiacomi, Matteo T; Alderson, T Reid; Carneiro, Marta G; Ab, Eiso; Siegal, Gregg; Baldwin, Andrew J

2017-07-19

Methyl groups are powerful probes for the analysis of structure, dynamics and function of supramolecular assemblies, using both solution- and solid-state NMR. Widespread application of the methodology has been limited due to the challenges associated with assigning spectral resonances to specific locations within a biomolecule. Here, we present Methyl Assignment by Graph Matching (MAGMA), for the automatic assignment of methyl resonances. A graph matching protocol examines all possibilities for each resonance in order to determine an exact assignment that includes a complete description of any ambiguity. MAGMA gives 100% accuracy in confident assignments when tested against both synthetic data, and 9 cross-validated examples using both solution- and solid-state NMR data. We show that this remarkable accuracy enables a user to distinguish between alternative protein structures. In a drug discovery application on HSP90, we show the method can rapidly and efficiently distinguish between possible ligand binding modes. By providing an exact and robust solution to methyl resonance assignment, MAGMA can facilitate significantly accelerated studies of supramolecular machines using methyl-based NMR spectroscopy.

Methylene-bis[(aminomethyl)phosphinic acids]: synthesis, acid-base and coordination properties.

PubMed

David, Tomáš; Procházková, Soňa; Havlíčková, Jana; Kotek, Jan; Kubíček, Vojtěch; Hermann, Petr; Lukeš, Ivan

2013-02-21

Three symmetrical methylene-bis[(aminomethyl)phosphinic acids] bearing different substituents on the central carbon atom, (NH(2)CH(2))PO(2)H-C(R(1))(R(2))-PO(2)H(CH(2)NH(2)) where R(1) = OH, R(2) = Me (H(2)L(1)), R(1) = OH, R(2) = Ph (H(2)L(2)) and R(1),R(2) = H (H(2)L(3)), were synthesized. Acid-base and complexing properties of the ligands were studied in solution as well as in the solid state. The ligands show unusually high basicity of the nitrogen atoms (log K(1) = 9.5-10, log K(2) = 8.5-9) if compared with simple (aminomethyl)phosphinic acids and, consequently, high stability constants of the complexes with studied divalent metal ions. The study showed the important role of the hydroxo group attached to the central carbon atom of the geminal bis(phosphinate) moiety. Deprotonation of the hydroxo group yields the alcoholate anion which tends to play the role of a bridging ligand and induces formation of polynuclear complexes. Solid-state structures of complexes [H(2)N=C(NH(2))(2)][Cu(2)(H(-1)L(2))(2)]CO(3)·10H(2)O and Li(2)[Co(4)(H(-1)L(1))(3)(OH)]·17.5H(2)O were determined by X-ray diffraction. The complexes show unexpected geometries forming dinuclear and cubane-like structures, respectively. The dinuclear copper(II) complex contains a bridging μ(2)-alcoholate group with the (-)O-P(=O)-CH(2)-NH(2) fragments of each ligand molecule chelated to the different central ion. In the cubane cobalt(II) complex, one μ(3)-hydroxide and three μ(3)-alcoholate anions are located in the cube vertices and both phosphinate groups of one ligand molecule are chelating the same cobalt(II) ion while each of its amino groups are bound to different neighbouring metal ions. All such three metal ions are bridged by the alcoholate group of a given ligand.

Ligand-dependent exciton dynamics and photovoltaic properties of PbS quantum dot heterojunction solar cells.

PubMed

Chang, Jin; Ogomi, Yuhei; Ding, Chao; Zhang, Yao Hong; Toyoda, Taro; Hayase, Shuzi; Katayama, Kenji; Shen, Qing

2017-03-01

The surface chemistry of colloidal quantum dots (QDs) plays an important role in determining the photoelectric properties of QD films and the corresponding quantum dot heterojunction solar cells (QDHSCs). To investigate the effects of the ligand structure on the photovoltaic performance and exciton dynamics of QDHSCs, PbS QDHSCs were fabricated by the solid state ligand exchange method with mercaptoalkanoic acid as the cross-linking ligand. Temperature-dependent photoluminescence and ultrafast transient absorption spectra show that the electronic coupling and charge transfer rate within QD ensembles were monotonically enhanced as the ligand length decreased. However, in practical QDHSCs, the second shortest ligand 3-mercaptopropionic acid (MPA) showed higher power conversion efficiency than the shortest ligand thioglycolic acid (TGA). This could be attributed to the difference in their surface trap states, supported by thermally stimulated current measurements. Moreover, compared with the non-conjugated ligand MPA, the conjugated ligand 4-mercaptobenzoic acid (MBA) introduces less trap states and has a similar charge transfer rate in QD ensembles, but has poor photovoltaic properties. This unexpected result could be contributed by the QD-ligand orbital mixing, leading to the charge transfer from QDs to ligands instead of charge transfer between adjacent QDs. This work highlights the significant effects of ligand structures on the photovoltaic properties and exciton dynamics of QDHSCs, which would shed light on the further development of QD-based photoelectric devices.

Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results.

PubMed

ten Brink, Tim; Exner, Thomas E

2009-06-01

In this work, we present a systematical investigation of the influence of ligand protonation states, stereoisomers, and tautomers on results obtained with the two protein-ligand docking programs GOLD and PLANTS. These different states were generated with a fully automated tool, called SPORES (Structure PrOtonation and Recognition System). First, the most probable protonations, as defined by this rule based system, were compared to the ones stored in the well-known, manually revised CCDC/ASTEX data set. Then, to investigate the influence of the ligand protonation state on the docking results, different protonation states were created. Redocking and virtual screening experiments were conducted demonstrating that both docking programs have problems in identifying the correct protomer for each complex. Therefore, a preselection of plausible protomers or the improvement of the scoring functions concerning their ability to rank different molecules/states is needed. Additionally, ligand stereoisomers were tested for a subset of the CCDC/ASTEX set, showing similar problems regarding the ranking of these stereoisomers as the ranking of the protomers.

Thermometric titration studies of mixed ligand complexes of thorium.

PubMed

Kugler, G C; Carey, G H

1970-10-01

Mixed-ligand chelates consisting of two different multidentate ligands linked to a central thorium(IV) ion have been prepared in aqueous solution and their heats of formation studied thermo metrically. Pyrocatechol, tiron, chromotropic acid, potassium hydrogen phthalate, 8-hydroxyquinoline-S-sulphonic acid, iminodiacetic acid, 5-sulphosalicylic acid and salicylic acid were used as the secondary ligands, while ethylenediaminetetra-acetate and 1, 2-diaminocyclohexane-N,N,N',N'-tetra-acetate were used as primary ligands. DeltaH values for the overall reactions are given, and where possible, the DeltaH and DeltaS values for the specific secondary ligand addition were calculated. The overall stability of the mixed-ligand chelates and the enhanced stability of EDTA mixed chelates relative to the analogous DCTA chelates were found to be due to entropy rather than enthalpy effects.

Synthesis, spectroscopic characterization, electrochemical behavior and computational analysis of mixed diamine ligand gold(III) complexes: antiproliferative and in vitro cytotoxic evaluations against human cancer cell lines.

PubMed

Al-Jaroudi, Said S; Monim-ul-Mehboob, M; Altaf, Muhammad; Al-Saadi, Abdulaziz A; Wazeer, Mohammed I M; Altuwaijri, Saleh; Isab, Anvarhusein A

2014-12-01

The gold(III) complexes of the type [(DACH)Au(en)]Cl3, 1,2-Diaminocyclohexane ethylenediamine gold(III) chloride [where 1,2-DACH = cis-, trans-1,2- and S,S-1,2diaminocyclohexane and en = ethylenediamine] have been synthesized and characterized using various analytical and spectroscopic techniques including elemental analysis, UV-Vis and FTIR spectra; and solution as well as solid-state NMR measurements. The solid-state (13)C NMR shows that 1,2-diaminocyclohexane (1,2-DACH) and ethylenediamine (en) are strongly bound to the gold(III) center via N donor atoms. The stability of the mixed diamine ligand gold(III) was determined by (1)H and (13)C NMR spectra. Their electrochemical behavior was studied by cyclic voltammetry. The structural details and relative stabilities of the four possible isomers of the complexes were also reported at the B3LYP/LANL2DZ level of theory. The coordination sphere of these complexes around gold(III) center adopts distorted square planar geometry. The computational study also demonstrates that trans- conformations is slightly more stable than the cis-conformations. The antiproliferative effects and cytotoxic properties of the mixed diamine ligand gold(III) complexes were evaluated in vitro on human gastric SGC7901 and prostate PC3 cancer cells using MTT assay. The antiproliferative study of the gold(III) complexes on PC3 and SGC7901 cells indicate that complex 1 is the most effective antiproliferative agent among mixed ligand based gold(III) complexes 1-3. The IC50 data reveal that the in vitro cytotoxicity of complexes 1 and 3 against SGC7901 cancer cells are fairly better than that of cisplatin.

Ligand versus metal protonation of an iron hydrogenase active site mimic.

PubMed

Eilers, Gerriet; Schwartz, Lennart; Stein, Matthias; Zampella, Giuseppe; de Gioia, Luca; Ott, Sascha; Lomoth, Reiner

2007-01-01

The protonation behavior of the iron hydrogenase active-site mimic [Fe2(mu-adt)(CO)4(PMe3)2] (1; adt=N-benzyl-azadithiolate) has been investigated by spectroscopic, electrochemical, and computational methods. The combination of an adt bridge and electron-donating phosphine ligands allows protonation of either the adt nitrogen to give [Fe2(mu-Hadt)(CO)4(PMe3)2]+ ([1 H]+), the Fe-Fe bond to give [Fe2(mu-adt)(mu-H)(CO)4(PMe3)2]+ ([1 Hy]+), or both sites simultaneously to give [Fe2(mu-Hadt)(mu-H)(CO)4(PMe3)2]2+ ([1 HHy]2 +). Complex 1 and its protonation products have been characterized in acetonitrile solution by IR, (1)H, and (31)P NMR spectroscopy. The solution structures of all protonation states feature a basal/basal orientation of the phosphine ligands, which contrasts with the basal/apical structure of 1 in the solid state. Density functional calculations have been performed on all protonation states and a comparison between calculated and experimental spectra confirms the structural assignments. The ligand protonated complex [1 H]+ (pKa=12) is the initial, metastable protonation product while the hydride [1 Hy]+ (pKa=15) is the thermodynamically stable singly protonated form. Tautomerization of cation [1 H]+ to [1 Hy]+ does not occur spontaneously. However, it can be catalyzed by HCl (k=2.2 m(-1) s(-1)), which results in the selective formation of cation [1 Hy]+. The protonations of the two basic sites have strong mutual effects on their basicities such that the hydride (pK(a)=8) and the ammonium proton (pK(a)=5) of the doubly protonated cationic complex [1 HHy]2+ are considerably more acidic than in the singly protonated analogues. The formation of dication [1 HHy]2+ from cation [1 H]+ is exceptionally slow with perchloric or trifluoromethanesulfonic acid (k=0.15 m(-1) s(-1)), while the dication is formed substantially faster (k>10(2) m(-1) s(-1)) with hydrobromic acid. Electrochemically, 1 undergoes irreversible reduction at -2.2 V versus ferrocene, and this potential shifts to -1.6, -1.1, and -1.0 V for the cationic complexes [1 H]+, [1 Hy]+, and [1 HHy]2+, respectively, upon protonation. The doubly protonated form [1 HHy]2+ is reduced at less negative potential than all previously reported hydrogenase models, although catalytic proton reduction at this potential is characterized by slow turnover.

A novel signal transduction protein: Combination of solute binding and tandem PAS-like sensor domains in one polypeptide chain: Periplasmic Ligand Binding Protein Dret_0059

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, R.; Wilton, R.; Cuff, M. E.

We report the structural and biochemical characterization of a novel periplasmic ligand-binding protein, Dret_0059, from Desulfohalobium retbaense DSM 5692, an organism isolated from the Salt Lake Retba in Senegal. The structure of the protein consists of a unique combination of a periplasmic solute binding protein (SBP) domain at the N-terminal and a tandem PAS-like sensor domain at the C-terminal region. SBP domains are found ubiquitously and their best known function is in solute transport across membranes. PAS-like sensor domains are commonly found in signal transduction proteins. These domains are widely observed as parts of many protein architectures and complexes butmore » have not been observed previously within the same polypeptide chain. In the structure of Dret_0059, a ketoleucine moiety is bound to the SBP, whereas a cytosine molecule is bound in the distal PAS-like domain of the tandem PAS-like domain. Differential scanning flourimetry support the binding of ligands observed in the crystal structure. There is significant interaction between the SBP and tandem PAS-like domains, and it is possible that the binding of one ligand could have an effect on the binding of the other. We uncovered three other proteins with this structural architecture in the non-redundant sequence data base, and predict that they too bind the same substrates. The genomic context of this protein did not offer any clues for its function. We did not find any biological process in which the two observed ligands are coupled. The protein Dret_0059 could be involved in either signal transduction or solute transport.« less

Spin exchange effects on the physicochemical properties of tetraoxolene-bridged bimetallic complexes.

PubMed

Guo, Dong; McCusker, James K

2007-04-16

The synthesis, physical, and spectroscopic properties of a series of metal complexes bridged by the redox-active chloranilate ligand are described. Compounds containing the (CAcat,cat)4- ligand, where (CAcat,cat)4- represents the fully reduced aromatic form of chloranilate, have been prepared by two different routes from H2CA and H4CA starting materials; the corresponding (CAsq,cat)3- analogue was obtained by one-electron oxidation with decamethylferrocenium tetrafluoroborate. Homo- and heterobimetallic complexes containing CrIII and GaIII with chloranilate have been prepared, yielding the following six complexes: [Ga2(tren)2(CAcat,cat)](BPh4)2 (1), [Ga2(tren)2(CAsq,cat)](BPh4)2(BF4) (2), [GaCr(tren)2(CAcat,cat)](BPh4)2 (3), [GaCr(tren)2(CAsq,cat)](BPh4)2(BF4) (4), [Cr2(tren)2(CAcat,cat)] (BPh4)2 (5), and [Cr2(tren)2(CAsq,cat)](BPh4)2(BF4) (6) (where tren is tris(2-aminoethyl)amine). Single-crystal X-ray structures have been obtained for complexes 1, 3, and 5; nearly identical C-C bond distances within the quinoidal ligand confirm the aromatic character of the bridge in each case. Complex 2 exhibits a temperature-independent magnetic moment of microeff = 1.64 +/- 0.04 microB in the solid state between 4 and 350 K, consistent with the CAsq,cat formulation of the ligand and an S = 1/2 ground state for complex 2. Complex 3 exhibits a value of microeff = 3.44 +/- 0.09 microB that is also temperature-independent, indicating an S = 3/2 ground state. Complexes 4-6 are all influenced by Heisenberg spin exchange. The temperature-independent behavior of complexes 4 and 6 indicate the presence of strong antiferromagnetic exchange between the CrIII and the (sq,cat) bridging radical yielding well-isolated ground states of S = 1 and 5/2 for 4 and 6, respectively. In contrast, complex 5 exhibits a weak intramolecular antiferromagnetic exchange interaction between the two CrIII centers (J = -2 cm-1 for H = -2Jŝ1.ŝ2) via superexchange through the diamagnetic CAcat,cat bridge. The absorption spectra of the CAsq,cat-containing complexes exhibit a number of sharp, relatively intense features in fluid solution. Group theoretical arguments coupled with a qualitative ligand-field analysis including the effects of Heisenberg spin exchange suggest that several of the observed transitions are a consequence of exchange interactions in both the ground- and excited-state manifolds of the compounds.

Determining the magnitude and direction of photoinduced ligand field switching in photochromic metal-organic complexes: molybdenum-tetracarbonyl spirooxazine complexes.

PubMed

Paquette, Michelle M; Patrick, Brian O; Frank, Natia L

2011-07-06

The ability to optically switch or tune the intrinsic properties of transition metals (e.g., redox potentials, emission/absorption energies, and spin states) with photochromic metal-ligand complexes is an important strategy for developing "smart" materials. We have described a methodology for using metal-carbonyl complexes as spectroscopic probes of ligand field changes associated with light-induced isomerization of photochromic ligands. Changes in ligand field between the ring-closed spirooxazine (SO) and ring-opened photomerocyanine (PMC) forms of photochromic azahomoadamantyl and indolyl phenanthroline-spirooxazine ligands are demonstrated through FT-IR, (13)C NMR, and computational studies of their molybdenum-tetracarbonyl complexes. The frontier molecular orbitals (MOs) of the SO and PMC forms differ considerably in both electron density distributions and energies. Of the multiple π* MOs in the SO and PMC forms of the ligands, the LUMO+1, a pseudo-b(1)-symmetry phenanthroline-based MO, mixes primarily with the Mo(CO)(4) fragment and provides the major pathway for Mo(d)→phen(π*) backbonding. The LUMO+1 is found to be 0.2-0.3 eV lower in energy in the SO form relative to the PMC form, suggesting that the SO form is a better π-acceptor. Light-induced isomerization of the photochromic ligands was therefore found to lead to changes in the energies of their frontier MOs, which in turn leads to changes in π-acceptor ability and ligand field strength. Ligand field changes associated with photoisomerizable ligands allow tuning of excited-state and ground-state energies that dictate energy/electron transfer, optical/electrical properties, and spin states of a metal center upon photoisomerization, positioning photochromic ligand-metal complexes as promising targets for smart materials.

Spectroscopic and electrochemical properties of group 12 acetates of di-2-pyridylketone thiophene-2-carboxylic acid hydrazone (dpktch-H) complexes. The structure of [Cd(η³-N,N,O-dpktch-H)₂].

PubMed

Bakir, Mohammed; Lawrence, Mark A W; McBean, Shameal

2015-07-05

The reaction between [dpktch] and [M(OAc)2] (M=group 12 metal atom) in refluxing CH3CN gave [M(η(2)-O,O-OAc)(η(3)-N,N,O-dpktch-H)]·nH2O (n=0 or 1). The infrared and (1)H NMR spectra are consistent with the coordination of [η(2)-O,O-OAc] and [η(3)-N,N,O-dpktch-H](-) and the proposed formulations. The electronic absorption spectra of [M(η(2)-O,O-OAc)(η(3)-N,N,O-dpktch-H)]·nH2O measured in non-aqueous solvents revealed a highly intense intra-ligand-charge transfer (ILCT) transition due to π-π∗ of dpk followed by dpk→thiophene charge transfer. The electronic transitions of [M(η(2)-O,O-OAc)(η(3)-N,N,O-dpktch-H)]·nH2O are solvent and concentration dependent. Spectrophotometric titrations of dmso solutions of [M(η(2)-O,O-OAc)(η(3)-N,N,O-dpktch-H)]·nH2O with benzoic acid revealed irreversible inter-conversion between [M(η(2)-O,O-OAc)(η(3)-N,N,O-dpktch-H)]·nH2O and it conjugate acid [M(η(2)-O,O-OAc)(η(3)-N,N,O-dpktch)]·nH2O pointing to ligand exchange between the acetate and benzoate anions. When CH2Cl2 solutions of [M(η(2)-O,O-OAc)(η(3)-N,N,O-dpktch-H)]·nH2O were titrated with dmso, changes appeared pointing to solvolysis or ligand exchange reactions. Electrochemical measurements on dmso solutions of [M(η(2)-O,O-OAc)(η(3)-N,N,O-dpktch-H)]·nH2O divulged irreversible redox transformations consistent with electrochemical decomposition of [M(η(2)-O,O-OAc)(η(3)-N,N,O-dpktch-H)]·nH2O. The solid state structure of a single crystal of [Cd(η(3)-N,N,O-dpktch-H)2] obtained from a dmso solution of [Cd(η(2)-O,O-OAc)(η(3)-N,N,O-dpktch-H)]·nH2O confirmed the ligand scrambling of [M(η(2)-O,O-OAc)(η(3)-N,N,O-dpktch-H)]·nH2O. The extended structure of [Cd(η(3)-N,N,O-dpktch-H)2] revealed stacks of [Cd(η(3)-N,N,O-dpktch-H)2] locked via a network of hydrogen bonds. A significant amount of empty space (35.5%) was observed in the solid state structure of [Cd(η(3)-N,N,O-dpktch-H)2]. Copyright © 2015 Elsevier B.V. All rights reserved.

Pyrazole bridged dinuclear Cu(II) and Zn(II) complexes as phosphatase models: Synthesis and activity

NASA Astrophysics Data System (ADS)

Naik, Krishna; Nevrekar, Anupama; Kokare, Dhoolesh Gangaram; Kotian, Avinash; Kamat, Vinayak; Revankar, Vidyanand K.

2016-12-01

Present work describes synthesis of dibridged dinuclear [Cu2L2(μ2-NN pyr)(NO3)2(H2O)2] and [Zn2L(μ-OH)(μ-NNpyr)(H2O)2] complexes derived from a pyrazole based ligand bis(2-hydroxy-3-methoxybenzylidene)-1H-pyrazole-3,5-dicarbohydrazide. The ligand shows dimeric chelate behaviour towards copper against monomeric for zinc counterpart. Spectroscopic evidences affirm octahedral environment around the metal ions in solution state and non-electrolytic nature of the complexes. Both the complexes are active catalysts towards phosphomonoester hydrolysis with first order kcat values in the range of 2 × 10-3s-1. Zinc complex exhibited promising catalytic efficiency for the hydrolysis. The dinuclear complexes hydrolyse via Lewis acid activation, whereby the phosphate esters are preferentially bound in a bidentate bridging fashion and subsequent nucleophilic attack to release phosphate group.

Bifunctional phenyl monophosphonic/sulfonic acid ion exchange resin and process for using the same

DOEpatents

Alexandratos, Spiro; Shelley, Christopher A.; Horwitz, E. Philip; Chiarizia, Renato

2001-01-01

A cross-linked water-insoluble ion exchange resin comprised of polymerized monomers having a phenyl ring is disclosed. A contemplated resin contains (i) polymerized phenyl ring-containing monomers having a phosphonic acid ligand linked to the phenyl ring, (ii) about 2 to about 5 millimoles per gram (mmol/g) of phosphorus as phosphonic acid ligands, and (iii) a sufficient amount of a sulfonic acid ligand such that the ratio of mmol/g of phosphonic acid to mmol/g sulfonic acid is up to 3:1. A process for removing polyvalent metal cations from aqueous solution, and a process for removing iron(III) cations from acidic copper(II) cation-containing solutions that utilize the contemplated resin or other resins are disclosed.

Bifunctional phenyl monophosphonic/sulfonic acid ion exchange resin and process for using the same

DOEpatents

Alexandratos, Spiro; Shelley, Christopher A.; Horwitz, E. Philip; Chiarizia, Renato; Gula, Michael J.; Xue, Sui; Harvey, James T.

2002-01-01

A cross-linked water-insoluble ion exchange resin comprised of polymerized monomers having a phenyl ring is disclosed. A contemplated resin contains (i) polymerized phenyl ring-containing monomers having a phosphonic acid ligand linked to the phenyl ring, (ii) about 2 to about 5 millimoles per gram (mmol/g) of phosphorus as phosphonic acid ligands, and (iii) a sufficient amount of a sulfonic acid ligand such that the ratio of mmol/g of phosphonic acid to mmol/g sulfonic acid is up to 3:1. A process for removing polyvalent metal cations from aqueous solution, and a process for removing iron(III) cations from acidic copper(II) cation-containing solutions that utilize the contemplated resin or other resins are disclosed.

Solution synthesis of germanium nanocrystals

DOEpatents

Gerung, Henry [Albuquerque, NM; Boyle, Timothy J [Kensington, MD; Bunge, Scott D [Cuyahoga Falls, OH

2009-09-22

A method for providing a route for the synthesis of a Ge(0) nanometer-sized material from. A Ge(II) precursor is dissolved in a ligand heated to a temperature, generally between approximately 100.degree. C. and 400.degree. C., sufficient to thermally reduce the Ge(II) to Ge(0), where the ligand is a compound that can bond to the surface of the germanium nanomaterials to subsequently prevent agglomeration of the nanomaterials. The ligand encapsulates the surface of the Ge(0) material to prevent agglomeration. The resulting solution is cooled for handling, with the cooling characteristics useful in controlling the size and size distribution of the Ge(0) materials. The characteristics of the Ge(II) precursor determine whether the Ge(0) materials that result will be nanocrystals or nanowires.

pK(a) based protonation states and microspecies for protein-ligand docking.

PubMed

ten Brink, Tim; Exner, Thomas E

2010-11-01

In this paper we present our reworked approach to generate ligand protonation states with our structure preparation tool SPORES (Structure PrOtonation and REcognition System). SPORES can be used for the preprocessing of proteins and protein-ligand complexes as e.g. taken from the Protein Data Bank as well as for the setup of 3D ligand databases. It automatically assigns atom and bond types, generates different protonation, tautomeric states as well as different stereoisomers. In the revised version, pKa calculations with the ChemAxon software MARVIN are used either to determine the likeliness of a combinatorial generated protonation state or to determine the titrable atoms used in the combinatorial approach. Additionally, the MARVIN software is used to predict microspecies distributions of ligand molecules. Docking studies were performed with our recently introduced program PLANTS (Protein-Ligand ANT System) on all protomers resulting from the three different selection methods for the well established CCDC/ASTEX clean data set demonstrating the usefulness of especially the latter approach.

pKa based protonation states and microspecies for protein-ligand docking

NASA Astrophysics Data System (ADS)

ten Brink, Tim; Exner, Thomas E.

2010-11-01

In this paper we present our reworked approach to generate ligand protonation states with our structure preparation tool SPORES (Structure PrOtonation and REcognition System). SPORES can be used for the preprocessing of proteins and protein-ligand complexes as e.g. taken from the Protein Data Bank as well as for the setup of 3D ligand databases. It automatically assigns atom and bond types, generates different protonation, tautomeric states as well as different stereoisomers. In the revised version, pKa calculations with the ChemAxon software MARVIN are used either to determine the likeliness of a combinatorial generated protonation state or to determine the titrable atoms used in the combinatorial approach. Additionally, the MARVIN software is used to predict microspecies distributions of ligand molecules. Docking studies were performed with our recently introduced program PLANTS (Protein-Ligand ANT System) on all protomers resulting from the three different selection methods for the well established CCDC/ASTEX clean data set demonstrating the usefulness of especially the latter approach.

Investigation of the Ligand-Nanoparticle Interface: A Cryogenic Approach for Preserving Surface Chemistry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karakoti, Ajay S.; Yang, Ping; Wang, Weina

2018-02-15

Ligand functionalized nanoparticles have replaced bare nanoparticles from most biological applications. These applications require tight control over size and stability of nanoparticles in aqueous medium. Understanding the mechanism of interaction of nanoparticle surfaces with functional groups of different organic ligands such as carboxylic acids is confounding despite the two decades of research on nanoparticles because of the inability to characterize their surfaces in their immediate environment. Often the surface interaction is understood by correlating the information available, in a piecemeal approach, from surface sensitive spectroscopic information of ligands and the bulk and surface information of nanoparticles. In present study wemore » report the direct interaction of 5-7 nm cerium oxide nanoparticles surface with acetic acid. In-situ XPS study was carried out by freezing the aqueous solution of nanoparticles to liquid nitrogen temperatures. Analysis of data collected concurrently from the ligands as well as functionalized frozen cerium oxide nanoparticles show that the acetic acid binds to the ceria surface in both dissociated and molecular state with equal population over the surface. The cerium oxide surface was populated predominantly with Ce4+ ions consistent with the thermal hydrolysis synthesis. DFT calculations reveal that the acetate ions bind more strongly to the cerium oxide nanoparticles as compared to the water and can replace the hydration sphere of nanoparticles resulting in high acetate/acetic surface coverage. These findings reveal molecular level interaction between the nanoparticle surfaces and ligands giving a better understanding of how materials behave in their immediate aqueous environment. This study also proposes a simple and elegant methodology to directly study the surface functional groups attached to nanoparticles in their immediate aqueous environment.« less

Fundamental Factors Impacting the Stability of Phosphonate-Derivatized Ruthenium Polypyridyl Sensitizers Adsorbed on Metal Oxide Surfaces.

PubMed

Raber, McKenzie; Brady, Matthew David; Troian-Gautier, Ludovic; Dickenson, John; Marquard, Seth L; Hyde, Jacob; Lopez, Santiago; Meyer, Gerald J; Meyer, Thomas J; Harrison, Daniel P

2018-06-08

A series of 18 ruthenium(II) polypyridyl complexes were synthesized and evaluated under electrochemically oxidative conditions, which generates the Ru(III) oxidation state and mimics the harsh conditions experienced during the kinetically-limited regime that can occur in dye-sensitized solar cells (DSSCs) and dye-sensitized photoelectrosynthesis cells (DSPECs), to further develop fundamental insights into the factors governing molecular sensitizer surface stability in aqueous 0.1 M HClO4 (aq). Both desorption and oxidatively induced ligand substitution were observed on planar fluorine doped tin oxide, FTO, electrodes, with a dependence on the E1/2 Ru(III/II) redox potential dictating the comparative ratios of the processes. Complexes such as RuP4OMe (E1/2 = 0.91 vs Ag/AgCl) displayed virtually only desorption, while complexes such as RuPbpz (E1/2 > 1.62 V vs Ag/AgCl) displayed only chemical decomposition. Comparing isomers of 4,4'- and 5,5-disubstituted-2,2'-bipyridine ancillary polypyridyl ligands, a dramatic increase in the rate of desorption of the Ru(III) complexes was observed for the 5,5'-ligands. Nanoscopic indium doped tin oxide thin films, nanoITO, were also sensitized and analyzed with cyclic voltammetry, UV-Vis absorption spectroscopy, and XPS, allowing for further distinction of desorption versus ligand substitution processes. Desorption loss to bulk solution associated with the planar surface of FTO is essentially non-existent on nanoITO, where both desorption and ligand substitution are shut down with RuP4OMe. These results revealed that minimizing time spent in the oxidized form, incorporating electron donating groups, maximizing hydrophobicity, and minimizing molecular bulk near the adsorbed ligand are critical to optimizing the performance of ruthenium(II) polypyridyl complexes in dye-sensitized solar cell devices.

Synthesis, characterization and electrochemistry studies of iron(III) complex with curcumin ligand.

PubMed

Özbolat, Gülüzar; Yegani, Arash Alizadeh; Tuli, Abdullah

2018-05-11

Iron overload is a serious clinical condition for humans and is a key target in drug development. The aim of this study was to investigate the coordination of iron(III) ions with curcumin ligand that may be used in the treatment of iron overload. Iron(III) complex of curcumin was synthesized and structurally characterized in its solid and solution state by FT-IR, UV-Vis, elemental analysis, and magnetic susceptibility. Electrochemical behaviour of the ligand and the complexes were examined using cyclic voltammetry. The cytotoxic activities of the ligand and the iron(III) complex were evaluated by the MTT assay. Curcumin reacted with iron in high concentrations at physiological pH at room temperature. Subsequently, a brown-red complex was formed. Data regarding magnetic susceptibility showed that the complexes with a 1:2 (metal/ligand) mole ratio had octahedral geometry. The complex showed higher anti-oxidant effect towards the cell line ECV304 at IC 50 values of 4.83 compared to curcumin. The complex exhibited very high cytotoxic activity and showed a cytotoxic effect that was much better than that of the ligand. The potentials for redox were calculated as 0.180 V and 0.350 V, respectively. The electrochemistry studies showed that Fe 3+ /Fe 2+ couple redox process occurred at low potentials. This value was within the range of compounds that are expected to show superoxide dismutase activity. This finding indicates that the iron complex is capable of removing free radicals. The observed cytotoxicity could be pursued to obtain a potential drug. Further studies investigating the use of curcumin for this purpose are needed. © 2018 John Wiley & Sons Australia, Ltd.

Model studies of the Cu(B) site of cytochrome c oxidase utilizing a Zn(II) complex containing an imidazole-phenol cross-linked ligand.

PubMed

Pesavento, Russell P; Pratt, Derek A; Jeffers, Jerry; van der Donk, Wilfred A

2006-07-21

Cytochrome c oxidase, the enzyme complex responsible for the four-electron reduction of O2 to H2O, contains an unusual histidine-tyrosine cross-link in its bimetallic heme a3-CuB active site. We have synthesised an unhindered, tripodal chelating ligand, BPAIP, containing the unusual ortho-imidazole-phenol linkage, which mimics the coordination environment of the CuB center. The ligand was used to investigate the physicochemical (pKa, oxidation potential) and coordination properties of the imidazole-phenol linkage when bound to a dication. Zn(II) coordination lowers the pKa of the phenol by 0.6 log units, and increases the potential of the phenolate/phenoxyl radical couple by approximately 50 mV. These results are consistent with inductive withdrawal of electron density from the phenolic ring. Spectroscopic data and theoretical calculations (DFT) were used to establish that the cationic complex [Zn(BPAIP)Br]+ has an axially distorted trigonal bipyramidal structure, with three coordinating nitrogen ligands (two pyridine and one imidazole) occupying the equatorial plane and the bromide and the tertiary amine nitrogen of the tripod in the axial positions. Interestingly, the Zn-Namine bonding interaction is weak or absent in [Zn(BPAIP)Br]+ and the complex gains stability in basic solutions, as indicated by 1H NMR spectroscopy. These observations are supported by theoretical calculations (DFT), which suggest that the electron-donating capacity of the equatorial imidazole ligand can be varied by modulation of the protonation and/or redox state of the cross-linked phenol. Deprotonation of the phenol makes the equatorial imidazole a stronger sigma-donor, resulting in an increased Zn-Nimd interaction and thereby leading to distortion of the axial ligand axis toward a more tetrahedral geometry.

The role of organic solvent radical cations in separations ligand degradation

DOE PAGES

Mezyk, Stephen P.; Mincher, Bruce J.; Dhiman, Surajdevprakash B.; ...

2015-11-04

The dodecane radical cation reaction rate constant with CMPO was measured using ps electron pulse radiolysis/absorption spectroscopy as k = (1.30 ± 0.11) x 1010 M -1 s -1 in dodecane/0.10 M CH 2Cl 2 solution. No reactivity increase occurred when these solutions were pre-contacted with nitric acid, similar to the behavior observed for TODGA. To corroborate these kinetic data with steady-state radiolysis measurements, where acid pre contacted CMPO showed significantly less degradation, it is proposed that the dodecane radical cation always reacts directly with TODGA, but for CMPO the charge-transfer occurs with the CMPO•HNO 3 complex formed in themore » acid contacted solvent.« less

Multiscale study of mononuclear Co II SMMs based on curcuminoid ligands

DOE PAGES

Díaz-Torres, Raúl; Menelaou, Melita; Roubeau, Olivier; ...

2016-01-07

This work introduces a novel family of Co II species having a curcuminoid (CCMoid) ligand, 9Accm, attached, namely [Co(9Accm) 2 (py) 2 ] (1) and [Co(9Accm) 2(2,2'-bpy)] (2), achieved in high yields by the use of a microwave reactor, and exhibiting two different arrangements for the 9Accm ligands, described as "cis"(2) and "trans"(1). The study of the similarities/differences of the magnetic, luminescent and surface behaviors of the two new species, 1 and 2, is the main objective of the present work. The determined single-crystal structures of both compounds are the only Co II -CCMoid structures described in the literature somore » far. Both compounds exhibit large positive D values, that of 1 (D = +74 cm -1 ) being three times larger than that of 2 (D = +24 cm -1 ), and behave as mononuclear Single-Molecule Magnets (SMMs) in the presence of an external magnetic field. Their similar structures but different anisotropy and SMM characteristics provide, for the first time, deep insight on the spin-orbital effects thanks to the use of CASSCF/NEVPT2 calculations implementing such contributions. Further magnetic studies were performed in solution by means of paramagnetic 1H NMR, where both compounds (1 and 2) are stable in CDCl 3 and display high symmetry. Paramagnetic NMR appears to be a useful diagnostic tool for the identification of such molecules in solution, where the resonance values found for the methine group (-CH-) of 9Accm vary significantly depending on the cis or trans disposition of the ligands. Fluorescence studies show that both systems display chelation enhancement of quenching (CHEQ) with regard to the free ligand, while 1 and 2 display similar quantum yields. Deposition of 1-2 on HOPG and Si(100) surfaces using spin-coating was studied using AFM; UV photoemission experiments under the same conditions display 2 as the most robust system. The measured occupied density of states of 2 with UV photoemission is in excellent agreement with theoretical DFT calculations.« less

A new titration system of a novel split-type superconducting magnet NMR spectrometer.

PubMed

Kitagawa, Isao; Tanaka, Hideki; Okada, Michiya; Kitaguchi, Hitoshi; Kohzuma, Takamitsu

2008-12-01

A new titration system for studying protein-ligand interactions has been developed. In this system, the sample solution is circulated in the route formed by an access path in a split superconducting magnet to maintain a constant protein concentration during the titration experiments. A concentration-control procedure for the ligand/protein ratio is devised, and the ligand/protein ratio is well controlled by this apparatus.

Vancomycin: ligand recognition, dimerization and super-complex formation.

PubMed

Jia, ZhiGuang; O'Mara, Megan L; Zuegg, Johannes; Cooper, Matthew A; Mark, Alan E

2013-03-01

The antibiotic vancomycin targets lipid II, blocking cell wall synthesis in Gram-positive bacteria. Despite extensive study, questions remain regarding how it recognizes its primary ligand and what is the most biologically relevant form of vancomycin. In this study, molecular dynamics simulation techniques have been used to examine the process of ligand binding and dimerization of vancomycin. Starting from one or more vancomycin monomers in solution, together with different peptide ligands derived from lipid II, the simulations predict the structures of the ligated monomeric and dimeric complexes to within 0.1 nm rmsd of the structures determined experimentally. The simulations reproduce the conformation transitions observed by NMR and suggest that proposed differences between the crystal structure and the solution structure are an artifact of the way the NMR data has been interpreted in terms of a structural model. The spontaneous formation of both back-to-back and face-to-face dimers was observed in the simulations. This has allowed a detailed analysis of the origin of the cooperatively between ligand binding and dimerization and suggests that the formation of face-to-face dimers could be functionally significant. The work also highlights the possible role of structural water in stabilizing the vancomycin ligand complex and its role in the manifestation of vancomycin resistance. © 2013 The Authors Journal compilation © 2013 FEBS.

Circularly Polarized Luminescence in Enantiopure Europium and Terbium Complexes with Modular, All-Oxygen Donor Ligands

PubMed Central

Seitz, Michael; Do, King; Ingram, Andrew J.; Moore, Evan G.; Muller, Gilles; Raymond, Kenneth N.

2009-01-01

Abstract: Circulaly polarized luminescence from terbium(III) complexed and excited by chiral antenna ligands gives strong emission The modular synthesis of three new octadentate, enantiopure ligands are reported - one with the bidentate chelating unit 2-hydroxyisophthalamide (IAM) and two with 1-hydroxy-2-pyridinone (1,2-HOPO) units. A new design principle is introduced for the chiral, non-racemic hexamines which constitute the central backbones for the presented class of ligands. The terbium(III) complex of the IAM ligand, as well as the europium(III) complexes of the 1,2-HOPO ligands are synthesized and characterized by various techniques (NMR, UV, CD, luminescence spectroscopy). All species exhibit excellent stability and moderate to high luminescence efficiency (quantum yields ΦEu = 0.05–0.08 and ΦTb = 0.30–0.57) in aqueous solution at physiological pH. Special focus is put onto the properties of the complexes in regard to circularly polarized luminescence (CPL). The maximum luminescence dissymmetry factors (glum) in aqueous solution are high with |glum|max = 0.08 – 0.40. Together with the very favorable general properties (good stability, high quantum yields, long lifetimes), the presented lanthanide complexes can be considered as good candidates for analytical probes based on CPL in biologically relevant environments. PMID:19639983

Can ligand addition to soil enhance Cd phytoextraction? A mechanistic model study.

PubMed

Lin, Zhongbing; Schneider, André; Nguyen, Christophe; Sterckeman, Thibault

2014-11-01

Phytoextraction is a potential method for cleaning Cd-polluted soils. Ligand addition to soil is expected to enhance Cd phytoextraction. However, experimental results show that this addition has contradictory effects on plant Cd uptake. A mechanistic model simulating the reaction kinetics (adsorption on solid phase, complexation in solution), transport (convection, diffusion) and root absorption (symplastic, apoplastic) of Cd and its complexes in soil was developed. This was used to calculate plant Cd uptake with and without ligand addition in a great number of combinations of soil, ligand and plant characteristics, varying the parameters within defined domains. Ligand addition generally strongly reduced hydrated Cd (Cd(2+)) concentration in soil solution through Cd complexation. Dissociation of Cd complex ([Formula: see text]) could not compensate for this reduction, which greatly lowered Cd(2+) symplastic uptake by roots. The apoplastic uptake of [Formula: see text] was not sufficient to compensate for the decrease in symplastic uptake. This explained why in the majority of the cases, ligand addition resulted in the reduction of the simulated Cd phytoextraction. A few results showed an enhanced phytoextraction in very particular conditions (strong plant transpiration with high apoplastic Cd uptake capacity), but this enhancement was very limited, making chelant-enhanced phytoextraction poorly efficient for Cd.

Ligand solvation in molecular docking.

PubMed

Shoichet, B K; Leach, A R; Kuntz, I D

1999-01-01

Solvation plays an important role in ligand-protein association and has a strong impact on comparisons of binding energies for dissimilar molecules. When databases of such molecules are screened for complementarity to receptors of known structure, as often occurs in structure-based inhibitor discovery, failure to consider ligand solvation often leads to putative ligands that are too highly charged or too large. To correct for the different charge states and sizes of the ligands, we calculated electrostatic and non-polar solvation free energies for molecules in a widely used molecular database, the Available Chemicals Directory (ACD). A modified Born equation treatment was used to calculate the electrostatic component of ligand solvation. The non-polar component of ligand solvation was calculated based on the surface area of the ligand and parameters derived from the hydration energies of apolar ligands. These solvation energies were subtracted from the ligand-receptor interaction energies. We tested the usefulness of these corrections by screening the ACD for molecules that complemented three proteins of known structure, using a molecular docking program. Correcting for ligand solvation improved the rankings of known ligands and discriminated against molecules with inappropriate charge states and sizes.

Ligand binding turns moth pheromone-binding protein into a pH sensor: effect on the Antheraea polyphemus PBP1 conformation.

PubMed

Katre, Uma V; Mazumder, Suman; Prusti, Rabi K; Mohanty, Smita

2009-11-13

In moths, pheromone-binding proteins (PBPs) are responsible for the transport of the hydrophobic pheromones to the membrane-bound receptors across the aqueous sensillar lymph. We report here that recombinant Antheraea polyphemus PBP1 (ApolPBP1) picks up hydrophobic molecule(s) endogenous to the Escherichia coli expression host that keeps the protein in the "open" (bound) conformation at high pH but switches to the "closed" (free) conformation at low pH. This finding has bearing on the solution structures of undelipidated lepidopteran moth PBPs determined thus far. Picking up a hydrophobic molecule from the host expression system could be a common feature for lipid-binding proteins. Thus, delipidation is critical for bacterially expressed lipid-binding proteins. We have shown for the first time that the delipidated ApolPBP1 exists primarily in the closed form at all pH levels. Thus, current views on the pH-induced conformational switch of PBPs hold true only for the ligand-bound open conformation of the protein. Binding of various ligands to delipidated ApolPBP1 studied by solution NMR revealed that the protein in the closed conformation switches to the open conformation only at or above pH 6.0 with a protein to ligand stoichiometry of approximately 1:1. Mutation of His(70) and His(95) to alanine drives the equilibrium toward the open conformation even at low pH for the ligand-bound protein by eliminating the histidine-dependent pH-induced conformational switch. Thus, the delipidated double mutant can bind ligand even at low pH in contrast to the wild type protein as revealed by fluorescence competitive displacement assay using 1-aminoanthracene and solution NMR.

High-Performance Quantum Dot Thin-Film Transistors with Environmentally Benign Surface Functionalization and Robust Defect Passivation.

PubMed

Jung, Su Min; Kang, Han Lim; Won, Jong Kook; Kim, JaeHyun; Hwang, ChaHwan; Ahn, KyungHan; Chung, In; Ju, Byeong-Kwon; Kim, Myung-Gil; Park, Sung Kyu

2018-01-31

The recent development of high-performance colloidal quantum dot (QD) thin-film transistors (TFTs) has been achieved with removal of surface ligand, defect passivation, and facile electronic doping. Here, we report on high-performance solution-processed CdSe QD-TFTs with an optimized surface functionalization and robust defect passivation via hydrazine-free metal chalcogenide (MCC) ligands. The underlying mechanism of the ligand effects on CdSe QDs has been studied with hydrazine-free ex situ reaction derived MCC ligands, such as Sn 2 S 6 4- , Sn 2 Se 6 4- , and In 2 Se 4 2- , to allow benign solution-process available. Furthermore, the defect passivation and remote n-type doping effects have been investigated by incorporating indium nanoparticles over the QD layer. Strong electronic coupling and solid defect passivation of QDs could be achieved by introducing electronically active MCC capping and thermal diffusion of the indium nanoparticles, respectively. It is also noteworthy that the diffused indium nanoparticles facilitate charge injection not only inter-QDs but also between source/drain electrodes and the QD semiconductors, significantly reducing contact resistance. With benign organic solvents, the Sn 2 S 6 4- , Sn 2 Se 6 4- , and In 2 Se 4 2- ligand based QD-TFTs exhibited field-effect mobilities exceeding 4.8, 12.0, and 44.2 cm 2 /(V s), respectively. The results reported here imply that the incorporation of MCC ligands and appropriate dopants provide a general route to high-performance, extremely stable solution-processed QD-based electronic devices with marginal toxicity, offering compatibility with standard complementary metal oxide semiconductor processing and large-scale on-chip device applications.

Tunable Keplerate Type-Cluster "Mo132 " Cavity with Dicarboxylate Anions.

PubMed

Lai, Thanh-Loan; Awada, Mouhamad; Floquet, Sébastien; Roch-Marchal, Catherine; Watfa, Nancy; Marrot, Jérôme; Haouas, Mohamed; Taulelle, Francis; Cadot, Emmanuel

2015-09-14

The internal functionalization of the Keplerate-type capsule Mo132 has been carried out by ligand exchange leading to the formation of glutarate and succinate containing species isolated as ammonium or dimethylammonium salts. Solution NMR analysis is consistent with asymmetric inner dicarboxylate ions containing one carboxylato group grafted onto the inner side of the spheroidal inorganic shell while the second hangs toward the center of the cavity. Such a disposition has been confirmed by the single-crystal X-ray diffraction analysis of the glutarate containing {Mo132 } species. A detailed NMR solution study of the ligand-exchange process allowed determining the binding constant KL of acetate (AcO(-) ), succinate (HSucc(-) ) or glutarate (HGlu(-) ) ligands at the 30 inner coordinating sites, which vary such as K AcO -

Solution structure of the chick TGFbeta type II receptor ligand-binding domain.

PubMed

Marlow, Michael S; Brown, Christopher B; Barnett, Joey V; Krezel, Andrzej M

2003-02-28

The transforming growth factor beta (TGFbeta) signaling pathway influences cell proliferation, immune responses, and extracellular matrix reorganization throughout the vertebrate life cycle. The signaling cascade is initiated by ligand-binding to its cognate type II receptor. Here, we present the structure of the chick type II TGFbeta receptor determined by solution NMR methods. Distance and angular constraints were derived from 15N and 13C edited NMR experiments. Torsion angle dynamics was used throughout the structure calculations and refinement. The 20 final structures were energy minimized using the generalized Born solvent model. For these 20 structures, the average backbone root-mean-square distance from the average structure is below 0.6A. The overall fold of this 109-residue domain is conserved within the superfamily of these receptors. Chick receptors fully recognize and respond to human TGFbeta ligands despite only 60% identity at the sequence level. Comparison with the human TGFbeta receptor determined by X-ray crystallography reveals different conformations in several regions. Sequence divergence and crystal packing interactions under low pH conditions are likely causes. This solution structure identifies regions were structural changes, however subtle, may occur upon ligand-binding. We also identified two very well conserved molecular surfaces. One was found to bind ligand in the crystallized human TGFbeta3:TGFbeta type II receptor complex. The other, newly identified area can be the interaction site with type I and/or type III receptors of the TGFbeta signaling complex.

Inorganic Chemistry Solutions to Semiconductor Nanocrystal Problems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alvarado, Samuel R.; Guo, Yijun; Ruberu, T. Purnima A.

2014-03-15

The optoelectronic and chemical properties of semiconductor nanocrystals heavily depend on their composition, size, shape and internal structure, surface functionality, etc. Available strategies to alter these properties through traditional colloidal syntheses and ligand exchange methods place a premium on specific reaction conditions and surfactant combinations. In this invited review, we apply a molecular-level understanding of chemical precursor reactivity to reliably control the morphology, composition and intimate architecture (core/shell vs. alloyed) of semiconductor nanocrystals. We also describe our work aimed at achieving highly selective, low-temperature photochemical methods for the synthesis of semiconductor–metal and semiconductor–metal oxide photocatalytic nanocomposites. In addition, we describemore » our work on surface modification of semiconductor nanocrystal quantum dots using new approaches and methods that bypass ligand exchange, retaining the nanocrystal's native ligands and original optical properties, as well as on spectroscopic methods of characterization useful in determining surface ligand organization and chemistry. Using recent examples from our group and collaborators, we demonstrate how these efforts have lead to faster, wider and more systematic application of semiconductor nanocrystal-based materials to biological imaging and tracking, and to photocatalysis of unconventional substrates. We believe techniques and methods borrowed from inorganic chemistry (including coordination, organometallic and solid state chemistry) have much to offer in reaching a better understanding of the synthesis, functionalization and real-life application of such exciting materials as semiconductor nanocrystals (quantum dots, rods, tetrapods, etc.).« less

Spectroscopic, structural and computational analysis of [Re(CO)3(dippM)Br](n+) (dippM = 1,1'-bis(diiso-propylphosphino)metallocene, M = Fe, n = 0 or 1; M = Co, n = 1).

PubMed

Furneaux, Aliza G; Piro, Nicholas A; Hernández Sánchez, Raúl; Gramigna, Kathryn M; Fey, Natalie; Robinson, Michael J; Kassel, W Scott; Nataro, Chip

2016-03-21

While the redox active backbone of bis(phosphino)ferrocene ligands is often cited as an important feature of these ligands in catalytic studies, the structural parameters of oxidized bis(phosphino)ferrocene ligands have not been thoroughly studied. The reaction of [Re(CO)3(dippf)Br] (dippf = 1,1'-bis(diiso-propylphosphino)ferrocene) and [NO][BF4] in methylene chloride yields the oxidized compound, [Re(CO)3(dippf)Br][BF4]. The oxidized species, [Re(CO)3(dippf)Br][BF4], and the neutral species, [Re(CO)3(dippf)Br], are compared using X-ray crystallography, cyclic voltammetry, visible spectroscopy, IR spectroscopy and zero-field (57)Fe Mössbauer spectroscopy. In addition, the magnetic moment of the paramagnetic [Re(CO)3(dippf)Br][BF4] was measured in the solid state using SQUID magnetometry and in solution by the Evans method. The electron transfer reaction of [Re(CO)3(dippf)Br][BF4] with acetylferrocene was also examined. For additional comparison, the cationic compound, [Re(CO)3(dippc)Br][PF6] (dippc = 1,1'-bis(diiso-propylphosphino)cobaltocenium), was prepared and characterized by cyclic voltammetry, X-ray crystallography, and NMR, IR and visible spectroscopies. Finally, DFT was employed to examine the oxidized dippf ligand and the oxidized rhenium complex, [Re(CO)3(dippf)Br](+).

Sub-millisecond ligand probing of cell receptors with multiple solution exchange

PubMed Central

Sylantyev, Sergiy; Rusakov, Dmitri A

2013-01-01

The accurate knowledge of receptor kinetics is crucial to our understanding of cell signal transduction in general and neural function in particular. The classical technique of probing membrane receptors on a millisecond scale involves placing a recording micropipette with a membrane patch in front of a double-barrel (θ-glass) application pipette mounted on a piezo actuator. Driven by electric pulses, the actuator can rapidly shift the θ-glass pipette tip, thus exposing the target receptors to alternating ligand solutions. However, membrane patches survive for only a few minutes, thus normally restricting such experiments to a single-application protocol. In order to overcome this deficiency, we have introduced pressurized supply microcircuits in the θ-glass channels, thus enabling repeated replacement of application solutions within 10–15 s. this protocol, which has been validated in our recent studies and takes 20–60 min to implement, allows the characterization of ligand-receptor interactions with high sensitivity, thereby also enabling a powerful paired-sample statistical design. PMID:23744290

Nucleophilic stabilization of water-based reactive ink for titania-based thin film inkjet printing

NASA Astrophysics Data System (ADS)

Gadea, C.; Marani, D.; Esposito, V.

2017-02-01

Drop on demand deposition (DoD) of titanium oxide thin films (<500 nm) is performed via a novel titanium-alkoxide-based solution that is tailored as a reactive ink for inkjet printing. The ink is developed as water-based solution by a combined use of titanium isopropoxide and n-methyldiethanolamine (MDEA) used as nucleophilic ligand. The function of the ligand is to control the fast hydrolysis/condensation reactions in water for the metal alkoxide before deposition, leading to formation of the TiO2 only after the jet process. The evolution of the titanium-ligand interactions at increasing amount of MDEA is here elucidated in terms of long term stability. The ink printability parameter (Z) is optimized, resulting in a reactive solution with printability, Z, >1, and chemical stability up to 600 h. Thin titanium oxide films (<500 nm) are proved on different substrates. Pure anatase phase is obtained after annealing at low temperature (ca. 400 °C).

Determination of the equilibrium constant of C60 fullerene binding with drug molecules.

PubMed

Mosunov, Andrei A; Pashkova, Irina S; Sidorova, Maria; Pronozin, Artem; Lantushenko, Anastasia O; Prylutskyy, Yuriy I; Parkinson, John A; Evstigneev, Maxim P

2017-03-01

We report a new analytical method that allows the determination of the magnitude of the equilibrium constant of complexation, K h , of small molecules to C 60 fullerene in aqueous solution. The developed method is based on the up-scaled model of C 60 fullerene-ligand complexation and contains the full set of equations needed to fit titration datasets arising from different experimental methods (UV-Vis spectroscopy, 1 H NMR spectroscopy, diffusion ordered NMR spectroscopy, DLS). The up-scaled model takes into consideration the specificity of C 60 fullerene aggregation in aqueous solution and allows the highly dispersed nature of C 60 fullerene cluster distribution to be accounted for. It also takes into consideration the complexity of fullerene-ligand dynamic equilibrium in solution, formed by various types of self- and hetero-complexes. These features make the suggested method superior to standard Langmuir-type analysis, the approach used to date for obtaining quantitative information on ligand binding with different nanoparticles.

Evolution of an adenine-copper cluster to a highly porous cuboidal framework: solution-phase ripening and gas-adsorption properties.

PubMed

Venkatesh, V; Pachfule, Pradip; Banerjee, Rahul; Verma, Sandeep

2014-09-15

The synthesis and directed evolution of a tetranuclear copper cluster, supported by 8-mercapto-N9-propyladenine ligand, to a highly porous three-dimensional cubic framework in the solid state is reported. The structure of this porous framework was unambiguously characterized by X-ray crystallography. The framework contains about 62 % solvent-accessible void; the presence of a free exocyclic amino group in the porous framework facilitates reversible adsorption of gas and solvent molecules. Oriented growth of framework in solution was also tracked by force and scanning electron microscopy studies, leading to identification of an intriguing ripening process, over a period of 30 days, which also revealed formation of cuboidal aggregates in solution. The elemental composition of these cuboidal aggregates was ascertained by EDAX analysis. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

How maltose influences structural changes to bind to maltose-binding protein: results from umbrella sampling simulation.

PubMed

Mascarenhas, Nahren Manuel; Kästner, Johannes

2013-02-01

A well-studied periplasmic-binding protein involved in the abstraction of maltose is maltose-binding protein (MBP), which undergoes a ligand-induced conformational transition from an open (ligand-free) to a closed (ligand-bound) state. Umbrella sampling simulations have been us to estimate the free energy of binding of maltose to MBP and to trace the potential of mean force of the unbinding event using the center-of-mass distance between the protein and ligand as the reaction coordinate. The free energy thus obtained compares nicely with the experimentally measured value justifying our theoretical basis. Measurement of the domain angle (N-terminal-domain - hinge - C-terminal-domain) along the unbinding pathway established the existence of three different states. Starting from a closed state, the protein shifts to an open conformation during the initial unbinding event of the ligand then resides in a semi-open conformation and later resides predominantly in an open-state. These transitions along the ligand unbinding pathway have been captured in greater depth using principal component analysis. It is proposed that in mixed-model, both conformational selection and an induced-fit mechanism combine to the ligand recognition process in MBP. Copyright © 2012 Wiley Periodicals, Inc.

Functional PEG–PAMAM-Tetraphosphonate Capped NaLnF4 Nanoparticles and their Colloidal Stability in Phosphate Buffer

PubMed Central

2015-01-01

Developing surface coatings for NaLnF4 nanoparticles (NPs) that provide long-term stability in solutions containing competitive ions such as phosphate remains challenging. An amine-functional polyamidoamine tetraphosphonate (NH2-PAMAM-4P) as a multidentate ligand for these NPs has been synthesized and characterized as a ligand for the surface of NaGdF4 and NaTbF4 nanoparticles. A two-step ligand exchange protocol was developed for introduction of the NH2-PAMAM-4P ligand on oleate-capped NaLnF4 NPs. The NPs were first treated with methoxy-poly(ethylene glycol)-monophosphoric acid (Mn = 750) in tetrahydrofuran. The mPEG750-OPO3-capped NPs were stable colloidal solutions in water, where they could be ligand-exchanged with NH2-PAMAM-4P. The surface amine groups on the NPs were available for derivatization to attach methoxy-PEG (Mn = 2000) and biotin-terminated PEG (Mn = 2000) chains. The surface coverage of ligands on the NPs was examined by thermal gravimetric analysis, and by a HABA analysis for biotin-containing NPs. Colloidal stability of the NPs was examined by dynamic light scattering. NaGdF4 and NaTbF4 NPs capped with mPEG2000–PAMAM-4P showed colloidal stability in DI water and in phosphate buffer (10 mM, pH 7.4). A direct comparison with NaTbF4 NPs capped with a mPEG2000-lysine-based tetradentate ligand that we reported previously (Langmuir2012, 28, 12861−1287022906305) showed that both ligands provided long-term stability in phosphate buffer, but that the lysine-based ligand provided better stability in phosphate-buffered saline. PMID:24898128

Functional PEG-PAMAM-tetraphosphonate capped NaLnF₄ nanoparticles and their colloidal stability in phosphate buffer.

PubMed

Zhao, Guangyao; Tong, Lemuel; Cao, Pengpeng; Nitz, Mark; Winnik, Mitchell A

2014-06-17

Developing surface coatings for NaLnF4 nanoparticles (NPs) that provide long-term stability in solutions containing competitive ions such as phosphate remains challenging. An amine-functional polyamidoamine tetraphosphonate (NH2-PAMAM-4P) as a multidentate ligand for these NPs has been synthesized and characterized as a ligand for the surface of NaGdF4 and NaTbF4 nanoparticles. A two-step ligand exchange protocol was developed for introduction of the NH2-PAMAM-4P ligand on oleate-capped NaLnF4 NPs. The NPs were first treated with methoxy-poly(ethylene glycol)-monophosphoric acid (M(n) = 750) in tetrahydrofuran. The mPEG750-OPO3-capped NPs were stable colloidal solutions in water, where they could be ligand-exchanged with NH2-PAMAM-4P. The surface amine groups on the NPs were available for derivatization to attach methoxy-PEG (M(n) = 2000) and biotin-terminated PEG (M(n) = 2000) chains. The surface coverage of ligands on the NPs was examined by thermal gravimetric analysis, and by a HABA analysis for biotin-containing NPs. Colloidal stability of the NPs was examined by dynamic light scattering. NaGdF4 and NaTbF4 NPs capped with mPEG2000-PAMAM-4P showed colloidal stability in DI water and in phosphate buffer (10 mM, pH 7.4). A direct comparison with NaTbF4 NPs capped with a mPEG2000-lysine-based tetradentate ligand that we reported previously (Langmuir 2012, 28, 12861-12870) showed that both ligands provided long-term stability in phosphate buffer, but that the lysine-based ligand provided better stability in phosphate-buffered saline.

Manipulating charge transfer excited state relaxation and spin crossover in iron coordination complexes with ligand substitution

DOE PAGES

Zhang, Wenkai; Kjaer, Kasper S.; Alonso-Mori, Roberto; ...

2016-08-25

Developing light-harvesting and photocatalytic molecules made with iron could provide a cost effective, scalable, and environmentally benign path for solar energy conversion. To date these developments have been limited by the sub-picosecond metal-to-ligand charge transfer (MLCT) electronic excited state lifetime of iron based complexes due to spin crossover – the extremely fast intersystem crossing and internal conversion to high spin metal-centered excited states. We revitalize a 30 year old synthetic strategy for extending the MLCT excited state lifetimes of iron complexes by making mixed ligand iron complexes with four cyanide (CN –) ligands and one 2,2'-bipyridine (bpy) ligand. This enablesmore » MLCT excited state and metal-centered excited state energies to be manipulated with partial independence and provides a path to suppressing spin crossover. We have combined X-ray Free-Electron Laser (XFEL) Kβ hard X-ray fluorescence spectroscopy with femtosecond time-resolved UV-visible absorption spectroscopy to characterize the electronic excited state dynamics initiated by MLCT excitation of [Fe(CN) 4(bpy)] 2–. The two experimental techniques are highly complementary; the time-resolved UV-visible measurement probes allowed electronic transitions between valence states making it sensitive to ligand-centered electronic states such as MLCT states, whereas the Kβ fluorescence spectroscopy provides a sensitive measure of changes in the Fe spin state characteristic of metal-centered excited states. Here, we conclude that the MLCT excited state of [Fe(CN) 4(bpy)] 2– decays with roughly a 20 ps lifetime without undergoing spin crossover, exceeding the MLCT excited state lifetime of [Fe(2,2'-bipyridine) 3] 2+ by more than two orders of magnitude.« less

Probing the Impact of Solvation on Photoexcited Spin Crossover Complexes with High-Precision X-ray Transient Absorption Spectroscopy

DOE PAGES

Liu, Cunming; Zhang, Jianxin; Lawson Daku, Latevi M.; ...

2017-11-10

Investigating the photoinduced electronic and structural response of bistable molecular building blocks incorporating transition metals in solution phase constitutes a necessary stepping stone for steering their properties towards applications and perfomance optimizations. Here, this paper presents a detailed X-ray transient absorption (XTA) spectroscopy study of a prototypical spin crossover (SCO) complex [Fe II(mbpy) 3] 2+ (where mbpy=4,4’-dimethyl-2,2’-bipyridine) with a [Fe IIN 6] first coordination shell in water (H 2O) and acetonitrile (CH 3CN). The unprecedented data quality of the XTA spectra together with the direct fitting of the difference spectra in k space using a large number of scattering pathsmore » enables resolving the subtle difference in the photoexcited structures of an Fe II complex in two solvents for the first time. Also, compared to the low spin (LS) 1A 1 state, the average Fe-N bond elongations for the photoinduced high spin (HS) 5T 2 state are found to be 0.181 ± 0.003 Å in H 2O and 0.199 ± 0.003 Å in CH 3CN. This difference in structural response is attributed to ligand-solvent interactions that are stronger in H 2O than in CH 3CN for the HS excited state. Our studies demonstrate that, although the metal center of [Fe II(mbpy) 3] 2+ could have been expected to be rather shielded by the three bidentate ligands with quasi-octahedral-coordination, the ligand field strength in the HS excited state is nevertheless indirectly affected by solvation that modifies the charge distribution within the Fe-N covalent bonds. More generally, this work highlights the importance of including solvation effects in order to develop a generalized understanding of the spin-state switching at the atomic level.« less

Crystal Structure of Oligomeric β1-Adrenergic G Protein- Coupled Receptors in Ligand-Free Basal State

PubMed Central

Huang, Jianyun; Chen, Shuai; Zhang, J. Jillian; Huang, Xin-Yun

2013-01-01

G protein-coupled receptors (GPCRs) mediate transmembrane signaling. Before ligand binding, GPCRs exist in a basal state. Crystal structures of several GPCRs bound with antagonists or agonists have been solved. However, the crystal structure of the ligand-free basal state of a GPCR, the starting point of GPCR activation and function, has not been determined. Here we report the X-ray crystal structure of the first ligand-free basal state of a GPCR in a lipid membrane-like environment. Oligomeric turkey β1-adrenergic receptors display two alternating dimer interfaces. One interface involves the transmembrane domain (TM) 1, TM2, the C-terminal H8, and the extracellular loop 1. The other interface engages residues from TM4, TM5, the intracellular loop 2 and the extracellular loop 2. Structural comparisons show that this ligand-free state is in an inactive conformation. This provides the structural information regarding GPCR dimerization and oligomerization. PMID:23435379

The relationship between metal toxicity and biotic ligand binding affinities in aquatic and soil organisms: a review.

PubMed

Ardestani, Masoud M; van Straalen, Nico M; van Gestel, Cornelis A M

2014-12-01

The biotic ligand model (BLM) is a theoretical, potentially mechanistic approach to assess metal bioavailability in soil and aquatic systems. In a BLM, toxicity is linked to the fraction of biotic ligand occupied, which in turn, depends on the various components of the solution, including activity of the metal. Bioavailability is a key factor in determining toxicity and uptake of metals in organisms. In this study, the present status of BLM development for soil and aquatic organisms is summarized. For all species and all metals, toxicity was correlated with the conditional biotic ligand binding constants. For almost all organisms, values for Ag, Cu, and Cd were higher than those for Zn and Ni. The constants derived for aquatic systems seem to be equally valid for soil organisms, but in the case of soils, bioavailability from the soil solution is greatly influenced by the presence of the soil solid phase. Copyright © 2014 Elsevier Ltd. All rights reserved.

Simple method to assess stability of immobilized peptide ligands against proteases.

PubMed

Giudicessi, Silvana L; Salum, María L; Saavedra, Soledad L; Martínez-Ceron, María C; Cascone, Osvaldo; Erra-Balsells, Rosa; Camperi, Silvia A

2017-09-01

Although peptides are used as affinity chromatography ligands, they could be digested by proteases. Usually, peptide stability is evaluated in solution, which differs from the resin-bounded peptide behavior. Furthermore, the study of the degradation products requires purification steps before analysis. Here, we describe an easy method to assess immobilized peptide stability. Sample peptides were synthesized on hydroxymethylbenzamide-ChemMatrix resin. Peptidyl-resin beads were then incubated with solutions containing proteases. Peptides were detached from the solid support with ammonia vapor and analyzed by matrix-assisted laser desorption/ionization and electrospray ionization mass spectrometry, allowing the detection of the whole peptides as well as their C-terminal degradation products. The method allowed a fast evaluation of peptide ligand stability in solid phase towards proteases that may be present in the crude sample before their use as ligands in affinity chromatography. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Díaz-Torres, Raúl; Menelaou, Melita; Roubeau, Olivier

This work introduces a novel family of Co II species having a curcuminoid (CCMoid) ligand, 9Accm, attached, namely [Co(9Accm) 2 (py) 2 ] (1) and [Co(9Accm) 2(2,2'-bpy)] (2), achieved in high yields by the use of a microwave reactor, and exhibiting two different arrangements for the 9Accm ligands, described as "cis"(2) and "trans"(1). The study of the similarities/differences of the magnetic, luminescent and surface behaviors of the two new species, 1 and 2, is the main objective of the present work. The determined single-crystal structures of both compounds are the only Co II -CCMoid structures described in the literature somore » far. Both compounds exhibit large positive D values, that of 1 (D = +74 cm -1 ) being three times larger than that of 2 (D = +24 cm -1 ), and behave as mononuclear Single-Molecule Magnets (SMMs) in the presence of an external magnetic field. Their similar structures but different anisotropy and SMM characteristics provide, for the first time, deep insight on the spin-orbital effects thanks to the use of CASSCF/NEVPT2 calculations implementing such contributions. Further magnetic studies were performed in solution by means of paramagnetic 1H NMR, where both compounds (1 and 2) are stable in CDCl 3 and display high symmetry. Paramagnetic NMR appears to be a useful diagnostic tool for the identification of such molecules in solution, where the resonance values found for the methine group (-CH-) of 9Accm vary significantly depending on the cis or trans disposition of the ligands. Fluorescence studies show that both systems display chelation enhancement of quenching (CHEQ) with regard to the free ligand, while 1 and 2 display similar quantum yields. Deposition of 1-2 on HOPG and Si(100) surfaces using spin-coating was studied using AFM; UV photoemission experiments under the same conditions display 2 as the most robust system. The measured occupied density of states of 2 with UV photoemission is in excellent agreement with theoretical DFT calculations.« less

Water-Soluble 2-Hydroxyisophthalamides for Sensitization of Lanthanide Luminescence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Samuel, Amanda P. S.; Moore, Evan G.; Melchior, Marco

2008-02-20

A series of octadentate ligands featuring the 2-hydroxyisophthalamide (IAM) antenna chromophore (to sensitize Tb(III) and Eu(III) luminescence) has been prepared and characterized. The length of the alkyl amine scaffold that links the four IAM moieties has been varied in order to investigate the effect of the ligand backbone on the stability and photophysical properties of the Ln(III) complexes. The amine backbones utilized in this study are N,N,N{prime},N{prime}-tetrakis-(2-aminoethyl)-ethane-1,2-diamine [H(2,2)-], N,N,N{prime},N{prime}-tetrakis-(2-aminoethyl)-propane-1,3-diamine [H(3,2)-] and N,N,N{prime},N{prime}-tetrakis-(2-aminoethyl)-butane-1,4-diamine [H(4,2)-]. These ligands also incorporate methoxyethylene [MOE] groups on each of the IAM chromophores to increase their water solubility. The aqueous ligand protonation constants and Tb(III) and Eu(III)more » formation constants were determined from solution thermodynamic studies. The resulting values indicate that at physiological pH, the Eu(III) and Tb(III) complexes of H(2,2)-IAM-MOE and H(4,2)-IAM-MOE are sufficiently stable to prevent dissociation at nanomolar concentrations. The photophysical measurements for the Tb(III) complexes gave overall quantum yield values of 0.56, 0.39, and 0.52 respectively for the complexes with H(2,2)-IAM-MOE, H(3,2)-IAM-MOE and H(4,2)-IAM-MOE, while the corresponding Eu(III) complexes displayed significantly weaker luminescence, with quantum yield values of 0.0014, 0.0015, and 0.0058, respectively. Analysis of the steady state Eu(III) emission spectra provides insight into the solution symmetries of the complexes. The combined solubility, stability and photophysical performance of the Tb(III) complexes in particular make them well suited to serve as the luminescent reporter group in high sensitivity time-resolved fluoroimmunoassays.« less

Protonation States of Homocitrate and Nearby Residues in Nitrogenase Studied by Computational Methods and Quantum Refinement.

PubMed

Cao, Lili; Caldararu, Octav; Ryde, Ulf

2017-09-07

Nitrogenase is the only enzyme that can break the triple bond in N 2 to form two molecules of ammonia. The enzyme has been thoroughly studied with both experimental and computational methods, but there is still no consensus regarding the atomic details of the reaction mechanism. In the most common form, the active site is a MoFe 7 S 9 C(homocitrate) cluster. The homocitrate ligand contains one alcohol and three carboxylate groups. In water solution, the triply deprotonated form dominates, but because the alcohol (and one of the carboxylate groups) coordinate to the Mo ion, this may change in the enzyme. We have performed a series of computational calculations with molecular dynamics (MD), quantum mechanical (QM) cluster, combined QM and molecular mechanics (QM/MM), QM/MM with Poisson-Boltzmann and surface area solvation, QM/MM thermodynamic cycle perturbations, and quantum refinement methods to settle the most probable protonation state of the homocitrate ligand in nitrogenase. The results quite conclusively point out a triply deprotonated form (net charge -3) with a proton shared between the alcohol and one of the carboxylate groups as the most stable at pH 7. Moreover, we have studied eight ionizable protein residues close to the active site with MD simulations and determined the most likely protonation states.

Experimental and theoretical investigations on spectroscopic properties of the imidazole-fused phenanthroline and its derivatives

NASA Astrophysics Data System (ADS)

Zhong, Rongfeng; Xu, Shengxian; Wang, Jinglan; Zhao, Feng; Xia, Hongying; Wang, Yibo

2016-05-01

Two phenanthroline derivatives, 1H-imidazo[4,5-f][1,10]phenanthroline (imPhen) and 2-(9H-fluoren-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline (Flu-imPhen), have been synthesized and characterized and the corresponding absorption and emission spectroscopic properties have been studied in CH2Cl2 solution. The imPhen exhibits the main two absorption bands at 282 nm and 229 nm and these bands are assigned as the typical π → π*(Phen) state. In addition, the weak absorption bands at 313 nm associated with a shoulder near 302 nm were assigned to the π → π*(Phen) state with partial charge transfer (CT) character. A similar absorption spectra are observed in the case of the Flu-imPhen in the region of 200-300 nm, while the region of 300-400 nm of the spectra are dominated by the characteristic π → π* transition of the fluorene moiety. imPhen shows the typical ligand-centered 1π → π* emission, while Flu-imPhen emits from the mixed 1π → π*/CT states. Density functional theory (DFT) and time-dependent density functional theory (TDDFT) were employed to rationalize the photophysical properties of these ligands studied. The theoretical data confirm the assignment of the experimental absorption spectra and the nature of the emitting states.

Pharmacokinetic Steady-States Highlight Interesting Target-Mediated Disposition Properties.

PubMed

Gabrielsson, Johan; Peletier, Lambertus A

2017-05-01

In this paper, we derive explicit expressions for the concentrations of ligand L, target R and ligand-target complex RL at steady state for the classical model describing target-mediated drug disposition, in the presence of a constant-rate infusion of ligand. We demonstrate that graphing the steady-state values of ligand, target and ligand-target complex, we obtain striking and often singular patterns, which yield a great deal of insight and understanding about the underlying processes. Deriving explicit expressions for the dependence of L, R and RL on the infusion rate, and displaying graphs of the relations between L, R and RL, we give qualitative and quantitive information for the experimentalist about the processes involved. Understanding target turnover is pivotal for optimising these processes when target-mediated drug disposition (TMDD) prevails. By a combination of mathematical analysis and simulations, we also show that the evolution of the three concentration profiles towards their respective steady-states can be quite complex, especially for lower infusion rates. We also show how parameter estimates obtained from iv bolus studies can be used to derive steady-state concentrations of ligand, target and complex. The latter may serve as a template for future experimental designs.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kohler, Lars; Hadt, Ryan G.; Hayes, Dugan

In this paper we describe the synthesis of a new phenanthroline ligand, 2,9-di(2,4,6-tri-isopropyl-phenyl)-1,10-phenanthroline (bL2) and its use as the blocking ligand in the preparation of two new heteroleptic Cu(I)diimine complexes. Analysis of the CuHETPHEN single crystal structures shows a distinct distortion from an ideal tetrahedral geometry around the Cu(I) center, forced by the secondary phenanthroline ligand rotating to accommodate the isopropyl groups of bL2. The increased steric bulk of bL2 as compared to the more commonly used 2,9-dimesityl-1,10-phenanthroline blocking ligand prohibits intramolecular ligand–ligand interaction, which is unique among CuHETPHEN complexes. The ground state optical and redox properties of CuHETPHEN complexesmore » are responsive to the substitution on the blocking ligand even though the differences in structure are far removed from the Cu(I) center. Transient optical spectroscopy was used to understand the excited state kinetics in both coordinating and non-coordinating solvents following visible excitation. Substitution of the blocking phenanthroline ligand has a significant impact on the 3MLCT decay and can be used to increase the excited state lifetime by 50%. Electronic structure calculations established relationships between ground and excited state properties, and general entatic state concepts are discussed for copper photosensitizers. This work contributes to the growing library of CuHETPHEN complexes and broadens the fundamental understanding of their ground and excited state properties.« less

Solution NMR investigation of the response of the lactose repressor core domain dimer to hydrostatic pressure.

PubMed

Fuglestad, Brian; Stetz, Matthew A; Belnavis, Zachary; Wand, A Joshua

2017-12-01

Previous investigations of the sensitivity of the lac repressor to high-hydrostatic pressure have led to varying conclusions. Here high-pressure solution NMR spectroscopy is used to provide an atomic level view of the pressure induced structural transition of the lactose repressor regulatory domain (LacI* RD) bound to the ligand IPTG. As the pressure is raised from ambient to 3kbar the native state of the protein is converted to a partially unfolded form. Estimates of rotational correlation times using transverse optimized relaxation indicates that a monomeric state is never reached and that the predominate form of the LacI* RD is dimeric throughout this pressure change. Spectral analysis suggests that the pressure-induced transition is localized and is associated with a volume change of approximately -115mlmol -1 and an average pressure dependent change in compressibility of approximately 30mlmol -1 kbar -1 . In addition, a subset of resonances emerge at high-pressures indicating the presence of a non-native but folded alternate state. Copyright © 2017 Elsevier B.V. All rights reserved.

Development of a Multi-Species Biotic Ligand Model Predicting the Toxicity of Trivalent Chromium to Barley Root Elongation in Solution Culture

PubMed Central

Song, Ningning; Zhong, Xu; Li, Bo; Li, Jumei; Wei, Dongpu; Ma, Yibing

2014-01-01

Little knowledge is available about the influence of cation competition and metal speciation on trivalent chromium (Cr(III)) toxicity. In the present study, the effects of pH and selected cations on the toxicity of trivalent chromium (Cr(III)) to barley (Hordeum vulgare) root elongation were investigated to develop an appropriate biotic ligand model (BLM). Results showed that the toxicity of Cr(III) decreased with increasing activity of Ca2+ and Mg2+ but not with K+ and Na+. The effect of pH on Cr(III) toxicity to barley root elongation could be explained by H+ competition with Cr3+ bound to a biotic ligand (BL) as well as by the concomitant toxicity of CrOH2+ in solution culture. Stability constants were obtained for the binding of Cr3+, CrOH2+, Ca2+, Mg2+ and H+ with binding ligand: log KCrBL 7.34, log KCrOHBL 5.35, log KCaBL 2.64, log KMgBL 2.98, and log KHBL 4.74. On the basis of those estimated parameters, a BLM was successfully developed to predict Cr(III) toxicity to barley root elongation as a function of solution characteristics. PMID:25119269

Development of a multi-species biotic ligand model predicting the toxicity of trivalent chromium to barley root elongation in solution culture.

PubMed

Song, Ningning; Zhong, Xu; Li, Bo; Li, Jumei; Wei, Dongpu; Ma, Yibing

2014-01-01

Little knowledge is available about the influence of cation competition and metal speciation on trivalent chromium (Cr(III)) toxicity. In the present study, the effects of pH and selected cations on the toxicity of trivalent chromium (Cr(III)) to barley (Hordeum vulgare) root elongation were investigated to develop an appropriate biotic ligand model (BLM). Results showed that the toxicity of Cr(III) decreased with increasing activity of Ca(2+) and Mg(2+) but not with K(+) and Na(+). The effect of pH on Cr(III) toxicity to barley root elongation could be explained by H(+) competition with Cr(3+) bound to a biotic ligand (BL) as well as by the concomitant toxicity of CrOH(2+) in solution culture. Stability constants were obtained for the binding of Cr(3+), CrOH(2+), Ca(2+), Mg(2+) and H(+) with binding ligand: log KCrBL 7.34, log KCrOHBL 5.35, log KCaBL 2.64, log KMgBL 2.98, and log KHBL 4.74. On the basis of those estimated parameters, a BLM was successfully developed to predict Cr(III) toxicity to barley root elongation as a function of solution characteristics.

Homogeneously catalysed conversion of aqueous formaldehyde to H2 and carbonate.

PubMed

Trincado, M; Sinha, Vivek; Rodriguez-Lugo, Rafael E; Pribanic, Bruno; de Bruin, Bas; Grützmacher, Hansjörg

2017-04-28

Small organic molecules provide a promising solution for the requirement to store large amounts of hydrogen in a future hydrogen-based energy system. Herein, we report that diolefin-ruthenium complexes containing the chemically and redox non-innocent ligand trop 2 dad catalyse the production of H 2 from formaldehyde and water in the presence of a base. The process involves the catalytic conversion to carbonate salt using aqueous solutions and is the fastest reported for acceptorless formalin dehydrogenation to date. A mechanism supported by density functional theory calculations postulates protonation of a ruthenium hydride to form a low-valent active species, the reversible uptake of dihydrogen by the ligand and active participation of both the ligand and the metal in substrate activation and dihydrogen bond formation.

Surface acoustic wave oxygen sensor

NASA Technical Reports Server (NTRS)

Collman, James P.; Oglesby, Donald M.; Upchurch, Billy T.; Leighty, Bradley D.; Zhang, Xumu; Herrmann, Paul C.

1994-01-01

A surface acoustic wave (SAW) device that responds to oxygen pressure was developed by coating a 158 MHz quartz surface acoustic wave (SAW) device with an oxygen binding agent. Two types of coatings were used. One type was prepared by dissolving an oxygen binding agent in a toluene solution of a copolymer containing the axial ligand. A second type was prepared with an oxygen binding porphyrin solution containing excess axial ligand without a polymer matrix. In the polymer based coatings, the copolymer served to provide the axial ligand to the oxygen binding agent and as a coating matrix on the surface of the SAW device. The oxygen sensing SAW device has been shown to bind oxygen following a Langmuir isotherm and may be used to measure the equilibrium constant of the oxygen binding compound in the coating matrix.

Mass spectrometric screening of ligands with lower off-rate from a clicked-based pooled library.

PubMed

Arai, Satoshi; Hirosawa, Shota; Oguchi, Yusuke; Suzuki, Madoka; Murata, Atsushi; Ishiwata, Shin'ichi; Takeoka, Shinji

2012-08-13

This paper describes a convenient screening method using ion trap electrospray ionization mass spectrometry to classify ligands to a target molecule in terms of kinetic parameters. We demonstrate this method in the screening of ligands to a hexahistidine tag from a pooled library synthesized by click chemistry. The ion trap mass spectrometry analysis revealed that higher stabilities of ligand-target complexes in the gas phase were related to lower dissociation rate constants, i.e., off-rates in solution. Finally, we prepared a fluorescent probe utilizing the ligand with lowest off-rate and succeeded in performing single molecule observations of hexahistidine-tagged myosin V walking on actin filaments.

Advanced mercury removal from gold leachate solutions prior to gold and silver extraction: a field study from an active gold mine in Peru.

PubMed

Matlock, Matthew M; Howerton, Brock S; Van Aelstyn, Mike A; Nordstrom, Fredrik L; Atwood, David A

2002-04-01

Mercury contamination in the Gold-Cyanide Process (GCP) is a serious health and environmental problem. Following the heap leaching of gold and silver ores with NaCN solutions, portions of the mercury-cyano complexes often adhere to the activated carbon (AC) used to extract the gold. During the electrowinning and retorting steps, mercury can be (and often is) emitted to the air as a vapor. This poses a severe health hazard to plant workers and the local environment. Additional concerns relate to the safety of workers when handling the mercury-laden AC. Currently, mercury treatment from the heap leach solution is nonexistent. This is due to the fact that chelating ligands which can effectively work under the adverse pH conditions (as present in the heap leachate solutions) do not exist. In an effort to economically and effectively treat the leachate solution prior to passing over the AC, a dipotassium salt of 1,3-benzenediamidoethanethiol (BDET2-) has been developed to irreversibly bind and precipitate the mercury. The ligand has proven to be highly effective by selectively reducing mercury levels from average initial concentrations of 34.5 ppm (parts per million) to 0.014 ppm within 10 min and to 0.008 ppm within 15 min. X-ray powder diffraction (XRD), proton nuclear magnetic resonance (1H NMR), Raman, and infrared (IR) spectroscopy demonstrate the formation of a mercury-ligand compound, which remains insoluble over pH ranges of 0.0-14.0. Leachate samples from an active gold mine in Peru have been analyzed using cold vapor atomic fluorescence (CVAF) and inductively coupled plasma optical emission spectroscopy (ICP-OES) for metal concentrations before and after treatment with the BDET2- ligand.

A novel signal transduction protein: Combination of solute binding and tandem PAS-like sensor domains in one polypeptide chain

DOE PAGES

Wu, R.; Wilton, R.; Cuff, M. E.; ...

2017-02-07

The tandem Per-Arnt-Sim (PAS) like sensors are commonly found in signal transduction proteins. The periplasmic solute binding protein (SBP) domains are found ubiquitously and are generally involved in solute transport. These domains are widely observed as parts of separate proteins but not within the same polypeptide chain. We report the structural and biochemical characterization of the extracellular ligand-binding receptor, Dret_0059 from Desulfohalobium retbaense DSM 5692, an organism isolated from the Retba salt lake in Senegal. The structure of Dret_0059 consists of a novel combination of SBP and TPAS sensor domains. The N-terminal region forms an SBP domain and the C-terminalmore » region folds into a tandem PAS-like domain structure. A ketoleucine moiety is bound to the SBP, whereas a cytosine molecule is bound in the distal PAS domain of the TPAS. The differential scanning flourimetry studies in solution support the ligands observed in the crystal structure. There are only two other proteins with this structural architecture in the non-redundant sequence data base and we predict that they too bind the same substrates. There is significant interaction between the SBP and TPAS domains, and it is quite conceivable that the binding of one ligand will have an effect on the binding of the other. Our attempts to remove the ligands bound to the protein during expression were not successful, therefore, it is not clear what the relative affects are. The genomic context of this receptor does not contain any protein components expected for transport function, hence, we suggest that Dret_0059 is likely involved in signal transduction and not in solute transport.« less

Measuring the Valence of Nanocrystal Surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Owen, Jonathan Scharle

2016-11-30

The goal of this project is to understand and control the interplay between nanocrystal stoichiometry, surface ligand binding and exchange, and the optoelectronic properties of semiconductor nanocrystals in solution and in thin solid films. We pursued three research directions with this goal in mind: 1) We characterized nanocrystal stoichiometry and its influence on the binding of L-type and X-type ligands, including the thermodynamics of binding and the kinetics of ligand exchange. 2) We developed a quantitative understanding of the relationship between surface ligand passivation and photoluminescence quantum yield. 3) We developed methods to replace the organic ligands on the nanocrystalmore » with halide ligands and controllably deposit these nanocrystals into thin films, where electrical measurements were used to investigate the electrical transport and internanocrystal electronic coupling.« less

Strengthening of the Coordination Shell by Counter Ions in Aqueous Th 4+ Solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Atta-Fynn, Raymond; Bylaska, Eric J.; de Jong, Wibe A.

The presence of counter ions in solutions containing highly charged metal cations can trigger processes such as ion-pair formation, hydrogen bond breakages and subsequent reformation, and ligand exchanges. In this work, it is shown how halide (Cl-, Br-) and perchlorate (ClO4-) anions affect the strength of the primary solvent coordination shells around Th4+ using explicit solvent and finite temperature ab initio molecular dynamics modeling methods. The 9-fold solvent geometry was found to be the most stable hydration structure in each aqueous solution. Relative to the dilute aqueous solution, the presence of the counter ions did not significantly alter the geometrymore » of the primary hydration shell. However, the free energy analyses indicated that the 10-fold hydrated states were thermodynamically accessible in dilute and bromide aqueous solutions within 1 kcal/mol. Analysis of the results showed that the hydrogen bond lifetimes were longer and solvent exchange energy barriers were larger in solutions with counter ions in comparison with the solution with no counter ions. This implies that the presence of the counter ions induces a strengthening of the Th4+ hydration shell.« less

Laser synthesis and spectroscopy of acetonitrile/silver nanoparticles

NASA Astrophysics Data System (ADS)

Akin, S. T.; Liu, X.; Duncan, M. A.

2015-11-01

Silver nanoparticles with acetonitrile ligands are produced in a laser ablation flow reactor. Excimer laser ablation produces gas phase metal clusters which are thermalized with helium or argon collisions in the flowtube, and reactions with acetonitrile vapor coordinate this ligand to the particle surface. The gaseous mixture is captured in a cryogenic trap; warming produces a solution of excess ligand and coated particles. TEM images reveal particle sizes of 10-30 nm diameter. UV-vis absorption and fluorescence spectra are compared to those of standard silver nanoparticles with surfactant coatings. Deep-UV ligand absorption is strongly enhanced by nanoparticle adsorption.

Cyclometalated products of [(COE)(2)RhCl](2) and 1,3-(RSCH(2))(2)C(6)H(4) (R = (t)Bu, (i)Pr) Are Dimeric. Synthesis, molecular structures, and solution dynamics of [mu-ClRh(H)(RSCH(2))(2)C(6)H(3)-2,6](2).

PubMed

Evans, Daniel R; Huang, Mingsheng; Seganish, W Michael; Chege, Esther W; Lam, Yiu-Fai; Fettinger, James C; Williams, Tracie L

2002-05-20

Two tridentate thioether pincer ligands, 1,3-(RSCH(2))(2)C(6)H(4) (R = (t)()Bu, 1a; R = (i)()Pr, 1b) underwent cyclometalation using [(COE)(2)RhCl](2) in air/moisture-free benzene at room temperature. The resultant complexes, [mu-ClRh(H)(RSCH(2))(2)C(6)H(3)-2,6](2) (R = (t)Bu, 2a; R = (i)Pr, 2b) are dimeric both in the solid state and in solution. A battery of variable-temperature one- and two-dimensional (1)H NMR experiments showed conclusively that both complexes undergo dynamic exchange in solution. Exchange between two dimeric diastereomers of 2a in solution occurred via rotation about the Rh-C(ipso) bond. The dynamic exchange of 2b was significantly more complex as an additional exchange mechanism, sulfur inversion, occurred, which resulted in the exchange between several diastereomers in solution.

The effect of intermolecular hydrogen bonding on the fluorescence of a bimetallic platinum complex.

PubMed

Zhao, Guang-Jiu; Northrop, Brian H; Han, Ke-Li; Stang, Peter J

2010-09-02

The bimetallic platinum complexes are known as unique building blocks and arewidely utilized in the coordination-driven self-assembly of functionalized supramolecular metallacycles. Hence, photophysical study of the bimetallic platinum complexes will be very helpful for the understanding on the optical properties and further applications of coordination-driven self-assembled supramolecular metallacycles. Herein, we report steady-state and time-resolved spectroscopic experiments as well as quantum chemistry calculations to investigate the significant intermolecular hydrogen bonding effects on the intramolecular charge transfer (ICT) fluorescence of a bimetallic platinum compound 4,4'-bis(trans-Pt(PEt(3))(2)OTf)benzophenone 3 in solution. We demonstrated that the fluorescent state of compound 3 can be assigned as a metal-to-ligand charge transfer (MLCT) state. Moreover, it was observed that the formation of intermolecular hydrogen bonds can effectively lengthen the fluorescence lifetime of 3 in alcoholic solvents compared with that in hexane solvent. At the same time, the electronically excited states of 3 in solution are definitely changed by intermolecular hydrogen bonding interactions. As a consequence, we propose a new fluorescence modulation mechanism by hydrogen bonding to explain different fluorescence emissions of 3 in hydrogen-bonding solvents and nonhydrogen-bonding solvents.

What a difference a 5f element makes: trivalent and tetravalent uranium halide complexes supported by one and two bis[2-(diisopropylphosphino)-4-methylphenyl]amido (PNP) ligands.

PubMed

Cantat, Thibault; Scott, Brian L; Morris, David E; Kiplinger, Jaqueline L

2009-03-02

The coordination behavior of the bis[2-(diisopropylphosphino)-4-methylphenyl]amido ligand (PNP) toward UI3(THF)4 and UCl4 has been investigated to access new uranium(III) and uranium(IV) halide complexes supported by one and two PNP ligands. The reaction between (PNP)K (6) and 1 equiv of UI3(THF)4 afforded the trivalent halide complex (PNP)UI2(4-tBu-pyridine)2 (7) in the presence of 4-tert-butylpyridine. The same reaction carried out with UCl4 and no donor ligand gave [(PNP)UCl3]2 (8), in which the uranium coordination sphere in the (PNP)UCl3 unit is completed by a bridging chloride ligand. When UCl4 is reacted with 1 equiv (PNP)K (6) in the presence of THF, trimethylphosphine oxide (TMPO), or triphenylphosphineoxide (TPPO), the tetravalent halide complexes (PNP)UCl3(THF) (9), (PNP)UCl3(TMPO)2 (10), and (PNP)UCl3(TPPO) (11), respectively, are formed in excellent yields. The bis(PNP) complexes of uranium(III), (PNP)2UI (12), and uranium(IV), (PNP)2UCl2 (13), were easily isolated from the analogous reactions between 2 equiv of 6 and UI3(THF)4 or UCl4, respectively. Complexes 12 and 13 represent the first examples of complexes featuring two PNP ligands coordinated to a single metal center. Complexes 7-13 have been characterized by single-crystal X-ray diffraction and 1H and 31P NMR spectroscopy. The X-ray structures demonstrate the ability of the PNP ligand to adopt new coordination modes upon coordination to uranium. The PNP ligand can adopt both pseudo-meridional and pseudo-facial geometries when it is kappa3-(P,N,P) coordinated, depending on the steric demand at the uranium metal center. Additionally, its hemilabile character was demonstrated with an unusual kappa2-(P,N) coordination mode that is maintained in both the solid-state and in solution. Comparison of the structures of the mono(PNP) and bis(PNP) complexes 7, 9, 11-13 with their respective C5Me5 analogues 1-4 undoubtedly show that a more sterically congested environment is provided by the PNP ligand. The electronic influence of replacing the C5Me5 ligands with PNP was investigated using electronic absorption spectroscopy and electrochemistry. For 12 and 13, a chemically reversible wave corresponding to the UIV/UIII redox transformation comparable to that for 3 and 4 was observed. However, a 350 mV shift of this couple to more negative potentials was observed on substitution of the bis(C5Me5) by the bis(PNP) framework, therefore pointing to a greater electronic density at the metal center in the PNP complexes. The UV-visible region of the electronic spectra for the mono(PNP) and bis(PNP) complexes appear to be dominated by PNP ligand-based transitions that are shifted to higher energy in the uranium complexes than in the simple ligand anion (6) spectrum, for both the UVI and UIII oxidation states. The near IR region in complexes 1-4 and 7, 9, 11-13 is dominated by f-f transitions derived from the 5f3 and 5f2 valence electronic configuration of the metal center. Though complexes of both ligand sets exhibit similar intensities in their f-f bands, a somewhat larger ligand-field splitting was observed for the PNP system, consistent with its higher electron donating ability.

New coordination compounds of Cr(III) used in leather tanning

NASA Astrophysics Data System (ADS)

Crudu, Marian; Sibiescu, Doina; Rosca, Ioan; Sutiman, Daniel; Vizitiu, Mihaela; Apostolescu, Gabriela

2009-01-01

Some new coordination compounds of Cr(III) using as ligand N-hydroxy - succinimide, were obtained and studied. The combination ratio, central atom: ligand were 1:1; 1:2 and 1:3. The new complex compounds were studied using UV-Vis spectroscopy, conductance and pH measurements. The studies of obtaining and of stability of the new compounds were accomplished in aqueous solutions using methods characteristic for coordination compounds: conductance and pH measurements. The combination ratios and the stability constants were determined with methods characteristic for studies in solutions.

High degree of polymerization in a fullerene-containing supramolecular polymer.

PubMed

Isla, Helena; Pérez, Emilio M; Martín, Nazario

2014-05-26

Supramolecular polymers based on dispersion forces typically show lower molecular weights (MW) than those based on hydrogen bonding or metal-ligand coordination. We present the synthesis and self-assembling properties of a monomer featuring two complementary units, a C60 derivative and an exTTF-based macrocycle, that interact mainly through π-π, charge-transfer, and van der Waals interactions. Thanks to the preorganization in the host part, a remarkable log K(a)=5.1±0.5 in CHCl3 at room temperature is determined for the host-guest couple. In accordance with the large binding constant, the monomer self-assembles in the gas phase, in solution, and in the solid state to form linear supramolecular polymers with a very high degree of polymerization. A MW above 150 kDa has been found experimentally in solution, while in the solid state the monomer forms extraordinarily long, straight, and uniform fibers with lengths reaching several microns. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Robust resistive memory devices using solution-processable metal-coordinated azo aromatics

NASA Astrophysics Data System (ADS)

Goswami, Sreetosh; Matula, Adam J.; Rath, Santi P.; Hedström, Svante; Saha, Surajit; Annamalai, Meenakshi; Sengupta, Debabrata; Patra, Abhijeet; Ghosh, Siddhartha; Jani, Hariom; Sarkar, Soumya; Motapothula, Mallikarjuna Rao; Nijhuis, Christian A.; Martin, Jens; Goswami, Sreebrata; Batista, Victor S.; Venkatesan, T.

2017-12-01

Non-volatile memories will play a decisive role in the next generation of digital technology. Flash memories are currently the key player in the field, yet they fail to meet the commercial demands of scalability and endurance. Resistive memory devices, and in particular memories based on low-cost, solution-processable and chemically tunable organic materials, are promising alternatives explored by the industry. However, to date, they have been lacking the performance and mechanistic understanding required for commercial translation. Here we report a resistive memory device based on a spin-coated active layer of a transition-metal complex, which shows high reproducibility (~350 devices), fast switching (<=30 ns), excellent endurance (~1012 cycles), stability (>106 s) and scalability (down to ~60 nm2). In situ Raman and ultraviolet-visible spectroscopy alongside spectroelectrochemistry and quantum chemical calculations demonstrate that the redox state of the ligands determines the switching states of the device whereas the counterions control the hysteresis. This insight may accelerate the technological deployment of organic resistive memories.

A Macrocyclic Chelator That Selectively Binds Ln 4+ over Ln 3+ by a Factor of 10 29

DOE PAGES

Pham, Tiffany A.; Altman, Alison B.; Stieber, S. Chantal E.; ...

2016-06-24

A tetravalent cerium macrocyclic complex (CeLK 4) was prepared with an octadentate terephthalamide ligand comprised of hard catecholate donors and characterized in the solution state by spectrophotometric titrations and electrochemistry and in the crystal by X-ray diffraction. The solution-state studies showed that L exhibits a remarkably high affinity toward Ce 4+, with log β 110 = 61(2) and ΔG = -348 kJ/mol, compared with log β 110 = 32.02(2) for the analogous Pr 3+ complex. In addition, L exhibits an unusual preference for forming CeL 4- relative to formation of the analogous actinide complex, ThL 4- , which has βmore » 110 = 53.7(5). The extreme stabilization of tetravalent cerium relative to its trivalent state is also evidenced by the shift of 1.91 V in the redox potential of the Ce 3+/Ce 4+ couple of the complex (measured at -0.454 V vs SHE). The unprecedented behavior prompted an electronic structure analysis using L 3 - and M 5,4-edge X-ray absorption near-edge structure (XANES) spectroscopies and configuration interaction calculations, which showed that 4f-orbital bonding in CeLK 4 has partial covalent character due to ligand-to-metal charge transfer (LMCT) in the ground state. The experimental results are presented in the context of earlier measurements on tetravalent cerium compounds, indicating that the amount of LMCT for CeLK 4 is similar to that observed for [Et 4N] 2[CeCl 6] and CeO 2 and significantly less than that for the organometallic sandwich compound cerocene, (C 8H 8) 2Ce. A simple model to rationalize changes in 4f orbital bonding for tri- and tetravalent lanthanide and actinide compounds is also provided.« less

Investigation of Rhodopsin Dynamics in its Signaling State by Solid-State Deuterium NMR Spectroscopy

PubMed Central

Struts, Andrey V.; Chawla, Udeep; Perera, Suchithranga M.D.C.; Brown, Michael F.

2017-01-01

Site-directed deuterium NMR spectroscopy is a valuable tool to study the structural dynamics of biomolecules in cases where solution NMR is inapplicable. Solid-state 2H NMR spectral studies of aligned membrane samples of rhodopsin with selectively labeled retinal provide information on structural changes of the chromophore in different protein states. In addition, solid-state 2H NMR relaxation time measurements allow one to study the dynamics of the ligand during the transition from the inactive to the active state. Here we describe the methodological aspects of solid-state 2H NMR spectroscopy for functional studies of rhodopsin, with an emphasis on the dynamics of the retinal cofactor. We provide complete protocols for the preparation of NMR samples of rhodopsin with 11-cis-retinal selectively deuterated at the methyl groups in aligned membranes. In addition, we review optimized conditions for trapping the rhodopsin photointermediates; and lastly we address the challenging problem of trapping the signaling state of rhodopsin in aligned membrane films. PMID:25697522

The Chelate Effect Redefined.

ERIC Educational Resources Information Center

da Silva, J. J. R. Frausto

1983-01-01

Discusses ambiguities of the accepted definition of the chelate effect, suggesting that it be defined in terms of experimental observation rather than mathematical abstraction. Indicates that the effect depends on free energy change in reaction, ligand basicity, pH of medium, type of chelates formed, and concentration of ligands in solution. (JN)

Synthesis, structure characterization and biological studies on a new aromatic hydrazone, 5-(2-(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)hydrazono)-2,2-dimethyl-1,3-dioxane-4,6-dione, and its transition metal complexes

NASA Astrophysics Data System (ADS)

Kumar, Shubha S.; Biju, S.; Sadasivan, V.

2018-03-01

A new aromatic hydrazone 5-(2-(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)hydrazono)-2,2-dimethyl-1,3-dioxane-4,6-dione has been synthesized by Japp-Klingemann reaction from diazotized 4-aminoantipyrine and Meldrum's acid. A few 3d-metal ion complexes of this hydrazone were synthesized. The compound and its complexes were characterized by UV-Visible, 1H NMR, ESR, Mass spectral, molar conductance and magnetic susceptibility measurements. The compound was found to exist in hydrazone form in solid state and solution from SXRD and 1H NMR study. The influence of pH on the molecule was studied and found that it shows azo/enol-hydrazone tautomerism in solution. This molecule act as a univalent tridentate ligand and the complexes were assigned to have a 1:2 stoichiometry (M:L). The antioxidant properties of the compounds were explored by DPPH assay and found that the ligand possesses better free radical scavenging effect than the complexes. Antimicrobial activities of these compounds were investigated and were found to be active.

Characterization and biological studies on Co(II), Ni(II) and Cu(II) complexes of carbohydrazones ending by pyridyl ring.

PubMed

Abu El-Reash, G M; El-Gammal, O A; Ghazy, S E; Radwan, A H

2013-03-01

The chelating behavior of ligands based on carbohydrazone core modified with pyridine end towards Co(II), Ni(II) and Cu(II) ions have been examined. The ligands derived from the condensation of carbohydrazide with 2-acetylpyridine (H(2)APC) and 4-acetylpyridine (H(2)APEC). The (1)H NMR, IR data and the binding energy calculations of H(2)APC revealed the presence of two stereoisomers syn and anti in the solid state and in the solution. The (1)H NMR, IR data and the binding energy calculations confirmed the presence of H(2)APEC in one keto form only in the solid state and in the solution. The spectroscopic data confirmed that H(2)APC behaves as a monobasic pentadentate in Co(II) and Cu(II) complexes and as mononegative tetradentate in Ni(II) complex. On the other hand, H(2)APEC acts as a mononegative tridentate in Co(II) complex, neutral tridentate in Ni(II) complex and neutral bidentate in Cu(II) complex. The electronic spectra and the magnetic measurements of complexes as well as the ESR of the copper complexes suggested the octahedral geometry. The bond length and bond angles were evaluated by DFT method using material studio program. The thermal behavior and the kinetic parameters of degradation were determined using Coats-Redfern and Horowitz-Metzger methods. The antioxidant (DDPH and ABTS methods), anti-hemolytic and in vitro Ehrlich ascites of the compounds have been screened. Copyright © 2012 Elsevier B.V. All rights reserved.

Interconversion of CO2 and formic acid by bio-inspired Ir complexes with pendent bases.

PubMed

Fujita, Etsuko; Muckerman, James T; Himeda, Yuichiro

2013-01-01

Recent investigations of the interconversion of CO2 and formic acid using Ru, Ir and Fe complexes are summarized in this review. During the past several years, both the reaction rates and catalyst stabilities have been significantly improved. Remarkably, the interconversion (i.e., reversibility) has also been achieved under mild conditions in environmentally benign water solvent by slightly changing the pH of the aqueous solution. Only a few catalysts seem to reflect a bio-inspired design such as the use of proton responsive ligands, ligands with pendent bases or acids for a second-coordination-sphere interaction, electroresponsive ligands, and/or ligands having a hydrogen bonding function with a solvent molecule or an added reagent. The most successful of these is an iridium dinuclear complex catalyst that at least has the first three of these characteristics associated with its bridging ligand. By utilizing an acid/base equilibrium for proton removal, the ligand becomes a strong electron donor, resulting in Ir(I) character with a vacant coordination site at each metal center in slightly basic solution. Complemented by DFT calculations, kinetic studies of the rates of formate production using a related family of Ir complexes with and without such functions on the ligand reveal that the rate-determining step for the CO2 hydrogenation is likely to be H2 addition through heterolytic cleavage involving a "proton relay" through the pendent base. The dehydrogenation of formic acid, owing to the proton responsive ligands changing character under slightly acidic pH conditions, is likely to occur by a mechanism with a different rate-determining step. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems. Copyright © 2012 Elsevier B.V. All rights reserved.

Disentangling Transient Charge Density and Metal–Ligand Covalency in Photoexcited Ferricyanide with Femtosecond Resonant Inelastic Soft X-ray Scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jay, Raphael M.; Norell, Jesper; Eckert, Sebastian

Soft X-ray spectroscopies are ideal probes of the local valence electronic structure of photocatalytically active metal sites. Here, we apply the selectivity of time-resolved resonant inelastic X-ray scattering at the iron L-edge to the transient charge distribution of an optically excited charge-transfer state in aqueous ferricyanide. Through comparison to steady-state spectra and quantum chemical calculations, the coupled effects of valence-shell closing and ligand-hole creation are experimentally and theoretically disentangled and described in terms of orbital occupancy, metal–ligand covalency, and ligand field splitting, thereby extending established steady-state concepts to the excited-state domain. π-Back-donation is found to be mainly determined by themore » metal site occupation, whereas the ligand hole instead influences σ-donation. Here, our results demonstrate how ultrafast resonant inelastic X-ray scattering can help characterize local charge distributions around catalytic metal centers in short-lived charge-transfer excited states, as a step toward future rationalization and tailoring of photocatalytic capabilities of transition-metal complexes.« less

Disentangling Transient Charge Density and Metal–Ligand Covalency in Photoexcited Ferricyanide with Femtosecond Resonant Inelastic Soft X-ray Scattering

DOE PAGES

Jay, Raphael M.; Norell, Jesper; Eckert, Sebastian; ...

2018-06-11

Soft X-ray spectroscopies are ideal probes of the local valence electronic structure of photocatalytically active metal sites. Here, we apply the selectivity of time-resolved resonant inelastic X-ray scattering at the iron L-edge to the transient charge distribution of an optically excited charge-transfer state in aqueous ferricyanide. Through comparison to steady-state spectra and quantum chemical calculations, the coupled effects of valence-shell closing and ligand-hole creation are experimentally and theoretically disentangled and described in terms of orbital occupancy, metal–ligand covalency, and ligand field splitting, thereby extending established steady-state concepts to the excited-state domain. π-Back-donation is found to be mainly determined by themore » metal site occupation, whereas the ligand hole instead influences σ-donation. Here, our results demonstrate how ultrafast resonant inelastic X-ray scattering can help characterize local charge distributions around catalytic metal centers in short-lived charge-transfer excited states, as a step toward future rationalization and tailoring of photocatalytic capabilities of transition-metal complexes.« less

Hydrogen and methanol exchange processes for (TMP)Rh-OCH3(CH3OH) in binary solutions of methanol and benzene.

PubMed

Sarkar, Sounak; Li, Shan; Wayland, Bradford B

2011-04-18

Tetramesityl porphinato rhodium(III) methoxide ((TMP)Rh-OCH(3)) binds with methanol in benzene to form a 1:1 methanol complex ((TMP)Rh-OCH(3)(CH(3)OH)) (1). Dynamic processes are observed to occur for the rhodium(III) methoxide methanol complex (1) that involve both hydrogen and methanol exchange. Hydrogen exchange between coordinated methanol and methoxide through methanol in solution results in an interchange of the environments for the non-equivalent porphyrin faces that contain methoxide and methanol ligands. Interchange of the environments of the coordinated methanol and methoxide sites in 1 produces interchange of the inequivalent mesityl o-CH(3) groups, but methanol ligand exchange occurs on one face of the porphyrin and the mesityl o-CH(3) groups remain inequivalent. Rate constants for dynamic processes are evaluated by full line shape analysis for the (1)H NMR of the mesityl o-CH(3) and high field methyl resonances of coordinated methanol and methoxide groups in 1. The rate constant for interchange of the inequivalent porphyrin faces is associated with hydrogen exchange between 1 and methanol in solution and is observed to increase regularly with the increase in the mole fraction of methanol. The rate constant for methanol ligand exchange between 1 and the solution varies with the solution composition and fluctuates in a manner that parallels the change in the activation energy for methanol diffusion which is a consequence of solution non-ideality from hydrogen bonded clusters.

A Pyridine Alkoxide Chelate Ligand That Promotes Both Unusually High Oxidation States and Water-Oxidation Catalysis

DOE PAGES

Michaelos, Thoe K.; Shopov, Dimitar Y.; Sinha, Shashi Bhushan; ...

2017-03-08

Here, water-oxidation catalysis is a critical bottleneck in the direct generation of solar fuels by artificial photosynthesis. Catalytic oxidation of difficult substrates such as water requires harsh conditions, so that the ligand must be designed both to stabilize high oxidation states of the metal center and to strenuously resist ligand degradation. Typical ligand choices either lack sufficient electron donor power or fail to stand up to the oxidizing conditions. This research on Ir-based water-oxidation catalysts (WOCs) has led us to identify a ligand, 2-(2'-pyridyl)-2-propanoate or “pyalk” that fulfills these requirements.

Functionalization of Cadmium Selenide Quantum Dots with Poly(ethylene glycol): Ligand Exchange, Surface Coverage, and Dispersion Stability.

PubMed

Wenger, Whitney Nowak; Bates, Frank S; Aydil, Eray S

2017-08-22

Semiconductor quantum dots synthesized using rapid mixing of precursors by injection into a hot solution of solvents and surfactants have surface ligands that sterically stabilize the dispersions in nonpolar solvents. Often, these ligands are exchanged to disperse the quantum dots in polar solvents, but quantitative studies of quantum dot surfaces before and after ligand exchange are scarce. We studied exchanging trioctylphosphine (TOP) and trioctylphosphine oxide (TOPO) ligands on as-synthesized CdSe quantum dots dispersed in hexane with a 2000 g/mol thiolated poly(ethylene glycol) (PEG) polymer. Using infrared spectroscopy we quantify the absolute surface concentration of TOP/TOPO and PEG ligands per unit area before and after ligand exchange. While 50-85% of the TOP/TOPO ligands are removed upon ligand exchange, only a few are replaced with PEG. Surprisingly, the remaining TOP/TOPO ligands outnumber the PEG ligands, but these few PEG ligands are sufficient to disperse the quantum dots in polar solvents such as chloroform, tetrahydrofuran, and water. Moreover, as-synthesized quantum dots once easily dispersed in hexane are no longer dispersible in nonpolar solvents after ligand exchange. A subtle coverage-dependent balance between attractive PEG-solvent interactions and repulsive TOP/TOPO-solvent interactions determines the dispersion stability.

On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein.

PubMed

Grosso, Marcos; Kalstein, Adrian; Parisi, Gustavo; Roitberg, Adrian E; Fernandez-Alberti, Sebastian

2015-06-28

The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use in combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data.

On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein

NASA Astrophysics Data System (ADS)

Grosso, Marcos; Kalstein, Adrian; Parisi, Gustavo; Roitberg, Adrian E.; Fernandez-Alberti, Sebastian

2015-06-01

The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use in combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data.

Covalent Coupling of Nanoparticles with Low-Density Functional Ligands to Surfaces via Click Chemistry

PubMed Central

Rianasari, Ina; de Jong, Michel P.; Huskens, Jurriaan; van der Wiel, Wilfred G.

2013-01-01

We demonstrate the application of the 1,3-dipolar cycloaddition (“click” reaction) to couple gold nanoparticles (Au NPs) functionalized with low densities of functional ligands. The ligand coverage on the citrate-stabilized Au NPs was adjusted by the ligand:Au surface atom ratio, while maintaining the colloidal stability of the Au NPs in aqueous solution. A procedure was developed to determine the driving forces governing the selectivity and reactivity of citrate-stabilized and ligand-functionalized Au NPs on patterned self-assembled monolayers. We observed selective and remarkably stable chemical bonding of the Au NPs to the complimentarily functionalized substrate areas, even when estimating that only 1–2 chemical bonds are formed between the particles and the substrate. PMID:23434666

Organic-inorganic hybrid perovskite quantum dots with high PLQY and enhanced carrier mobility through crystallinity control by solvent engineering and solid-state ligand exchange.

PubMed

Woo Choi, Jin; Woo, Hee Chul; Huang, Xiaoguang; Jung, Wan-Gil; Kim, Bong-Joong; Jeon, Sie-Wook; Yim, Sang-Youp; Lee, Jae-Suk; Lee, Chang-Lyoul

2018-05-22

The photoluminescence quantum yield (PLQY) and charge carrier mobility of organic-inorganic perovskite QDs were enhanced by the optimization of crystallinity and surface passivation as well as solid-state ligand exchange. The crystallinity of perovskite QDs was determined by the Effective solvent field (Esol) of various solvents for precipitation. The solvent with high Esol could more quickly countervail the localized field generated by the polar solvent, and it causes fast crystallization of the dissolved precursor, which results in poor crystallinity. The post-ligand adding process (PLAP) and post-ligand exchange process (PLEP) increase the PLQY of perovskite QDs by reducing non-radiative recombination and the density of surface defect states through surface passivation. Particularly, the post ligand exchange process (PLEP) in the solid-state improved the charge carrier mobility of perovskite QDs in addition to the PLQY enhancement. The ligand exchange with short alkyl chain length ligands could improve the packing density of perovskite QDs in films by reducing the inter-particle distance between perovskite QDs. The maximum hole mobility of 6.2 × 10-3 cm2 V-1 s-1, one order higher than that of pristine QDs without the PLEP, is obtained at perovskite QDs with hexyl ligands. By using PLEP treatment, compared to the pristine device, a 2.5 times higher current efficiency in perovskite QD-LEDs was achieved due to the improved charge carrier mobility and PLQY.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, R.; Wilton, R.; Cuff, M. E.

The tandem Per-Arnt-Sim (PAS) like sensors are commonly found in signal transduction proteins. The periplasmic solute binding protein (SBP) domains are found ubiquitously and are generally involved in solute transport. These domains are widely observed as parts of separate proteins but not within the same polypeptide chain. We report the structural and biochemical characterization of the extracellular ligand-binding receptor, Dret_0059 from Desulfohalobium retbaense DSM 5692, an organism isolated from the Retba salt lake in Senegal. The structure of Dret_0059 consists of a novel combination of SBP and TPAS sensor domains. The N-terminal region forms an SBP domain and the C-terminalmore » region folds into a tandem PAS-like domain structure. A ketoleucine moiety is bound to the SBP, whereas a cytosine molecule is bound in the distal PAS domain of the TPAS. The differential scanning flourimetry studies in solution support the ligands observed in the crystal structure. There are only two other proteins with this structural architecture in the non-redundant sequence data base and we predict that they too bind the same substrates. There is significant interaction between the SBP and TPAS domains, and it is quite conceivable that the binding of one ligand will have an effect on the binding of the other. Our attempts to remove the ligands bound to the protein during expression were not successful, therefore, it is not clear what the relative affects are. The genomic context of this receptor does not contain any protein components expected for transport function, hence, we suggest that Dret_0059 is likely involved in signal transduction and not in solute transport.« less

Cyclometalated gold(III) trioxadiborrin complexes: studies of the bonding and excited states.

PubMed

Ayoub, Nicholas A; Browne, Amberle R; Anderson, Bryce L; Gray, Thomas G

2016-03-07

Trioxadiborrins are chelating ligands that assemble in dehydration reactions of boronic acids. They are structurally related to β-diketonate ligands, but have a 2-charge. Little is known of the bonding properties of trioxadiborrin ligands. Presented here are density-functional theory (DFT) studies of cyclometalated gold(III) trioxadiborrins. Substituent effects are evaluated, and comparison is made to the cyclometalating 2-(4-tolyl)pyridine (tpy) ligand on gold. The tpy ligand binds more strongly than any trioxadiborrin ligand considered here, and the two ligands bind competitively to gold. The 1,3-diphenyl trioxadiborrin ligand of 1 has a larger absolute binding enthalpy to gold than its β-diketonate analogue. Conjugation between boron and aryl substituents delocalizes charge and attenuates the trioxadiborrin's binding capacity. Steric effects that disrupt conjugation between boron and aryl substituents cause the trioxadiborrin to chelate more tightly. Fragment bond orders are divided into in-plane and out-of-plane contributions for square planar 1. In-plane bonding accounts for 88% of bond order between (tpy)Au2+ and the trioxadiborrin ligand. Cyclometalated gold(III) trioxadiborrin complexes were previously shown to be phosphorescent. Spin-unrestricted triplet-state geometry optimizations find that the ten largest excited-state distortions all occur on the tpy ligand. A plot of spin density in triplet 1 shows spin to reside predominantly on tpy. The 77 K luminescence spectrum of 1 is reported here. Time-dependent DFT and configuration interaction singles calculations (corrected for doubles excitations) overestimate the emission energy by ∼ 0.12 eV.

New Equilibrium Models of Drug-Receptor Interactions Derived from Target-Mediated Drug Disposition.

PubMed

Peletier, Lambertus A; Gabrielsson, Johan

2018-05-14

In vivo analyses of pharmacological data are traditionally based on a closed system approach not incorporating turnover of target and ligand-target kinetics, but mainly focussing on ligand-target binding properties. This study incorporates information about target and ligand-target kinetics parallel to binding. In a previous paper, steady-state relationships between target- and ligand-target complex versus ligand exposure were derived and a new expression of in vivo potency was derived for a circulating target. This communication is extending the equilibrium relationships and in vivo potency expression for (i) two separate targets competing for one ligand, (ii) two different ligands competing for a single target and (iii) a single ligand-target interaction located in tissue. The derived expressions of the in vivo potencies will be useful both in drug-related discovery projects and mechanistic studies. The equilibrium states of two targets and one ligand may have implications in safety assessment, whilst the equilibrium states of two competing ligands for one target may cast light on when pharmacodynamic drug-drug interactions are important. The proposed equilibrium expressions for a peripherally located target may also be useful for small molecule interactions with extravascularly located targets. Including target turnover, ligand-target complex kinetics and binding properties in expressions of potency and efficacy will improve our understanding of within and between-individual (and across species) variability. The new expressions of potencies highlight the fact that the level of drug-induced target suppression is very much governed by target turnover properties rather than by the target expression level as such.

Square-antiprismatic eight-coordinate complexes of divalent first-row transition metal cations: a density functional theory exploration of the electronic-structural landscape.

PubMed

Conradie, Jeanet; Patra, Ashis K; Harrop, Todd C; Ghosh, Abhik

2015-02-16

Density functional theory (in the form of the PW91, BP86, OLYP, and B3LYP exchange-correlation functionals) has been used to map out the low-energy states of a series of eight-coordinate square-antiprismatic (D2d) first-row transition metal complexes, involving Mn(II), Fe(II), Co(II), Ni(II), and Cu(II), along with a pair of tetradentate N4 ligands. Of the five complexes, the Mn(II) and Fe(II) complexes have been synthesized and characterized structurally and spectroscopically, whereas the other three are as yet unknown. Each N4 ligand consists of a pair of terminal imidazole units linked by an o-phenylenediimine unit. The imidazole units are the strongest ligands in these complexes and dictate the spatial disposition of the metal three-dimensional orbitals. Thus, the dx(2)-y(2) orbital, whose lobes point directly at the coordinating imidazole nitrogens, has the highest orbital energy among the five d orbitals, whereas the dxy orbital has the lowest orbital energy. In general, the following orbital ordering (in order of increasing orbital energy) was found to be operative: dxy < dxz = dyz ≤ dz(2) < dx(2)-y(2). The square-antiprism geometry does not lead to large energy gaps between the d orbitals, which leads to an S = 2 ground state for the Fe(II) complex. Nevertheless, the dxy orbital has significantly lower energy relative to that of the dxz and dyz orbitals. Accordingly, the ground state of the Fe(II) complex corresponds unambiguously to a dxy(2)dxz(1)dyz(1)dz(2)(1)dx(2)-y(2)(1) electronic configuration. Unsurprisingly, the Mn(II) complex has an S = 5/2 ground state and no low-energy d-d excited states within 1.0 eV of the ground state. The Co(II) complex, on the other hand, has both a low-lying S = 1/2 state and multiple low-energy S = 3/2 states. Very long metal-nitrogen bonds are predicted for the Ni(II) and Cu(II) complexes; these bonds may be too fragile to survive in solution or in the solid state, and the complexes may therefore not be isolable. Overall, the different exchange-correlation functionals provided a qualitatively consistent and plausible picture of the low-energy d-d excited states of the complexes.

Platinum CCC-NHC benzimidazolyl pincer complexes: synthesis, characterization, photostability, and theoretical investigation of a blue-green emitter.

PubMed

Huckaba, Aron J; Cao, Bei; Hollis, T Keith; Valle, Henry U; Kelly, John T; Hammer, Nathan I; Oliver, Allen G; Webster, Charles Edwin

2013-06-28

The recently reported metallation/transmetallation route for the synthesis of CCC-bis(NHC) pincer ligand architectures was extended to 1,3-bis(3'-(trimethylsilylmethyl)-benzimidizol-1'-yl)benzene. The precursor was metallated with Zr(NMe2)4 and transmetallated to Pt using [Pt(COD)Cl2]. This Pt complex was found to resist photobleaching under UV irradiation in ambient conditions. Density functional theory (DFT) computations were used to generate the emission spectrum of the complex and reveal that this spectrum is the result of a transition from the triplet excited state (T1) to the ground state (S0). The Pt complex's molecular structure was determined by X-ray crystallography. The UV-vis absorption and emission spectra in solution and the solid-state emission spectra are reported. The solid-state photostability data and the radiative lifetime is also reported.

Spectroscopic and computational insight into the activation of O2 by the mononuclear Cu center in polysaccharide monooxygenases.

PubMed

Kjaergaard, Christian H; Qayyum, Munzarin F; Wong, Shaun D; Xu, Feng; Hemsworth, Glyn R; Walton, Daniel J; Young, Nigel A; Davies, Gideon J; Walton, Paul H; Johansen, Katja Salomon; Hodgson, Keith O; Hedman, Britt; Solomon, Edward I

2014-06-17

Strategies for O2 activation by copper enzymes were recently expanded to include mononuclear Cu sites, with the discovery of the copper-dependent polysaccharide monooxygenases, also classified as auxiliary-activity enzymes 9-11 (AA9-11). These enzymes are finding considerable use in industrial biofuel production. Crystal structures of polysaccharide monooxygenases have emerged, but experimental studies are yet to determine the solution structure of the Cu site and how this relates to reactivity. From X-ray absorption near edge structure and extended X-ray absorption fine structure spectroscopies, we observed a change from four-coordinate Cu(II) to three-coordinate Cu(I) of the active site in solution, where three protein-derived nitrogen ligands coordinate the Cu in both redox states, and a labile hydroxide ligand is lost upon reduction. The spectroscopic data allowed for density functional theory calculations of an enzyme active site model, where the optimized Cu(I) and (II) structures were consistent with the experimental data. The O2 reactivity of the Cu(I) site was probed by EPR and stopped-flow absorption spectroscopies, and a rapid one-electron reduction of O2 and regeneration of the resting Cu(II) enzyme were observed. This reactivity was evaluated computationally, and by calibration to Cu-superoxide model complexes, formation of an end-on Cu-AA9-superoxide species was found to be thermodynamically favored. We discuss how this thermodynamically difficult one-electron reduction of O2 is enabled by the unique protein structure where two nitrogen ligands from His1 dictate formation of a T-shaped Cu(I) site, which provides an open coordination position for strong O2 binding with very little reorganization energy.

Structural determinants of ligand binding in the ternary complex of human ileal bile acid binding protein with glycocholate and glycochenodeoxycholate obtained from solution NMR.

PubMed

Horváth, Gergő; Bencsura, Ákos; Simon, Ágnes; Tochtrop, Gregory P; DeKoster, Gregory T; Covey, Douglas F; Cistola, David P; Toke, Orsolya

2016-02-01

Besides aiding digestion, bile salts are important signal molecules exhibiting a regulatory role in metabolic processes. Human ileal bile acid binding protein (I-BABP) is an intracellular carrier of bile salts in the epithelial cells of the distal small intestine and has a key role in the enterohepatic circulation of bile salts. Positive binding cooperativity combined with site selectivity of glycocholate and glycochenodeoxycholate, the two most abundant bile salts in the human body, make human I-BABP a unique member of the family of intracellular lipid binding proteins. Solution NMR structure of the ternary complex of human I-BABP with glycocholate and glycochenodeoxycholate reveals an extensive network of hydrogen bonds and hydrophobic interactions stabilizing the bound bile salts. Conformational changes accompanying bile salt binding affects four major regions in the protein including the C/D, E/F and G/H loops as well as the helical segment. Most of these protein regions coincide with a previously described network of millisecond time scale fluctuations in the apo protein, a motion absent in the bound state. Comparison of the heterotypic doubly ligated complex with the unligated form provides further evidence of a conformation selection mechanism of ligand entry. Structural and dynamic aspects of human I-BABP-bile salt interaction are discussed and compared with characteristics of ligand binding in other members of the intracellular lipid binding protein family. The coordinates of the 10 lowest energy structures of the human I-BABP : GCDA : GCA complex as well as the distance restraints used to calculate the final ensemble have been deposited in the Brookhaven Protein Data Bank with accession number 2MM3. © 2015 FEBS.

Mixed-ligand approach to design of heterometallic single-source precursors with discrete molecular structure.

PubMed

Lieberman, Craig M; Navulla, Anantharamulu; Zhang, Haitao; Filatov, Alexander S; Dikarev, Evgeny V

2014-05-05

Heterometallic single-source precursors for the Pb/Fe = 1:1 oxide materials, PbFe(β-dik)4 (β-dik = hexafluoroacetylacetonate (hfac, 1), acetylacetonate (acac, 2), and trifluoroacetylacetonate (tfac, 4)), have been isolated by three different solid-state synthetic methods. The crystal structures of heterometallic diketonates 1, 2, and 4 were found to contain polymeric chains built on alternating [Fe(β-dik)2] and [Pb(β-dik)2] units that are held together by bridging M-O interactions. Heterometallic precursors are highly volatile, but soluble only in coordinating solvents, in which they dissociate into solvated homometallic fragments. In order to design the heterometallic precursor with a proper metal/metal ratio and with a discrete molecular structure, we used a combination of two different diketonate ligands. Heteroleptic complex Pb2Fe2(hfac)6(acac)2 (5) has been obtained by optimized stoichiometric reaction of an addition of homo-Fe(acac)2 to heterometallic Pb2Fe(hfac)6 (3) diketonate that can be run in solution on a high scale. The combination of two ligands with electron-withdrawing and electron-donating groups allows changing the connectivity pattern within the heterometallic assembly and yields the precursor with a discrete tetranuclear structure. In accord with its molecular structure, heteroleptic complex 5 is soluble even in noncoordinating solvents and was found to retain its heterometallic structure in solution. Thermal decomposition of heterometallic precursors in air at 750 °C resulted in the target Pb2Fe2O5 oxide, a prospective multiferroic material. Prolonging the annealing time or increasing the decomposition temperature leads to another phase-pure lead-iron oxide PbFe12O19 that is a representative of the important family of magnetic hexaferrites.

pi-Selective stationary phases: (II) Adsorption behavior of substituted aromatic compounds on n-alkyl-phenyl stationary phases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gritti, Fabrice; Guiochon, Georges A; Mayfield, Kirsty

2010-01-01

The frontal analysis method was used to measure the adsorption isotherms of phenol, 4-chlorophenol, p-cresol, 4-methoxyphenol and caffeine on a series of columns packed with home-made alkyl-phenyl bonded silica particles. These ligands consist of a phenyl ring tethered to the silica support via a carbon chain of length ranging from 0 to 4 atoms. The adsorption isotherm models that fit best to the data account for solute-solute interactions that are likely caused by p-p interactions occurring between aromatic compounds and the phenyl group of the ligand. These interactions are the dominant factor responsible for the separation of low molecular weightmore » aromatic compounds on these phenyl-type stationary phases. The saturation capacities depend on whether the spacer of the ligands have an even or an odd number of carbon atoms, with the even alkyl chain lengths having a greater saturation capacity than the odd alkyl chain lengths. The trends in the adsorption equilibrium constant are also significantly different for the even and the odd chain length ligands.« less

Improved Accuracy of Low Affinity Protein-Ligand Equilibrium Dissociation Constants Directly Determined by Electrospray Ionization Mass Spectrometry

NASA Astrophysics Data System (ADS)

Jaquillard, Lucie; Saab, Fabienne; Schoentgen, Françoise; Cadene, Martine

2012-05-01

There is continued interest in the determination by ESI-MS of equilibrium dissociation constants (KD) that accurately reflect the affinity of a protein-ligand complex in solution. Issues in the measurement of KD are compounded in the case of low affinity complexes. Here we present a KD measurement method and corresponding mathematical model dealing with both gas-phase dissociation (GPD) and aggregation. To this end, a rational mathematical correction of GPD (fsat) is combined with the development of an experimental protocol to deal with gas-phase aggregation. A guide to apply the method to noncovalent protein-ligand systems according to their kinetic behavior is provided. The approach is validated by comparing the KD values determined by this method with in-solution KD literature values. The influence of the type of molecular interactions and instrumental setup on fsat is examined as a first step towards a fine dissection of factors affecting GPD. The method can be reliably applied to a wide array of low affinity systems without the need for a reference ligand or protein.

A nickel tripeptide as a metallodithiolate ligand anchor for resin-bound organometallics.

PubMed

Green, Kayla N; Jeffery, Stephen P; Reibenspies, Joseph H; Darensbourg, Marcetta Y

2006-05-17

The molecular structure of the acetyl CoA synthase enzyme has clarified the role of individual nickel atoms in the dinickel active site which mediates C-C and C-S coupling reactions. The NiN2S2 portion of the biocatalyst (N2S2 = a cysteine-glycine-cysteine or CGC4- tripeptide ligand) serves as an S-donor ligand comparable to classical bidentate ligands operative in organometallic chemistry, ligating the second nickel which is redox and catalytically active. Inspired by this biological catalyst, the synthesis of NiN2S2 metalloligands, including the solid-phase synthesis of resin-bound Ni(CGC)2-, and sulfur-based derivatization with W(CO)5 and Rh(CO)2+ have been carried out. Through comparison to analogous well-characterized, solution-phase complexes, Attenuated Total Reflectance FTIR spectroscopy establishes the presence of unique heterobimetallic complexes, of the form [Ni(CGC)]M(CO)x, both in solution and immobilized on resin beads. This work provides the initial step toward exploitation of such an evolutionarily optimized nickel peptide as a solid support anchor for hybrid bioinorganic-organometallic catalysts.

Water-soluble platinum nanoparticles stabilized by sulfonated N-heterocyclic carbenes: influence of the synthetic approach.

PubMed

Baquero, Edwin A; Tricard, Simon; Coppel, Yannick; Flores, Juan C; Chaudret, Bruno; de Jesús, Ernesto

2018-03-28

The synthesis of metal nanoparticles (NPs) under controlled conditions in water remains a challenge in nanochemistry. Two different approaches to obtain platinum NPs, which involve the treatment of aqueous solutions of preformed sulfonated (NHC)Pt(ii) dimethyl complexes with carbon monoxide, and of (NHC)Pt(0) diolefin complexes with dihydrogen (NHC = N-heterocyclic carbene), are disclosed here. The resulting NPs were found to be highly stable in water under air for an indefinite time period. Coordination of the NHC ligands to the platinum surface via the carbenic carbon was monitored by solid-state NMR spectroscopy, and the presence of a platinum-carbon bond was unambiguously evidenced by the determination of a 13 C- 195 Pt coupling constant (1106 and 1050 Hz for NPs containing 13 C labeled-NHC ligands and prepared under CO and H 2 , respectively). The coordination of CO to the (NHC)Pt(ii) precursors prior to formation of the NPs was confirmed by NMR spectroscopy. When using a disulfonated NHC ligand, a second coordination sphere containing bis(NHC)Pt(ii) complexes is described. Under CO, the formation of NPs was found to be slower than in a previously reported thermal method (Angew. Chem., Int. Ed., 2014, 53, 13220-13224), but led to NPs of similar sizes, whereas under H 2 , the synthesis of platinum NPs progressed even more slowly and produced larger NPs. In addition to the influence of the synthetic approach, the present study highlights the importance of ligand design for NP stabilization.

The coordination behaviour of ferrocene-based pyridylphosphine ligands towards Zn(II), Cd(II) and Hg(II).

PubMed

Siemeling, Ulrich; Klemann, Thorsten; Bruhn, Clemens; Schulz, Jiří; Štěpnička, Petr

2011-05-07

The reaction of Group 12 metal dihalides MX(2) with the P,N-ligands [Fe(C(5)H(4)-PPh(2))(C(5)H(4)-2-py)] (1) (2-py = pyrid-2-yl), [Fe(C(5)H(4)-PPh(2))(C(5)H(4)-CH(2)-2-py)] (2) and [Fe(C(5)H(4)-PPh(2))(C(5)H(4)-3-py)] (3) (3-py = pyrid-3-yl) was investigated. For a 1 : 1 molar ratio of MX(2) and the respective ligand, three structure types were found in the solid state, viz. chelate, cyclic dimer and chain-like coordination polymer. The M(II) coordination environment is distorted pseudo-tetrahedral in each case. The P-M-N angle is much larger in the chelates (≥119°) than in the ligand-bridged structures (≤109°). 1 prefers the formation of chelates [MX(2)(1-κ(2)N,P)]. 3 forms coordination polymers [MX(2)(μ-3)](n). With the more flexible 2 all three structure types can occur. Dynamic coordination equilibria were observed in solution for the molecular complexes obtained with 1 and 2. NMR data indicate that the N- and P-donor sites interact most strongly with Zn(II) and Hg(II), respectively. While the formation of bis(phosphine)mercury complexes (soft-soft) was easily achieved, no bis(pyridine)zinc complex (borderline-borderline) could be obtained, which is surprising in view of the HSAB principle.

Chemical bonding in aqueous hexacyano cobaltate from photon- and electron-detection perspectives

PubMed Central

Lalithambika, Sreeju Sreekantan Nair; Atak, Kaan; Seidel, Robert; Neubauer, Antje; Brandenburg, Tim; Xiao, Jie; Winter, Bernd; Aziz, Emad F.

2017-01-01

The electronic structure of the [Co(CN)6]3− complex dissolved in water is studied using X-ray spectroscopy techniques. By combining electron and photon detection methods from the solutions ionized or excited by soft X-rays we experimentally identify chemical bonding between the metal center and the CN ligand. Non-resonant photoelectron spectroscopy provides solute electron binding energies, and nitrogen 1 s and cobalt 2p resonant core-level photoelectron spectroscopy identifies overlap between metal and ligand orbitals. By probing resonances we are able to qualitatively determine the ligand versus metal character of the respective occupied and non-occupied orbitals, purely by experiment. For the same excitations we also detect the emitted X-rays, yielding the complementary resonant inelastic X-ray scattering spectra. For a quantitative interpretation of the spectra, we perform theoretical electronic-structure calculations. The latter provide both orbital energies and orbital character which are found to be in good agreement with experimental energies and with experimentally inferred orbital mixing. We also report calculated X-ray absorption spectra, which in conjunction with our orbital-structure analysis, enables us to quantify various bonding interactions with a particular focus on the water-solvent – ligand interaction and the strength of π-backbonding between metal and ligand. PMID:28098216

Dramatic enhancement of enzymatic activity in organic solvents by lyoprotectants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dabulis, K.; Klibanov, A.M.

1993-03-05

When seven different hydrolytic enzymes (four proteases and three lipases) were lyophilized from aqueous solution containing a ligand, N-Ac-L-Phe-NH[sub 2], their catalytic activity in anhydrous solvents was far greater (one to two orders of magnitude) than that of the enzymes lyophilized without the ligand. This ligand-induced activation was expressed regardless of whether the substrate employed in organic solvents structurally resembled the ligand. Furthermore, nonligand lyoprotectants [sorbitol, other sugars, and poly(ethylene glycol)] also dramatically enhanced enzymatic activity in anhydrous solvents when present in enzyme aqueous solution prior to lyophilization. The effects of the ligand and of the lyoprotectants were nonadditive, suggestingmore » the same mechanism of action. Excipient-activated and nonactivated enzymes exhibited identical activities in water. Also, addition of the excipients directly to suspensions of nonactivated enzymes in organic solvents had no appreciable effect on catalytic activity. These observations indicate that the mechanism of the excipient-induced activation is based on the ability of the excipients to alleviate reversible denaturation of enzymes upon lyophilization. Activity enhancement induced by the excipients is displayed even after their removal by washing enzymes with anhydrous solvents. Subtilisin Carlsberg, lyophilized with sorbitol, was found to be a much more efficient practical catalyst than its regular' counterpart.« less

Ligand-induced Epitope Masking

PubMed Central

Mould, A. Paul; Askari, Janet A.; Byron, Adam; Takada, Yoshikazu; Jowitt, Thomas A.; Humphries, Martin J.

2016-01-01

We previously demonstrated that Arg-Gly-Asp (RGD)-containing ligand-mimetic inhibitors of integrins are unable to dissociate pre-formed integrin-fibronectin complexes (IFCs). These observations suggested that amino acid residues involved in integrin-fibronectin binding become obscured in the ligand-occupied state. Because the epitopes of some function-blocking anti-integrin monoclonal antibodies (mAbs) lie near the ligand-binding pocket, it follows that the epitopes of these mAbs may become shielded in the ligand-occupied state. Here, we tested whether function-blocking mAbs directed against α5β1 can interact with the integrin after it forms a complex with an RGD-containing fragment of fibronectin. We showed that the anti-α5 subunit mAbs JBS5, SNAKA52, 16, and P1D6 failed to disrupt IFCs and hence appeared unable to bind to the ligand-occupied state. In contrast, the allosteric anti-β1 subunit mAbs 13, 4B4, and AIIB2 could dissociate IFCs and therefore were able to interact with the ligand-bound state. However, another class of function-blocking anti-β1 mAbs, exemplified by Lia1/2, could not disrupt IFCs. This second class of mAbs was also distinguished from 13, 4B4, and AIIB2 by their ability to induce homotypic cell aggregation. Although the epitope of Lia1/2 was closely overlapping with those of 13, 4B4, and AIIB2, it appeared to lie closer to the ligand-binding pocket. A new model of the α5β1-fibronectin complex supports our hypothesis that the epitopes of mAbs that fail to bind to the ligand-occupied state lie within, or very close to, the integrin-fibronectin interface. Importantly, our findings imply that the efficacy of some therapeutic anti-integrin mAbs could be limited by epitope masking. PMID:27484800

Harvesting solar energy by means of charge-separating nanocrystals and their solids.

PubMed

Diederich, Geoffrey; O'Connor, Timothy; Moroz, Pavel; Kinder, Erich; Kohn, Elena; Perera, Dimuthu; Lorek, Ryan; Lambright, Scott; Imboden, Martene; Zamkov, Mikhail

2012-08-23

Conjoining different semiconductor materials in a single nano-composite provides synthetic means for the development of novel optoelectronic materials offering a superior control over the spatial distribution of charge carriers across material interfaces. As this study demonstrates, a combination of donor-acceptor nanocrystal (NC) domains in a single nanoparticle can lead to the realization of efficient photocatalytic materials, while a layered assembly of donor- and acceptor-like nanocrystals films gives rise to photovoltaic materials. Initially the paper focuses on the synthesis of composite inorganic nanocrystals, comprising linearly stacked ZnSe, CdS, and Pt domains, which jointly promote photoinduced charge separation. These structures are used in aqueous solutions for the photocatalysis of water under solar radiation, resulting in the production of H2 gas. To enhance the photoinduced separation of charges, a nanorod morphology with a linear gradient originating from an intrinsic electric field is used. The inter-domain energetics are then optimized to drive photogenerated electrons toward the Pt catalytic site while expelling the holes to the surface of ZnSe domains for sacrificial regeneration (via methanol). Here we show that the only efficient way to produce hydrogen is to use electron-donating ligands to passivate the surface states by tuning the energy level alignment at the semiconductor-ligand interface. Stable and efficient reduction of water is allowed by these ligands due to the fact that they fill vacancies in the valence band of the semiconductor domain, preventing energetic holes from degrading it. Specifically, we show that the energy of the hole is transferred to the ligand moiety, leaving the semiconductor domain functional. This enables us to return the entire nanocrystal-ligand system to a functional state, when the ligands are degraded, by simply adding fresh ligands to the system. To promote a photovoltaic charge separation, we use a composite two-layer solid of PbS and TiO2 films. In this configuration, photoinduced electrons are injected into TiO2 and are subsequently picked up by an FTO electrode, while holes are channeled to a Au electrode via PbS layer. To develop the latter we introduce a Semiconductor Matrix Encapsulated Nanocrystal Arrays (SMENA) strategy, which allows bonding PbS NCs into the surrounding matrix of CdS semiconductor. As a result, fabricated solids exhibit excellent thermal stability, attributed to the heteroepitaxial structure of nanocrystal-matrix interfaces, and show compelling light-harvesting performance in prototype solar cells.

Synthesis, characterization, crystal structure and HSA binding of two new N,O,O-donor Schiff-base ligands derived from dihydroxybenzaldehyde and tert-butylamine

NASA Astrophysics Data System (ADS)

Khosravi, Iman; Hosseini, Farnaz; Khorshidifard, Mahsa; Sahihi, Mehdi; Rudbari, Hadi Amiri

2016-09-01

Two new o-hydroxy Schiff-bases compounds, L1 and L2, were derived from the 1:1 M condensation of 2,3-dihydroxybenzaldehyde and 2,4-dihydroxybenzaldehyde with tert-butylamine and were characterized by elemental analysis, FT-IR, 1H and 13C NMR spectroscopies. The crystal structure of L2 was also determined by single crystal X-ray analysis. The crystal structure of L2 showed that the compound exists as a zwitterionic form in the solid state, with the H atom of the phenol group being transferred to the imine N atom. It adopts an E configuration about the central Cdbnd N double bond. Furthermore, binding of these Schiff base ligands to Human Serum Albumin (HSA) was investigated by fluorescence quenching, absorption spectroscopy, molecular docking and molecular dynamics (MD) simulation methods. The fluorescence emission of HSA was quenched by ligands. Also, suitable models were used to analyze the UV-vis absorption spectroscopy data for titration of HSA solution by various amounts of Schiff bases. The spectroscopic studies revealed that these Schiff bases formed 1:1 complex with HSA. Energy transfer mechanism of quenching was discussed and the values of 3.35 and 1.57 nm as the mean distances between the bound ligands and the HSA were calculated for L1 and L2, respectively. Molecular docking results indicated that the main active binding site for these Schiff bases ligands is in subdomain IB. Moreover, MD simulation results suggested that this Schiff base complex can interact with HSA, with a slight modification of its tertiary structure.

Investigation of the Ligand–Nanoparticle Interface: A Cryogenic Approach for Preserving Surface Chemistry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karakoti, Ajay S.; Yang, Ping; Wang, Weina

Ligand functionalized nanoparticles have replaced bare nanoparticles from most biological applications. These applications require tight control over size and stability of nanoparticles in aqueous medium. Understanding the mechanism of interaction of nanoparticle surfaces with functional groups of different organic ligands such as carboxylic acids is confounding despite the two decades of research on nanoparticles because of the inability to characterize their surfaces in their immediate environment. Often the surface interaction is understood by correlating the information available, in a piecemeal approach, from surface sensitive spectroscopic information of ligands and the bulk and surface information of nanoparticles. In present study wemore » report the direct interaction of 5-7 nm cerium oxide nanoparticles surface with acetic acid. In-situ XPS study was carried out by freezing the aqueous solution of nanoparticles to liquid nitrogen temperatures. Analysis of data collected concurrently from the ligands as well as functionalized frozen cerium oxide nanoparticles show that the acetic acid binds to the ceria surface in both dissociated and molecular state with equal population over the surface. The cerium oxide surface was populated predominantly with Ce4+ ions consistent with the thermal hydrolysis synthesis. DFT calculations reveal that the acetate ions bind more strongly to the cerium oxide nanoparticles as compared to the water and can replace the hydration sphere of nanoparticles resulting in high acetate/acetic surface coverage. These findings reveal molecular level interaction between the nanoparticle surfaces and ligands giving a better understanding of how materials behave in their immediate aqueous environment. This study also proposes a simple and elegant methodology to directly study the surface functional groups attached to nanoparticles in their immediate aqueous environment.« less

Effects of sulfate ligand on uranyl carbonato surface species on ferrihydrite surfaces

USGS Publications Warehouse

Arai, Yuji; Fuller, C.C.

2012-01-01

Understanding uranium (U) sorption processes in permeable reactive barriers (PRB) are critical in modeling reactive transport for evaluating PRB performance at the Fry Canyon demonstration site in Utah, USA. To gain insight into the U sequestration mechanism in the amorphous ferric oxyhydroxide (AFO)-coated gravel PRB, U(VI) sorption processes on ferrihydrite surfaces were studied in 0.01 M Na2SO4 solutions to simulate the major chemical composition of U-contaminatedgroundwater (i.e., [SO42-]~13 mM L-1) at the site. Uranyl sorption was greater at pH 7.5 than that at pH 4 in both air- and 2% pCO2-equilibrated systems. While there were negligible effects of sulfate ligands on the pH-dependent U(VI) sorption (<24 h) in both systems, X-ray absorption spectroscopy (XAS) analysis showed sulfate ligand associated U(VI) surface species at the ferrihydrite–water interface. In air-equilibrated systems, binary and mono-sulfate U(VI) ternary surface species co-existed at pH 5.43. At pH 6.55–7.83, a mixture of mono-sulfate and bis-carbonato U(VI) ternary surface species became more important. At 2% pCO2, there was no contribution of sulfate ligands on the U(VI) ternary surface species. Instead, a mixture of bis-carbonato inner-sphere (38%) and tris-carbonato outer-sphere U(VI) ternary surface species (62%) was found at pH 7.62. The study suggests that the competitive ligand (bicarbonate and sulfate) coordination on U(VI) surface species might be important in evaluating the U solid-state speciation in the AFO PRB at the study site where pCO2 fluctuates between 1 and 2 pCO2%.

Rational design of dicarboxylato platinum(II) complexes with purine-mimetic ligands as novel anticancer agents.

PubMed

Hoffmann, Kamil; Wiśniewska, Joanna; Wojtczak, Andrzej; Sitkowski, Jerzy; Denslow, Agnieszka; Wietrzyk, Joanna; Jakubowski, Mateusz; Łakomska, Iwona

2017-07-01

Six novel platinum(II) complexes containing purine-mimetic ligands (5,7-dimethyl-1,2,4-triazolo[1,5-a]pyrimidine (dmtp), 7-isobutyl-5-methyl-1,2,4-triazolo[1,5-a]pyrimidine (ibmtp), 5,7-ditertbutyl-1,2,4-triazolo[1,5-a]pyrimidine (dbtp)) and dicarboxylato ligands (glutarato (glut) or cyclobutane-1,1-dicarboxylato (CBDC)) have been prepared and characterized with multinuclear magnetic resonance ( 1 H, 13 C, 15 N, 195 Pt) NMR, infrared (IR) and X-ray crystallography. Spectroscopic data in solid state and in solution unambiguously confirm the square-planar geometry of Pt(II) with two monodentate N3-bonded 5,7-disubstituted-1,2,4-triazolo[1,5-a]pyrimidine ligands and one O-chelating dicarboxylato ligand. Next, the effect of all the platinum(II) compounds on the viability of normal or cancer cells and their putative mechanisms of action have been investigated. Of the studied platinum(II) complexes, two ([Pt(glut)(dbtp) 2 ] and [Pt(CBDC)(dbtp) 2 ]) overcame the cisplatin resistance in human ovarian tumor cells (A2780cis or OVCAR-3) and arrested the cell cycle at S phase in mice mammary gland cancer cells (4T1), which indicates a mechanism of action different from that of cisplatin. Interestingly, preliminary in vivo toxicity assays revealed that both compounds tested in mice ([Pt(glut)(dbtp) 2 ] 3 and [Pt(CBDC)(dbtp) 2 ] 6) were less toxic in vivo than cisplatin or oxaliplatin. Additionally, compound 6 did not cause myelosuppression and showed over fivefold less accumulation in the liver than its glutarato analog 3. Copyright © 2017 Elsevier Inc. All rights reserved.

Stabilization of Functional Recombinant Cannabinoid Receptor CB2 in Detergent Micelles and Lipid Bilayers

PubMed Central

Vukoti, Krishna; Kimura, Tomohiro; Macke, Laura; Gawrisch, Klaus; Yeliseev, Alexei

2012-01-01

Elucidation of the molecular mechanisms of activation of G protein-coupled receptors (GPCRs) is among the most challenging tasks for modern membrane biology. For studies by high resolution analytical methods, these integral membrane receptors have to be expressed in large quantities, solubilized from cell membranes and purified in detergent micelles, which may result in a severe destabilization and a loss of function. Here, we report insights into differential effects of detergents, lipids and cannabinoid ligands on stability of the recombinant cannabinoid receptor CB2, and provide guidelines for preparation and handling of the fully functional receptor suitable for a wide array of downstream applications. While we previously described the expression in Escherichia coli, purification and liposome-reconstitution of multi-milligram quantities of CB2, here we report an efficient stabilization of the recombinant receptor in micelles - crucial for functional and structural characterization. The effects of detergents, lipids and specific ligands on structural stability of CB2 were assessed by studying activation of G proteins by the purified receptor reconstituted into liposomes. Functional structure of the ligand binding pocket of the receptor was confirmed by binding of 2H-labeled ligand measured by solid-state NMR. We demonstrate that a concerted action of an anionic cholesterol derivative, cholesteryl hemisuccinate (CHS) and high affinity cannabinoid ligands CP-55,940 or SR-144,528 are required for efficient stabilization of the functional fold of CB2 in dodecyl maltoside (DDM)/CHAPS detergent solutions. Similar to CHS, the negatively charged phospholipids with the serine headgroup (PS) exerted significant stabilizing effects in micelles while uncharged phospholipids were not effective. The purified CB2 reconstituted into lipid bilayers retained functionality for up to several weeks enabling high resolution structural studies of this GPCR at physiologically relevant conditions. PMID:23056277

Effects of sulfate ligand on uranyl carbonato surface species on ferrihydrite surfaces.

PubMed

Arai, Yuji; Fuller, C C

2012-01-01

Understanding uranium (U) sorption processes in permeable reactive barriers (PRB) are critical in modeling reactive transport for evaluating PRB performance at the Fry Canyon demonstration site in Utah, USA. To gain insight into the U sequestration mechanism in the amorphous ferric oxyhydroxide (AFO)-coated gravel PRB, U(VI) sorption processes on ferrihydrite surfaces were studied in 0.01 M Na(2)SO(4) solutions to simulate the major chemical composition of U-contaminated groundwater (i.e., [SO(4)(2-)] ~13 mM L(-1)) at the site. Uranyl sorption was greater at pH 7.5 than that at pH 4 in both air- and 2% pCO(2)-equilibrated systems. While there were negligible effects of sulfate ligands on the pH-dependent U(VI) sorption (<24 h) in both systems, X-ray absorption spectroscopy (XAS) analysis showed sulfate ligand associated U(VI) surface species at the ferrihydrite-water interface. In air-equilibrated systems, binary and mono-sulfate U(VI) ternary surface species co-existed at pH 5.43. At pH 6.55-7.83, a mixture of mono-sulfate and bis-carbonato U(VI) ternary surface species became more important. At 2% pCO(2), there was no contribution of sulfate ligands on the U(VI) ternary surface species. Instead, a mixture of bis-carbonato inner-sphere (38%) and tris-carbonato outer-sphere U(VI) ternary surface species (62%) was found at pH 7.62. The study suggests that the competitive ligand (bicarbonate and sulfate) coordination on U(VI) surface species might be important in evaluating the U solid-state speciation in the AFO PRB at the study site where pCO(2) fluctuates between 1 and 2 pCO(2)%. Copyright © 2011 Elsevier Inc. All rights reserved.

Ligand-Induced Stabilization of a Duplex-like Architecture Is Crucial for the Switching Mechanism of the SAM-III Riboswitch.

PubMed

Suresh, Gorle; Srinivasan, Harini; Nanda, Shivani; Priyakumar, U Deva

2016-06-21

Riboswitches are structured RNA motifs that control gene expression by sensing the concentrations of specific metabolites and make up a promising new class of antibiotic targets. S-Adenosylmethionine (SAM)-III riboswitch, mainly found in lactic acid bacteria, is involved in regulating methionine and SAM biosynthetic pathways. SAM-III riboswitch regulates the gene expression by switching the translation process on and off with respect to the absence and presence of the SAM ligand, respectively. In this study, an attempt is made to understand the key conformational transitions involved in ligand binding using atomistic molecular dynamics (MD) simulations performed in an explicit solvent environment. G26 is found to recognize the SAM ligand by forming hydrogen bonds, whereas the absence of the ligand leads to opening of the binding pocket. Consistent with experimental results, the absence of the SAM ligand weakens the base pairing interactions between the nucleobases that are part of the Shine-Dalgarno (SD) and anti-Shine-Dalgarno (aSD) sequences, which in turn facilitates recognition of the SD sequence by ribosomes. Detailed analysis reveals that a duplex-like structure formed by nucleotides from different parts of the RNA and the adenine base of the ligand is crucial for the stability of the completely folded state in the presence of the ligand. Previous experimental studies have shown that the SAM-III riboswitch exists in equilibrium between the unfolded and partially folded states in the absence of the ligand, which completely folds upon binding of the ligand. Comparison of the results presented here to the available experimental data indicates the structures obtained using the MD simulations resemble the partially folded state. Thus, this study provides a detailed understanding of the fully and partially folded structures of the SAM-III riboswitch in the presence and absence of the ligand, respectively. This study hypothesizes a dual role for the SAM ligand, which facilitates conformational switching between partially and fully folded states by forming a stable duplex-like structure and strengthening the interactions between SD and aSD nucleotides.

Syntheses, structures and luminescent properties of zero-/two-dimensional Cd(II) and Eu(III) complexes

NASA Astrophysics Data System (ADS)

Fan, Rui-Qing; Wang, Li-Yuan; Wang, Ping; Chen, Hong; Sun, Cun-fa; Yang, Yu-Lin; Su, Qing

2012-12-01

Three metal-organic complexes Cd(HBIDC)(phen)2·4H2O (1), [Cd(BIC)(phen)]n (2) and {[Eu(HBIDC)(H2BIDC)(H2O)]·H2O}n (3) (H3BIDC=benzimidazole-5,6-dicarboxylic acid, H2BIC=benzimidazole-6-carboxylic acid, phen=1,10-phenanthroline) have been synthesized under hydro(solvo)thermal conditions and structurally characterized by elemental analysis, IR spectrum, and single-crystal X-ray diffraction. With similar reaction conditions, reactions of the same ligand with different metal cations selected from different blocks (d-block and f-block) result in different coordination modes of carboxylate groups and final frameworks of complexes 1 and 3. The decarboxylation was observed in complex 2 and resulted in the formation of BIC2- ligand. Complexes 1-3 have intense fluorescent emissions at room temperature in dimethylsulfoxide (DMSO) solution and in the solid-state, which indicate they are potential fluorescence materials. The quantum yields and fluorescence lifetimes of these three complexes were systematically studied.

A surprising role for conformational entropy in protein function

PubMed Central

Wand, A. Joshua; Moorman, Veronica R.; Harpole, Kyle W.

2014-01-01

Formation of high-affinity complexes is critical for the majority of enzymatic reactions involving proteins. The creation of the family of Michaelis and other intermediate complexes during catalysis clearly involves a complicated manifold of interactions that are diverse and complex. Indeed, computing the energetics of interactions between proteins and small molecule ligands using molecular structure alone remains a grand challenge. One of the most difficult contributions to the free energy of protein-ligand complexes to experimentally access is that due to changes in protein conformational entropy. Fortunately, recent advances in solution nuclear magnetic resonance (NMR) relaxation methods have enabled the use of measures-of-motion between conformational states of a protein as a proxy for conformational entropy. This review briefly summarizes the experimental approaches currently employed to characterize fast internal motion in proteins, how this information is used to gain insight into conformational entropy, what has been learned and what the future may hold for this emerging view of protein function. PMID:23478875

Conformational selection in a protein-protein interaction revealed by dynamic pathway analysis

DOE PAGES

Chakrabarti, Kalyan S.; Agafonov, Roman V.; Pontiggia, Francesco; ...

2015-12-24

Molecular recognition plays a central role in biology, and protein dynamics has been acknowledged to be important in this process. However, it is highly debated whether conformational changes happen before ligand binding to produce a binding-competent state (conformational selection) or are caused in response to ligand binding (induced fit). Proposals for both mechanisms in protein/protein recognition have been primarily based on structural arguments. However, the distinction between them is a question of the probabilities of going via these two opposing pathways. Here we present a direct demonstration of exclusive conformational selection in protein/protein recognition by measuring the flux for rhodopsinmore » kinase binding to its regulator recoverin, an important molecular recognition in the vision system. Using NMR spectroscopy, stopped-flow kinetics and isothermal titration calorimetry we show that recoverin populates a minor conformation in solution that exposes a hydrophobic binding pocket responsible for binding rhodopsin kinase. Lastly, protein dynamics in free recoverin limits the overall rate of binding.« less

Conformational selection in a protein-protein interaction revealed by dynamic pathway analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chakrabarti, Kalyan S.; Agafonov, Roman V.; Pontiggia, Francesco

Molecular recognition plays a central role in biology, and protein dynamics has been acknowledged to be important in this process. However, it is highly debated whether conformational changes happen before ligand binding to produce a binding-competent state (conformational selection) or are caused in response to ligand binding (induced fit). Proposals for both mechanisms in protein/protein recognition have been primarily based on structural arguments. However, the distinction between them is a question of the probabilities of going via these two opposing pathways. Here we present a direct demonstration of exclusive conformational selection in protein/protein recognition by measuring the flux for rhodopsinmore » kinase binding to its regulator recoverin, an important molecular recognition in the vision system. Using NMR spectroscopy, stopped-flow kinetics and isothermal titration calorimetry we show that recoverin populates a minor conformation in solution that exposes a hydrophobic binding pocket responsible for binding rhodopsin kinase. Lastly, protein dynamics in free recoverin limits the overall rate of binding.« less

Probing the coordination environment of Ti(3+) ions coordinated to nitrogen-containing Lewis bases.

PubMed

Morra, E; Maurelli, S; Chiesa, M; Van Doorslaer, S

2015-08-28

Multi-frequency continuous-wave and pulsed EPR techniques are employed to investigate the coordination of nitrogen-containing ligands to Ti(3+)-chloro complexes. Frozen solutions of TiCl3 and TiCl3(Py)3 dissolved in nitrogen-containing solvents have been investigated together with the TiCl3(Py)3 solid-state complex. For these different systems, the hyperfine and nuclear quadrupole data of Ti(3+)-bound (14)N nuclei are reported and discussed in the light of DFT computations, allowing for a detailed description of the microscopic structure of these systems.

Robust, transformable, and crystalline single-node organometallic networks constructed from ditopic m-terphenyl isocyanides

DOE PAGES

Agnew, Douglas W.; Gembicky, Milan; Moore, Curtis E.; ...

2016-11-01

Here, the preparation of 3D and 2D Cu(I) coordination networks using ditopic m-terphenyl isocyanides is described. The incorporation of sterically encumbering substituents enables the controlled, solid-state preparation of Cu(I) tris-isocyanide nodes with a labile solvent ligand in a manner mirroring solution-phase chemistry of monomeric complexes. The protection afforded by the m-terphenyl groups is also shown to engender significant stability towards heat as well as acidic or basic conditions, resulting in robust single-metal-node networks that can transition from 3D to 2D extended structures.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grosso, Marcos; Kalstein, Adrian; Parisi, Gustavo

The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use inmore » combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data.« less

Conformation and dynamics of the ligand shell of a water-soluble Au102 nanoparticle.

PubMed

Salorinne, Kirsi; Malola, Sami; Wong, O Andrea; Rithner, Christopher D; Chen, Xi; Ackerson, Christopher J; Häkkinen, Hannu

2016-01-21

Inorganic nanoparticles, stabilized by a passivating layer of organic molecules, form a versatile class of nanostructured materials with potential applications in material chemistry, nanoscale physics, nanomedicine and structural biology. While the structure of the nanoparticle core is often known to atomic precision, gaining precise structural and dynamical information on the organic layer poses a major challenge. Here we report a full assignment of (1)H and (13)C NMR shifts to all ligands of a water-soluble, atomically precise, 102-atom gold nanoparticle stabilized by 44 para-mercaptobenzoic acid ligands in solution, by using a combination of multidimensional NMR methods, density functional theory calculations and molecular dynamics simulations. Molecular dynamics simulations augment the data by giving information about the ligand disorder and visualization of possible distinct ligand conformations of the most dynamic ligands. The method demonstrated here opens a way to controllable strategies for functionalization of ligated nanoparticles for applications.

Conformation and dynamics of the ligand shell of a water-soluble Au102 nanoparticle

PubMed Central

Salorinne, Kirsi; Malola, Sami; Wong, O. Andrea; Rithner, Christopher D.; Chen, Xi; Ackerson, Christopher J.; Häkkinen, Hannu

2016-01-01

Inorganic nanoparticles, stabilized by a passivating layer of organic molecules, form a versatile class of nanostructured materials with potential applications in material chemistry, nanoscale physics, nanomedicine and structural biology. While the structure of the nanoparticle core is often known to atomic precision, gaining precise structural and dynamical information on the organic layer poses a major challenge. Here we report a full assignment of 1H and 13C NMR shifts to all ligands of a water-soluble, atomically precise, 102-atom gold nanoparticle stabilized by 44 para-mercaptobenzoic acid ligands in solution, by using a combination of multidimensional NMR methods, density functional theory calculations and molecular dynamics simulations. Molecular dynamics simulations augment the data by giving information about the ligand disorder and visualization of possible distinct ligand conformations of the most dynamic ligands. The method demonstrated here opens a way to controllable strategies for functionalization of ligated nanoparticles for applications. PMID:26791253

Microreactor and method for preparing a radiolabeled complex or a biomolecule conjugate

DOEpatents

Reichert, David E; Kenis, Paul J. A.; Wheeler, Tobias D; Desai, Amit V; Zeng, Dexing; Onal, Birce C

2015-03-17

A microreactor for preparing a radiolabeled complex or a biomolecule conjugate comprises a microchannel for fluid flow, where the microchannel comprises a mixing portion comprising one or more passive mixing elements, and a reservoir for incubating a mixed fluid. The reservoir is in fluid communication with the microchannel and is disposed downstream of the mixing portion. A method of preparing a radiolabeled complex includes flowing a radiometal solution comprising a metallic radionuclide through a downstream mixing portion of a microchannel, where the downstream mixing portion includes one or more passive mixing elements, and flowing a ligand solution comprising a bifunctional chelator through the downstream mixing portion. The ligand solution and the radiometal solution are passively mixed while in the downstream mixing portion to initiate a chelation reaction between the metallic radionuclide and the bifunctional chelator. The chelation reaction is completed to form a radiolabeled complex.

Hydrogel Tethering Enhances Interdomain Stabilization of Single-Chain Antibodies.

PubMed

Xiong, Yijia; Ford, Nicole R; Hecht, Karen A; Roesijadi, Guritno; Squier, Thomas C

2017-11-15

Here, we identify the importance of molecular crowding agents in the functional stabilization of scFv antibodies. Antibodies were tethered through an engineered calmodulin (CaM)-binding peptide into a stimulus-responsive hydrogel composed of poly(ethylene glycol) (PEG)-functionalized CaM. Macromolecular crowding is modulated by transient heating, which decreases effective pore sizes. Using a fluorescent ligand bound to the scFv, frequency-domain fluorescence spectroscopy was used to assess the structural coupling between the V H and the V L domains and relationships with functional stabilization. There is minimal structural coupling between the V H and the V L domains in solution, as is apparent from the substantial rotational mobility for the bound ligand, that is suggestive of an independent mobility for the V H and the V L domains. In comparison, the hydrogel matrix acts to structurally couple the V H and the V L domains, resulting in a reduction in rotational mobility and a retention of ligand binding in the presence of 8.0 M urea. Under these same conditions, ligand binding is disrupted for scFv antibodies in solution. Increases in the stabilization of scFv antibodies in hydrogels is not simply the result of molecular crowding because decreases in pore size act to destabilize ligand binding. Rather, our results suggest that the functional stabilization of the scFv antibody within the PEG hydrogel matrix includes important factors involving protein solvation that stabilize interdomain interactions between the V H and the V L domains necessary for ligand binding.

Synthesis, electrochemical, structural, spectroscopic and biological activities of mixed ligand copper (II) complexes with 2-{[(Z)-(5-bromo-2-hydroxyphenyl)methylidene]amino}benzoic acid and nitrogenous bases

NASA Astrophysics Data System (ADS)

Choudhary, Mukesh; Patel, R. N.; Rawat, S. P.

2014-02-01

Three new copper (II) complexes viz. [Cu(L1)(bipy)]ṡ2H2O 1, [Cu(L1)(dmp)]ṡCH3CN 2, [Cu(L1)(phen)] 3 where L1H2 = 2-{[(Z)-(5-bromo-2-hydroxyphenyl)methylidene]amino}benzoic acid, bipy = 2,2‧-bipyridine; dmp = 2,9-dimethyl 1,10-phenanthroline, phen = 1,10-phenanthroline have been synthesized and characterized by physic-chemical and spectroscopic methods. The solid-state structures of 1 and 2 were determined by single crystal X-ray crystallography, which revealed distorted square pyramidal geometry. In solid-state structure, 1 is self-assembled via intermolecular π…π stacking and the distances between centroids of aromatic ring is 3.525 Å. L1H2 is a diprotic tridentate Schiff base ligand having ONO donor site. Infrared spectra, ligand field spectra and magnetic susceptibility measurements agree with the observed crystal structures. The EPR spectra of these complexes in frozen DMSO solutions showed a single at g ca. 2. The trend in g-value (g|| > g⊥ > 2.0023) suggests that the unpaired electron on copper (II) has d character. Copper (II) complexes 1-3 yielded an irreversible couple corresponding to the Cu (II)/Cu (I) redox process. Superoxide dismutase activity of all these complexes has been revealed to catalyze the dismutation of superoxide (O2-) and IC50 values were evaluated and discussed. Antimicrobial and antifungal activities of these complexes were also investigated.

Complexes of horseradish peroxidase with formate, acetate, and carbon monoxide.

PubMed

Carlsson, Gunilla H; Nicholls, Peter; Svistunenko, Dimitri; Berglund, Gunnar I; Hajdu, Janos

2005-01-18

Carbon monoxide, formate, and acetate interact with horseradish peroxidase (HRP) by binding to subsites within the active site. These ligands also bind to catalases, but their interactions are different in the two types of enzymes. Formate (notionally the "hydrated" form of carbon monoxide) is oxidized to carbon dioxide by compound I in catalase, while no such reaction is reported to occur in HRP, and the CO complex of ferrocatalase can only be obtained indirectly. Here we describe high-resolution crystal structures for HRP in its complexes with carbon monoxide and with formate, and compare these with the previously determined HRP-acetate structure [Berglund, G. I., et al. (2002) Nature 417, 463-468]. A multicrystal X-ray data collection strategy preserved the correct oxidation state of the iron during the experiments. Absorption spectra of the crystals and electron paramagnetic resonance data for the acetate and formate complexes in solution correlate electronic states with the structural results. Formate in ferric HRP and CO in ferrous HRP bind directly to the heme iron with iron-ligand distances of 2.3 and 1.8 A, respectively. CO does not bind to the ferric iron in the crystal. Acetate bound to ferric HRP stacks parallel with the heme plane with its carboxylate group 3.6 A from the heme iron, and without an intervening solvent molecule between the iron and acetate. The positions of the oxygen atoms in the bound ligands outline a potential access route for hydrogen peroxide to the iron. We propose that interactions in this channel ensure deprotonation of the proximal oxygen before binding to the heme iron.

The Free Energy Landscape of Small Molecule Unbinding

PubMed Central

Huang, Danzhi; Caflisch, Amedeo

2011-01-01

The spontaneous dissociation of six small ligands from the active site of FKBP (the FK506 binding protein) is investigated by explicit water molecular dynamics simulations and network analysis. The ligands have between four (dimethylsulphoxide) and eleven (5-diethylamino-2-pentanone) non-hydrogen atoms, and an affinity for FKBP ranging from 20 to 0.2 mM. The conformations of the FKBP/ligand complex saved along multiple trajectories (50 runs at 310 K for each ligand) are grouped according to a set of intermolecular distances into nodes of a network, and the direct transitions between them are the links. The network analysis reveals that the bound state consists of several subbasins, i.e., binding modes characterized by distinct intermolecular hydrogen bonds and hydrophobic contacts. The dissociation kinetics show a simple (i.e., single-exponential) time dependence because the unbinding barrier is much higher than the barriers between subbasins in the bound state. The unbinding transition state is made up of heterogeneous positions and orientations of the ligand in the FKBP active site, which correspond to multiple pathways of dissociation. For the six small ligands of FKBP, the weaker the binding affinity the closer to the bound state (along the intermolecular distance) are the transition state structures, which is a new manifestation of Hammond behavior. Experimental approaches to the study of fragment binding to proteins have limitations in temporal and spatial resolution. Our network analysis of the unbinding simulations of small inhibitors from an enzyme paints a clear picture of the free energy landscape (both thermodynamics and kinetics) of ligand unbinding. PMID:21390201

The free energy landscape of small molecule unbinding.

PubMed

Huang, Danzhi; Caflisch, Amedeo

2011-02-01

The spontaneous dissociation of six small ligands from the active site of FKBP (the FK506 binding protein) is investigated by explicit water molecular dynamics simulations and network analysis. The ligands have between four (dimethylsulphoxide) and eleven (5-diethylamino-2-pentanone) non-hydrogen atoms, and an affinity for FKBP ranging from 20 to 0.2 mM. The conformations of the FKBP/ligand complex saved along multiple trajectories (50 runs at 310 K for each ligand) are grouped according to a set of intermolecular distances into nodes of a network, and the direct transitions between them are the links. The network analysis reveals that the bound state consists of several subbasins, i.e., binding modes characterized by distinct intermolecular hydrogen bonds and hydrophobic contacts. The dissociation kinetics show a simple (i.e., single-exponential) time dependence because the unbinding barrier is much higher than the barriers between subbasins in the bound state. The unbinding transition state is made up of heterogeneous positions and orientations of the ligand in the FKBP active site, which correspond to multiple pathways of dissociation. For the six small ligands of FKBP, the weaker the binding affinity the closer to the bound state (along the intermolecular distance) are the transition state structures, which is a new manifestation of Hammond behavior. Experimental approaches to the study of fragment binding to proteins have limitations in temporal and spatial resolution. Our network analysis of the unbinding simulations of small inhibitors from an enzyme paints a clear picture of the free energy landscape (both thermodynamics and kinetics) of ligand unbinding.

Enhancing the Performance of CdSe/CdS Dot-in-Rod Light-Emitting Diodes via Surface Ligand Modification.

PubMed

Rastogi, Prachi; Palazon, Francisco; Prato, Mirko; Di Stasio, Francesco; Krahne, Roman

2018-02-14

The surface ligands on colloidal nanocrystals (NCs) play an important role in the performance of NC-based optoelectronic devices such as photovoltaic cells, photodetectors, and light-emitting diodes (LEDs). On one hand, the NC emission depends critically on the passivation of the surface to minimize trap states that can provide nonradiative recombination channels. On the other hand, the electrical properties of NC films are dominated by the ligands that constitute the barriers for charge transport from one NC to its neighbor. Therefore, surface modifications via ligand exchange have been employed to improve the conductance of NC films. However, in LEDs, such surface modifications are more critical because of their possible detrimental effects on the emission properties. In this work, we study the role of surface ligand modifications on the optical and electrical properties of CdSe/CdS dot-in-rods (DiRs) in films and investigate their performance in all-solution-processed LEDs. The DiR films maintain high photoluminescence quantum yield, around 40-50%, and their electroluminescence in the LED preserves the excellent color purity of the photoluminescence. In the LEDs, the ligand exchange boosted the luminance, reaching a fourfold increase from 2200 cd/m 2 for native surfactants to 8500 cd/m 2 for the exchanged aminoethanethiol (AET) ligands. Moreover, the efficiency roll-off, operational stability, and shelf life are significantly improved, and the external quantum efficiency is modestly increased from 5.1 to 5.4%. We relate these improvements to the increased conductivity of the emissive layer and to the better charge balance of the electrically injected carriers. In this respect, we performed ultraviolet photoelectron spectroscopy (UPS) to obtain a deeper insight into the band alignment of the LED structure. The UPS data confirm similar flat-band offsets of the emitting layer to the electron- and hole-transport layers in the case of AET ligands, which translates to more symmetric barriers for charge injection of electrons and holes. Furthermore, the change in solubility of the NCs induced by the ligand exchange allows for a layer-by-layer deposition process of the DiR films, which yields excellent homogeneity and good thickness control and enables the fabrication of all the LED layers (except for cathode and anode) by spin-coating.

A facile method to prepare "green" nano-phosphors with a large Stokes-shift and solid-state enhanced photophysical properties based on surface-modified gold nanoclusters.

PubMed

Cheng, C H; Huang, H Y; Talite, M J; Chou, W C; Yeh, J M; Yuan, C T

2017-12-15

Colloidal nano-materials, such as quantum dots (QDs) have been applied to light-conversion nano-phosphors due to their unique tunable emission. However, most of the QDs involve toxic elements and are synthesized in a hazardous solvent. In addition, conventional QD nano-phosphors with a small Stokes shift suffered from reabsorption losses and aggregation-induced quenching in the solid state. Here, we demonstrate a facile, matrix-free method to prepare eco-friendly nano-phosphors with a large Stokes shift based on aqueous thiolate-stabilized gold nanoclusters (GSH-AuNCs) with simple surface modifications. Our method is just to drop GSH-AuNCs solution on the aluminum foil and then surface-modified AuNCs (Al-GSH-AuNCs) can be spontaneously precipitated out of the aqueous solution. Compared with pristine GSH-AuNCs in solution, the Al-GSH-AuNCs exhibit enhanced solid-state PL quantum yields, lengthened PL lifetime, and spectral blue shift, which can be attributed to the aggregation-induced emission enhancement facilitated by surface modifications. Such surface-treatment induced aggregation of AuNCs can restrict the surface-ligand motion, leading to the enhancement of PL properties in the solid state. In addition, the Al-GSH-AuNCs nano-phosphors with a large Stokes shift can mitigate the aggregation-induced PL quenching and reabsorption losses, which would be potential candidates for "green" nano-phosphors. Copyright © 2017 Elsevier Inc. All rights reserved.

Metal–organic complexation in the marine environment

PubMed Central

Luther, George W; Rozan, Timothy F; Witter, Amy; Lewis, Brent

2001-01-01

We discuss the voltammetric methods that are used to assess metal–organic complexation in seawater. These consist of titration methods using anodic stripping voltammetry (ASV) and cathodic stripping voltammetry competitive ligand experiments (CSV-CLE). These approaches and a kinetic approach using CSV-CLE give similar information on the amount of excess ligand to metal in a sample and the conditional metal ligand stability constant for the excess ligand bound to the metal. CSV-CLE data using different ligands to measure Fe(III) organic complexes are similar. All these methods give conditional stability constants for which the side reaction coefficient for the metal can be corrected but not that for the ligand. Another approach, pseudovoltammetry, provides information on the actual metal–ligand complex(es) in a sample by doing ASV experiments where the deposition potential is varied more negatively in order to destroy the metal–ligand complex. This latter approach gives concentration information on each actual ligand bound to the metal as well as the thermodynamic stability constant of each complex in solution when compared to known metal–ligand complexes. In this case the side reaction coefficients for the metal and ligand are corrected. Thus, this method may not give identical information to the titration methods because the excess ligand in the sample may not be identical to some of the actual ligands binding the metal in the sample. PMID:16759421

Sky-blue emitting bridged diiridium complexes: beneficial effects of intramolecular π-π stacking.

PubMed

Congrave, Daniel G; Hsu, Yu-Ting; Batsanov, Andrei S; Beeby, Andrew; Bryce, Martin R

2018-02-06

The potential of intramolecular π-π interactions to influence the photophysical properties of diiridium complexes is an unexplored topic, and provides the motivation for the present study. A series of diarylhydrazide-bridged diiridium complexes functionalised with phenylpyridine (ppy)-based cyclometalating ligands is reported. It is shown by NMR studies in solution and single crystal X-ray analysis that intramolecular π-π interactions between the bridging and cyclometalating ligands rigidify the complexes leading to high luminescence quantum efficiencies in solution and in doped films. Fluorine substituents on the phenyl rings of the bridge promote the intramolecular π-π interactions. Notably, these non-covalent interactions are harnessed in the rational design and synthesis of the first examples of highly emissive sky-blue diiridium complexes featuring conjugated bridging ligands, for which they play a vital role in the structural and photophysical properties. Experimental results are supported by computational studies.

Nanocomposite and method of making thereof

DOEpatents

Tangirala, Ravisubhash; Milliron, Delia J.; Llordes, Anna

2016-03-15

An embodiment of an inorganic nanocomposite includes a nanoparticle phase and a matrix phase. The nanoparticle phase includes nanoparticles that are arranged in a repeating structure. In an embodiment, the nanoparticles have a spherical or pseudo-spherical shape and are incompatible with hydrazine. In another embodiment, the nanoparticles have neither a spherical nor pseudo-spherical shape. The matrix phase lies between the nanoparticles of the nanoparticle phase. An embodiment of a method of making an inorganic nanocomposite of the present invention includes forming a nanoparticle superlattice on a substrate. The nanoparticle superlattice includes nanoparticles. Each nanoparticle has organic ligands attached to a surface of the nanoparticle. The organic ligands separate adjacent nanoparticles within the nanoparticle superlattice. The method also includes forming a solution that includes an inorganic precursor. The nanoparticle superlattice is placed in the solution for a sufficient time for the inorganic precursor to replace the organic ligands.

Hypervalent surface interactions for colloidal stability and doping of silicon nanocrystals

PubMed Central

Wheeler, Lance M.; Neale, Nathan R.; Chen, Ting; Kortshagen, Uwe R.

2013-01-01

Colloidal semiconductor nanocrystals have attracted attention for cost-effective, solution-based deposition of quantum-confined thin films for optoelectronics. However, two significant challenges must be addressed before practical nanocrystal-based devices can be realized. The first is coping with the ligands that terminate the nanocrystal surfaces. Though ligands provide the colloidal stability needed to cast thin films from solution, these ligands dramatically hinder charge carrier transport in the resulting film. Second, after a conductive film is achieved, doping has proven difficult for further control of the optoelectronic properties of the film. Here we report the ability to confront both of these challenges by exploiting the ability of silicon to engage in hypervalent interactions with hard donor molecules. For the first time, we demonstrate the significant potential of applying the interaction to the nanocrystal surface. In this study, hypervalent interactions are shown to provide colloidal stability as well as doping of silicon nanocrystals. PMID:23893292

The Synthesis, Characterization and Reactivity of a Series of Ruthenium N-triphos Ph Complexes.

PubMed

Phanopoulos, Andreas; Long, Nicholas; Miller, Philip

2015-04-10

Herein we report the synthesis of a tridentate phosphine ligand N(CH2PPh2)3 (N-triphos(Ph)) (1) via a phosphorus based Mannich reaction of the hydroxylmethylene phosphine precursor with ammonia in methanol under a nitrogen atmosphere. The N-triphos(Ph) ligand precipitates from the solution after approximately 1 hr of reflux and can be isolated analytically pure via simple cannula filtration procedure under nitrogen. Reaction of the N-triphos(Ph) ligand with [Ru3(CO)12] under reflux affords a deep red solution that show evolution of CO gas on ligand complexation. Orange crystals of the complex [Ru(CO)2{N(CH2PPh2)3}-κ(3)P] (2) were isolated on cooling to RT. The (31)P{(1)H} NMR spectrum showed a characteristic single peak at lower frequency compared to the free ligand. Reaction of a toluene solution of complex 2 with oxygen resulted in the instantaneous precipitation of the carbonate complex [Ru(CO3)(CO){N(CH2PPh2)3}-κ(3)P] (3) as an air stable orange solid. Subsequent hydrogenation of 3 under 15 bar of hydrogen in a high-pressure reactor gave the dihydride complex [RuH2(CO){N(CH2PPh2)3}-κ(3)P] (4), which was fully characterized by X-ray crystallography and NMR spectroscopy. Complexes 3 and 4 are potentially useful catalyst precursors for a range of hydrogenation reactions, including biomass-derived products such as levulinic acid (LA). Complex 4 was found to cleanly react with LA in the presence of the proton source additive NH4PF6 to give [Ru(CO){N(CH2PPh2)3}-κ(3)P{CH3CO(CH2)2CO2H}-κ(2)O](PF6) (6).

The Synthesis, Characterization and Reactivity of a Series of Ruthenium N-triphosPh Complexes

PubMed Central

Phanopoulos, Andreas; Long, Nicholas; Miller, Philip

2015-01-01

Herein we report the synthesis of a tridentate phosphine ligand N(CH2PPh2)3 (N-triphosPh) (1) via a phosphorus based Mannich reaction of the hydroxylmethylene phosphine precursor with ammonia in methanol under a nitrogen atmosphere. The N-triphosPh ligand precipitates from the solution after approximately 1 hr of reflux and can be isolated analytically pure via simple cannula filtration procedure under nitrogen. Reaction of the N-triphosPh ligand with [Ru3(CO)12] under reflux affords a deep red solution that show evolution of CO gas on ligand complexation. Orange crystals of the complex [Ru(CO)2{N(CH2PPh2)3}-κ3P] (2) were isolated on cooling to RT. The 31P{1H} NMR spectrum showed a characteristic single peak at lower frequency compared to the free ligand. Reaction of a toluene solution of complex 2 with oxygen resulted in the instantaneous precipitation of the carbonate complex [Ru(CO3)(CO){N(CH2PPh2)3}-κ3P] (3) as an air stable orange solid. Subsequent hydrogenation of 3 under 15 bar of hydrogen in a high-pressure reactor gave the dihydride complex [RuH2(CO){N(CH2PPh2)3}-κ3P] (4), which was fully characterized by X-ray crystallography and NMR spectroscopy. Complexes 3 and 4 are potentially useful catalyst precursors for a range of hydrogenation reactions, including biomass-derived products such as levulinic acid (LA). Complex 4 was found to cleanly react with LA in the presence of the proton source additive NH4PF6 to give [Ru(CO){N(CH2PPh2)3}-κ3P{CH3CO(CH2)2CO2H}-κ2O](PF6) (6). PMID:25938678

Bis(hydroxylamino)triazines: High Selectivity and Hydrolytic Stability of Hydroxylamine-Based Ligands for Uranyl Compared to Vanadium(V) and Iron(III).

PubMed

Hadjithoma, Sofia; Papanikolaou, Michael G; Leontidis, Epameinondas; Kabanos, Themistoklis A; Keramidas, Anastasios D

2018-06-08

The development of ligands with high selectivity and affinity for uranium is critical in the extraction of uranium from human body, radioactive waste, and seawater. A scientific challenge is the improvement of the selectivity of chelators for uranium over other heavy metals, including iron and vanadium. Flat ligands with hard donor atoms that satisfy the geometric and electronic requirements of the U VI O 2 2+ exhibit high selectivity for the uranyl moiety. The bis(hydroxylamino)(triazine) ligand, 2,6-bis[hydroxy(methyl)amino]-4-morpholino-1,3,5-triazine (H 2 bihyat), a strong binder for hard metal ions (Fe III , Ti IV , V V , and Mo VI ), reacted with [U VI O 2 (NO 3 ) 2 (H 2 O) 2 ]·4H 2 O in aqueous solution and resulted in the isolation of the complexes [U VI O 2 (bihyat)(H 2 O)], [U VI O 2 (bihyat) 2 ] 2- , and {[U VI O 2 (bihyat)(μ-OH)]} 2 2- . These three species are in equilibrium in aqueous solution, and their abundance varies with the concentration of H 2 bihyat and the pH. Reaction of H 2 bihyat with [U VI O 2 (NO 3 ) 2 (H 2 O) 2 ]·4H 2 O in CH 3 CN gave the trinuclear complex [U VI 3 O 6 (bihyat) 2 (μ-bihyat) 2 ] 2- , which is the major species in organic solvents. The dynamics between the U VI O 2 2+ and the free ligand H 2 bihyat in aqueous and dimethyl sulfoxide solutions; the metal binding ability of the H 2 bihyat over pyridine-2,6-dicarboxylic acid (H 2 dipic) or glutarimidedioxime for U VI O 2 2+ , and the selectivity of the H 2 bihyat to bind U VI O 2 2+ in comparison to V V O 4 3- and Fe III in either U VI O 2 2+ /V V O 4 3- or U VI O 2 2+ /Fe III solutions were examined by NMR and UV-vis spectroscopies. The results revealed that H 2 bihyat is a superior ligand for U VI O 2 2+ with high selectivity compared to Fe III and V V O 4 3- , which increases at higher pHs. Thus, this type of ligand might find applications in the extraction of uranium from the sea and its removal from the environment and the human body.

Synthesis and characterisation of luminescent rhenium tricarbonyl complexes with axially coordinated 1,2,3-triazole ligands.

PubMed

Uppal, Baljinder S; Booth, Rebecca K; Ali, Noreen; Lockwood, Cindy; Rice, Craig R; Elliott, Paul I P

2011-08-07

A series of 1-alkyl-4-aryl-1,2,3-triazoles (1-methyl-4-phenyl-1,2,3-triazole (1a); 1-propyl-4-phenyl-1,2,3-triazole (1b); 1-benzyl-4-phenyl-1,2,3-triazole (1c); 1-propyl-4-p-tolyl-1,2,3-triazole (1d)) have been prepared through a one-pot procedure involving in situ generation of the alkyl azide from a halide precursor followed by copper catalysed alkyne/azide cycloaddition (CuAAC) with the appropriate aryl alkyne. Cationic Re(I) complexes [Re(bpy)(CO)(3)(1a-d)]PF(6) (2a-d) were then prepared by stirring [Re(bpy)(CO)(3)Cl] with AgPF(6) in dichloromethane in the presence of ligands 1a-d. X-ray crystal structures were obtained for 2a and 2b. In the solid state, 2a adopts a highly distorted geometry, which is not seen for 2b, in which the plane of the triazole ligand tilts by 13° with respect to the Re-N bond as a result of a π-stacking interaction between the Ph substituent and one of the rings of the bpy ligand. This π-stacking interaction also results in severe twisting of the bpy ligand. Infrared spectra of 2a-d exhibit ν(CO) bands at ∼2035 and ∼1926 cm(-1) suggesting that these ligands are marginally better donors than pyridine (ν(CO) = 2037, 1932 cm(-1)). The complexes are luminescent in aerated dichloromethane at room temperature with emission maxima at 542 to 552 nm comparable to that of the pyridine analogue (549 nm) and blue shifted relative to the parent chloride complex. Long luminescent lifetimes are observed for the triazole complexes (475 to 513 ns) in aerated dichloromethane solutions at room temperature.

Synthesis, Photochemical, and Redox Properties of Gold(I) and Gold(III) Pincer Complexes Incorporating a 2,2′:6′,2″-Terpyridine Ligand Framework

PubMed Central

2015-01-01

Reaction of [Au(C6F5)(tht)] (tht = tetrahydrothiophene) with 2,2′:6′,2″-terpyridine (terpy) leads to complex [Au(C6F5)(η1-terpy)] (1). The chemical oxidation of complex (1) with 2 equiv of [N(C6H4Br-4)3](PF6) or using electrosynthetic techniques affords the Au(III) complex [Au(C6F5)(η3-terpy)](PF6)2 (2). The X-ray diffraction study of complex 2 reveals that the terpyridine acts as tridentate chelate ligand, which leads to a slightly distorted square-planar geometry. Complex 1 displays fluorescence in the solid state at 77 K due to a metal (gold) to ligand (terpy) charge transfer transition, whereas complex 2 displays fluorescence in acetonitrile due to excimer or exciplex formation. Time-dependent density functional theory calculations match the experimental absorption spectra of the synthesized complexes. In order to further probe the frontier orbitals of both complexes and study their redox behavior, each compound was separately characterized using cyclic voltammetry. The bulk electrolysis of a solution of complex 1 was analyzed by spectroscopic methods confirming the electrochemical synthesis of complex 2. PMID:26496068

Probing receptor-ligand interactions by sedimentation equilibrium

NASA Astrophysics Data System (ADS)

Philo, John S.

1997-05-01

While sedimentation equilibrium is most commonly used to characterize the molecular weight and state of association of single proteins, this technique is also a very powerful tool for probing the interactions between two or more different proteins, and can characterize both the binding stoichiometry and the equilibrium constants. To resolve the complex binding interactions that can occur in such systems, it is crucial to globally fit data from many experiments to a common binding model, including samples made with different mixing ratios and a wide range of total concentration. It is often also essential to constrain the parameters during fitting so that the fits correctly reproduce the molar ratio of proteins used in making each sample. We have applied this methodology to probe mechanisms of receptor activation for a number of hematopoietic receptors and their cognate ligands, using receptor extracellular domains expressed as soluble proteins. Such data can potentially help in the design of improved or new protein therapeutics, as well as in efforts to create small- molecular mimetics of protein hormones through structure- based drug design. Sedimentation equilibrium has shown that stem cell factor, erythropoietin, and granulocyte-colony stimulating factor can each dimerize their respective receptors in solution, but the mechanism of ligand-induced receptor dimerization for these three systems are strikingly different.

Alternative binding modes identified for growth and differentiation factor-associated serum protein (GASP) family antagonism of myostatin.

PubMed

Walker, Ryan G; Angerman, Elizabeth B; Kattamuri, Chandramohan; Lee, Yun-Sil; Lee, Se-Jin; Thompson, Thomas B

2015-03-20

Myostatin, a member of the TGF-β family of ligands, is a strong negative regulator of muscle growth. As such, it is a prime therapeutic target for muscle wasting disorders. Similar to other TGF-β family ligands, myostatin is neutralized by binding one of a number of structurally diverse antagonists. Included are the antagonists GASP-1 and GASP-2, which are unique in that they specifically antagonize myostatin. However, little is known from a structural standpoint describing the interactions of GASP antagonists with myostatin. Here, we present the First low resolution solution structure of myostatin-free and myostatin-bound states of GASP-1 and GASP-2. Our studies have revealed GASP-1, which is 100 times more potent than GASP-2, preferentially binds myostatin in an asymmetrical 1:1 complex, whereas GASP-2 binds in a symmetrical 2:1 complex. Additionally, C-terminal truncations of GASP-1 result in less potent myostatin inhibitors that form a 2:1 complex, suggesting that the C-terminal domains of GASP-1 are the primary mediators for asymmetric complex formation. Overall, this study provides a new perspective on TGF-β antagonism, where closely related antagonists can utilize different ligand-binding strategies. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Alternative Binding Modes Identified for Growth and Differentiation Factor-associated Serum Protein (GASP) Family Antagonism of Myostatin*

PubMed Central

Walker, Ryan G.; Angerman, Elizabeth B.; Kattamuri, Chandramohan; Lee, Yun-Sil; Lee, Se-Jin; Thompson, Thomas B.

2015-01-01

Myostatin, a member of the TGF-β family of ligands, is a strong negative regulator of muscle growth. As such, it is a prime therapeutic target for muscle wasting disorders. Similar to other TGF-β family ligands, myostatin is neutralized by binding one of a number of structurally diverse antagonists. Included are the antagonists GASP-1 and GASP-2, which are unique in that they specifically antagonize myostatin. However, little is known from a structural standpoint describing the interactions of GASP antagonists with myostatin. Here, we present the First low resolution solution structure of myostatin-free and myostatin-bound states of GASP-1 and GASP-2. Our studies have revealed GASP-1, which is 100 times more potent than GASP-2, preferentially binds myostatin in an asymmetrical 1:1 complex, whereas GASP-2 binds in a symmetrical 2:1 complex. Additionally, C-terminal truncations of GASP-1 result in less potent myostatin inhibitors that form a 2:1 complex, suggesting that the C-terminal domains of GASP-1 are the primary mediators for asymmetric complex formation. Overall, this study provides a new perspective on TGF-β antagonism, where closely related antagonists can utilize different ligand-binding strategies. PMID:25657005

trans-Methylpyridine cyclen versus cross-bridged trans-methylpyridine cyclen. Synthesis, acid-base and metal complexation studies (metal = Co2+, Cu2+, and Zn2+).

PubMed

Bernier, Nicolas; Costa, Judite; Delgado, Rita; Félix, Vítor; Royal, Guy; Tripier, Raphaël

2011-05-07

The synthesis of the cross-bridged cyclen CRpy(2) {4,10-bis((pyridin-2-yl)methyl)-1,4,7,10-tetraazabicyclo[5.5.2]tetradecane}, a constrained analogue of the previously described trans-methylpyridine cyclen Cpy(2) is reported. The additional ethylene bridge confers to CRpy(2) proton-sponge type behaviour which was explored by NMR and potentiometric studies. Transition metal complexes have been synthesized (by complexation of both ligands with Co(2+), Cu(2+) and Zn(2+)) and characterized in solution and in the solid state. The single crystal X-ray structures of [CoCpy(2)](2+), [CuCpy(2)](2+) and [ZnCpy(2)](2+) complexes were determined. Stability constants of the complexes, including those of the cross-bridged derivative, were determined using potentiometric titration data and the kinetic inertness of the [CuCRpy(2)](2+) complex in an acidic medium (half-life values) was evaluated by spectrophotometry. The pre-organized structure of the cross-bridged ligand imposes an additional strain for the complexation leading to complexes with smaller thermodynamic stability in comparison with the related non-bridged ligand. The electrochemical study involving cyclic voltammetry underlines the importance of the ethylene cross-bridge on the redox properties of the transition metal complexes.

Plutonium: Advancing our Understanding to Support Sustainable Nuclear Fuel Cycles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lines, Amanda M.; Adami, Susan R.; Casella, Amanda

With Global energy needs increasing, real energy solutions to meet demands now, are needed. Fossil fuels are not an ideal candidate to meet these needs because of their negative impact on the environment. Renewables such as wind and solar have huge potential, but still need major technological advancements (particularly in the area of battery storage) before they can effectively meet growing world needs. The best option for meeting large energy needs without a large carbon footprint is nuclear energy. Of course, nuclear energy can face a fair amount of opposition and concern. However, through modern engineering and science many ofmore » these concerns can now be addressed. Many safety concerns can be met by engineering advancements, but perhaps the biggest area of concern is what to do with the used nuclear fuel after it is removed from the reactor. Currently the United States (and several other countries) utilize an open fuel cycle, meaning fuel is only used once and then discarded. It should be noted that fuel coming out of a reactor has utilized approximately 1% of the total energy that could be produced by the uranium in the fuel rod. The answer here is to close the fuel cycle and recycle the nuclear materials. By reprocessing used nuclear fuel, all the U can be repurposed without requiring disposal. The various fission products can be removed and either discarded (hugely reduced waste volume) or more reasonably, utilized in specialty reactors to make more energy or needed research/medical isotopes. While reprocessing technology is currently advanced enough to meet energy needs, completing research to improve and better understand these techniques is still needed. Better understanding behavior of fission products is one area of important research. Despite it being discovered over 75 years ago, plutonium is still an exciting element to study because of the complex solution chemistry it exhibits. In aqueous solutions Pu can exist simultaneously in multiple oxidation states, including 3+, 4+, and 6+. It also readily forms a variety of metal-ligand complexes depending on solution pH and available ligands. Understanding of the behavior of Pu in solution remains an important area of research today, with relevance to developing sustainable nuclear fuel cycles, minimizing its impact on the environment, and detecting and preventing the spread of nuclear weapons technology.« less

Chaperonin-based biolayer interferometry to assess the kinetic stability of metastable, aggregation-prone proteins

PubMed Central

Lea, Wendy A.; Naik, Subhashchandra; Chaudhri, Tapan; Machen, Alexandra J.; O’Neil, Pierce T.; McGinn-Straub, Wesley; Tischer, Alexander; Auton, Matthew T.; Burns, Joshua R.; Baldwin, Michael R.; Khar, Karen R.; Karanicolas, John; Fisher, Mark T.

2017-01-01

Stabilizing the folded state of metastable and/or aggregation-prone proteins through exogenous ligand binding is an appealing strategy to decrease disease pathologies brought on by protein folding defects or deleterious kinetic transitions. Current methods of examining ligand binding to these marginally stable native states are limited, because protein aggregation typically interferes with analysis. Here, we describe a rapid method for assessing the kinetic stability of folded proteins and monitoring the effects of ligand stabilization for both intrinsically stable proteins (monomers, oligomers, multi-domain) and metastable proteins (e.g. low Tm) that uses a new GroEL chaperonin-based biolayer interferometry (BLI) denaturant-pulse platform. A kinetically controlled denaturation isotherm is generated by exposing a target protein immobilized on a BLI biosensor to increasing denaturant concentrations (urea or GnHCl) in a pulsatile manner to induce partial or complete unfolding of the attached protein population. Following the rapid removal of the denaturant, the extent of hydrophobic unfolded/partially folded species that remain is detected by increased GroEL binding. Since this kinetic denaturant pulse is brief, the amplitude of the GroEL binding to the immobilized protein depends on the duration of exposure to denaturant, the concentration of denaturant, wash times, and the underlying protein unfolding/refolding kinetics; fixing all other parameters and plotting GroEL binding amplitude versus denaturant pulse concentration results in a kinetically controlled denaturation isotherm. When folding osmolytes or stabilizing ligands are added to the immobilized target proteins before and during the denaturant pulse, the diminished population of unfolded/partially folded protein is manifested by a decreased GroEL binding and/or a marked shift in these kinetically controlled denaturation profiles to higher denaturant concentrations. This particular platform approach can be used to identify small molecules/solution conditions that can stabilize or destabilize thermally stable proteins, multi-domain proteins, oligomeric proteins, and most importantly, aggregation prone metastable proteins. PMID:27505032

Synthesis, crystal structure and antimicrobial activities of two isomeric gold(I) complexes with nitrogen-containing heterocycle and triphenylphosphine ligands, [Au(L)(PPh3)] (HL = pyrazole and imidazole).

PubMed

Nomiya, K; Noguchi, R; Ohsawa, K; Tsuda, K; Oda, M

2000-03-01

Two isomeric gold(I)-triphenylphosphine complexes with nitrogen-containing heterocycles, [Au(L)(PPh3) (HL = pyrazole (1), imidazole (2)) were isolated as colorless cubic crystals for 1 and colorless plate crystals for 2, respectively. The crystal structures of 1 and 2 were determined by single-crystal X-ray diffraction. These complexes were also fully characterized by complete elemental analyses, thermogravimetric/differential thermal analyses (TG/DTA) and FT-IR in the solid state and by solution NMR (31P, 1H and 13C) spectroscopy and molecular weight measurements in acetone solution. These complexes consisted of a monomeric 2-coordinate AuNP core both in the solid state and in solution. The molecular structures of 1 and 2 were compared with those of related gold(I) complexes, [Au(1,2,3-triz)(PPh3)] (3, Htriz = triazole), [Au(1,2,4-triz)(PPh3)]2 (4) as a dimer through a gold(I)-gold(I) bond in the solid state, and [Au(tetz)(PPh3)] (5, Htetz = tetrazole). Selective and effective antimicrobial activities against two gram-positive bacteria (B. subtilis, S. aureus) and modest activities against one yeast (C. albicans) found in these gold(I) complexes 1-4 are noteworthy, in contrast to poor activities observed in the corresponding silver(I) complexes.

Thermodynamic Stability of Heterodimetallic [LnLn'] Complexes: Synthesis and DFT Studies

DOE PAGES

Gonzalez-Fabra, Joan; Bandeira, Nuno A. G.; Velasco, Veronica; ...

2017-03-27

The solid-state and solution configurations of the heterodimetallic complexes (Hpy)[LaEr(HL) 3(NO 3)(py)(H 2O)] (1), (Hpy)[CeEr(HL) 3(NO 3)(py)(H 2O)] (2), (Hpy)[CeGd(HL) 3(NO 3)(py)(H 2O)] (3), (Hpy)[PrSm(HL) 3(NO 3)(py)(H 2O)] (4), and (Hpy) 2[LaYb(HL) 3(NO 3)(H 2O)](NO 3) (5), in which H 3L is 6-(3-oxo-3-(2-hydroxyphenyl)propionyl)pyridine-2-carboxylic acid and py is pyridine, were analyzed experimentally and by using DFT calculations. Complexes 3, 4, and 5 are described here for the first time, and were analyzed by using single-crystal X-ray diffraction and mass spectrometry. The theoretical study was also extended to the [LaCe] and [LaLu] analogues. The results are consistent with a remarkable selectivity ofmore » the metal distribution within the molecule in the solid state, enhanced by the size difference between the different ions. This selectivity was reduced in solution, particularly for ions with the most similar radii. This unique entry into 4f–4f" heterometallic chemistry establishes for the first time the difference between the selectivity in solution and that in the solid state, as a result of changes to the coordination that follow the dissociation of terminal ligands upon dissolution of the complexes.« less

Complementary Spectroscopic Assays for Investigating Protein-Ligand Binding Activity: A Project for the Advanced Chemistry Laboratory

ERIC Educational Resources Information Center

Mascotti, David P.; Waner, Mark J.

2010-01-01

A protein-ligand binding, guided-inquiry laboratory project with potential application across the advanced undergraduate curriculum is described. At the heart of the project are fluorescence and spectrophotometric assays utilizing biotin-4-fluorescein and streptavidin. The use of the same stock solutions for an assay that may be examined by two…

Hydroxyalkyl phosphine gold complexes for use as diagnostic and therapeutic pharmaceuticals and method of making same

DOEpatents

Katti, Kattesh V.; Berning, Douglas E.; Volkert, Wynn A.; Ketring, Alan R.

1998-01-01

A complex and method for making same for use as a diagnostic or therapeutic pharmaceutical includes a ligand comprising at least one hydroxyalkyl phosphine donor group bound to a gold atom to form a gold-ligand complex that is stable in aqueous solutions containing oxygen, serum and other body fluids.

Hydroxyalkyl phosphine gold complexes for use as diagnostic and therapeutic pharmaceuticals and method of making same

DOEpatents

Katti, K.V.; Berning, D.E.; Volkert, W.A.; Ketring, A.R.

1998-12-01

A complex and method for making a diagnostic or therapeutic pharmaceutical includes a ligand comprising at least one hydroxyalkyl phosphine donor group bound to a gold atom to form a gold-ligand complex that is stable in aqueous solutions containing oxygen, serum and other body fluids. 20 figs.

Coupled metal partitioning dynamics and toxicodynamics at biointerfaces: a theory beyond the biotic ligand model framework.

PubMed

Duval, Jérôme F L

2016-04-14

A mechanistic understanding of the processes governing metal toxicity to microorganisms (bacteria, algae) calls for an adequate formulation of metal partitioning at biointerfaces during cell exposure. This includes the account of metal transport dynamics from bulk solution to biomembrane and the kinetics of metal internalisation, both potentially controlling the intracellular and surface metal fractions that originate cell growth inhibition. A theoretical rationale is developed here for such coupled toxicodynamics and interfacial metal partitioning dynamics under non-complexing medium conditions with integration of the defining cell electrostatic properties. The formalism explicitly considers intertwined metal adsorption at the biointerface, intracellular metal excretion, cell growth and metal depletion from bulk solution. The theory is derived under relevant steady-state metal transport conditions on the basis of coupled Nernst-Planck equation and continuous logistic equation modified to include metal-induced cell growth inhibition and cell size changes. Computational examples are discussed to identify limitations of the classical Biotic Ligand Model (BLM) in evaluating metal toxicity over time. In particular, BLM is shown to severely underestimate metal toxicity depending on cell exposure time, metal internalisation kinetics, cell surface electrostatics and initial cell density. Analytical expressions are provided for the interfacial metal concentration profiles in the limit where cell-growth is completely inhibited. A rigorous relationship between time-dependent cell density and metal concentrations at the biosurface and in bulk solution is further provided, which unifies previous equations formulated by Best and Duval under constant cell density and cell size conditions. The theory is sufficiently flexible to adapt to toxicity scenarios with involved cell survival-death processes.

Crystal packing modifies ligand binding affinity: the case of aldose reductase.

PubMed

Cousido-Siah, Alexandra; Petrova, Tatiana; Hazemann, Isabelle; Mitschler, André; Ruiz, Francesc X; Howard, Eduardo; Ginell, Stephan; Atmanene, Cédric; Van Dorsselaer, Alain; Sanglier-Cianférani, Sarah; Joachimiak, Andrzej; Podjarny, Alberto

2012-11-01

The relationship between the structures of protein-ligand complexes existing in the crystal and in solution, essential in the case of fragment-based screening by X-ray crystallography (FBS-X), has been often an object of controversy. To address this question, simultaneous co-crystallization and soaking of two inhibitors with different ratios, Fidarestat (FID; K(d) = 6.5 nM) and IDD594 (594; K(d) = 61 nM), which bind to h-aldose reductase (AR), have been performed. The subatomic resolution of the crystal structures allows the differentiation of both inhibitors, even when the structures are almost superposed. We have determined the occupation ratio in solution by mass spectrometry (MS) Occ(FID)/Occ(594) = 2.7 and by X-ray crystallography Occ(FID)/Occ(594) = 0.6. The occupancies in the crystal and in solution differ 4.6 times, implying that ligand binding potency is influenced by crystal contacts. A structural analysis shows that the Loop A (residues 122-130), which is exposed to the solvent, is flexible in solution, and is involved in packing contacts within the crystal. Furthermore, inhibitor 594 contacts the base of Loop A, stabilizing it, while inhibitor FID does not. This is shown by the difference in B-factors of the Loop A between the AR-594 and AR-FID complexes. A stable loop diminishes the entropic energy barrier to binding, favoring 594 versus FID. Therefore, the effect of the crystal environment should be taken into consideration in the X-ray diffraction analysis of ligand binding to proteins. This conclusion highlights the need for additional methodologies in the case of FBS-X to validate this powerful screening technique, which is widely used. Copyright © 2012 Wiley Periodicals, Inc.

A novel signal transduction protein: Combination of solute binding and tandem PAS-like sensor domains in one polypeptide chain.

PubMed

Wu, R; Wilton, R; Cuff, M E; Endres, M; Babnigg, G; Edirisinghe, J N; Henry, C S; Joachimiak, A; Schiffer, M; Pokkuluri, P R

2017-04-01

We report the structural and biochemical characterization of a novel periplasmic ligand-binding protein, Dret_0059, from Desulfohalobium retbaense DSM 5692, an organism isolated from Lake Retba, in Senegal. The structure of the protein consists of a unique combination of a periplasmic solute binding protein (SBP) domain at the N-terminal and a tandem PAS-like sensor domain at the C-terminal region. SBP domains are found ubiquitously, and their best known function is in solute transport across membranes. PAS-like sensor domains are commonly found in signal transduction proteins. These domains are widely observed as parts of many protein architectures and complexes but have not been observed previously within the same polypeptide chain. In the structure of Dret_0059, a ketoleucine moiety is bound to the SBP, whereas a cytosine molecule is bound in the distal PAS-like domain of the tandem PAS-like domain. Differential scanning flourimetry support the binding of ligands observed in the crystal structure. There is significant interaction between the SBP and tandem PAS-like domains, and it is possible that the binding of one ligand could have an effect on the binding of the other. We uncovered three other proteins with this structural architecture in the non-redundant sequence data base, and predict that they too bind the same substrates. The genomic context of this protein did not offer any clues for its function. We did not find any biological process in which the two observed ligands are coupled. The protein Dret_0059 could be involved in either signal transduction or solute transport. © 2017 The Protein Society.

NMR and computational methods applied to the 3- dimensional structure determination of DNA and ligand-DNA complexes in solution

NASA Astrophysics Data System (ADS)

Smith, Jarrod Anson

2D homonuclear 1H NMR methods and restrained molecular dynamics (rMD) calculations have been applied to determining the three-dimensional structures of DNA and minor groove-binding ligand-DNA complexes in solution. The structure of the DNA decamer sequence d(GCGTTAACGC)2 has been solved both with a distance-based rMD protocol and an NOE relaxation matrix backcalculation-based protocol in order to probe the relative merits of the different refinement methods. In addition, three minor groove binding ligand-DNA complexes have been examined. The solution structure of the oligosaccharide moiety of the antitumor DNA scission agent calicheamicin γ1I has been determined in complex with a decamer duplex containing its high affinity 5'-TCCT- 3' binding sequence. The structure of the complex reinforces the belief that the oligosaccharide moiety is responsible for the sequence selective minor-groove binding activity of the agent, and critical intermolecular contacts are revealed. The solution structures of both the (+) and (-) enantiomers of the minor groove binding DNA alkylating agent duocarmycin SA have been determined in covalent complex with the undecamer DNA duplex d(GACTAATTGTC).d(GAC AATTAGTC). The results support the proposal that the alkylation activity of the duocarmycin antitumor antibiotics is catalyzed by a binding-induced conformational change in the ligand which activates the cyclopropyl group for reaction with the DNA. Comparisons between the structures of the two enantiomers covalently bound to the same DNA sequence at the same 5'-AATTA-3 ' site have provided insight into the binding orientation and site selectivity, as well as the relative rates of reactivity of these two agents.

Thermodynamics of water structural reorganization due to geometric confinement

NASA Astrophysics Data System (ADS)

Stroberg, Wylie; Lichter, Seth

2015-03-01

Models of aqueous solvation have successfully quantified the behavior of water near convex bodies. However, many important processes occurring in aqueous solution involve interactions between solutes and surfaces with complicated non-convex geometries. Examples include the folding of proteins, hydrophobic association of solutes, ligand-receptor binding, and water confined within nanotubes and pores. For these geometries, models for solvation of convex bodies fail to account for the added interactions associated with structural confinement. Due to water's propensity to form networks of hydrogen bonds, small alterations to the confining geometry can induce large structural rearrangement within the water. We perform systematic Monte Carlo simulations of water confined to cylindrical cavities of varying aspect ratio to investigate how small geometric changes to the confining geometry may cause large changes to the structure and thermodynamic state of water. Using the Wang-Landau algorithm, we obtain free energies, enthalpies, entropies, and heat capacities across a broad range of temperatures, and show how these quantities are influenced by the structural rearrangement of water molecules due to geometric perturbations.

Structure-function relationship of reduced cytochrome c probed by complete solution structure determination in 30% acetonitrile/water solution.

PubMed

Sivakolundu, Sivashankar G; Mabrouk, Patricia Ann

2003-05-01

The complete solution structure of ferrocytochrome c in 30% acetonitrile/70% water has been determined using high-field 1D and 2D (1)H NMR methods and deposited in the Protein Data Bank with codes 1LC1 and 1LC2. This is the first time a complete solution protein structure has been determined for a protein in nonaqueous media. Ferrocyt c retains a native protein secondary structure (five alpha-helices and two omega loops) in 30% acetonitrile. H18 and M80 residues are the axial heme ligands, as in aqueous solution. Residues believed to be axial heme ligands in the alkaline-like conformers of ferricyt c, specifically H33 and K72, are positioned close to the heme iron. The orientations of both heme propionates are markedly different in 30% acetonitrile/70% water. Comparative structural analysis of reduced cyt c in 30% acetonitrile/70% water solution with cyt c in different environments has given new insight into the cyt c folding mechanism, the electron transfer pathway, and cell apoptosis.

Fe N-Heterocyclic Carbene Complexes as Promising Photosensitizers.

PubMed

Liu, Yizhu; Persson, Petter; Sundström, Villy; Wärnmark, Kenneth

2016-08-16

The photophysics and photochemistry of transition metal complexes (TMCs) has long been a hot field of interdisciplinary research. Rich metal-based redox processes, together with a high variety in electronic configurations and excited-state dynamics, have rendered TMCs excellent candidates for interconversion between light, chemical, and electrical energies in intramolecular, supramolecular, and interfacial arrangements. In specific applications such as photocatalytic organic synthesis, photoelectrochemical cells, and light-driven supramolecular motors, light absorption by a TMC-based photosensitizer and subsequent excited-state energy or electron transfer constitute essential steps. In this context, TMCs based on rare and expensive metals, such as ruthenium and iridium, are frequently employed as photosensitizers, which is obviously not ideal for large-scale implementation. In the search for abundant and environmentally benign solutions, six-coordinate Fe(II) complexes (Fe(II)L6) have been widely considered as highly desirable alternatives. However, not much success has been achieved due to the extremely short-lived triplet metal-to-ligand charge transfer ((3)MLCT) excited state that is deactivated by low-lying metal-centered (MC) states on a 100 fs time scale. A fundamental strategy to design useful Fe-based photosensitizers is thus to destabilize the MC states relative to the (3)MLCT state by increasing the ligand field strength, with special focus on making eg σ* orbitals on the Fe center energetically less accessible. Previous efforts to directly transplant successful strategies from Ru(II)L6 complexes unfortunately met with limited success in this regard, despite their close chemical kinship. In this Account, we summarize recent promising results from our and other groups in utilizing strongly σ-donating N-heterocyclic carbene (NHC) ligands to make strong-field Fe(II)L6 complexes with significantly extended (3)MLCT lifetimes. Already some of the first homoleptic bis(tridentate) complexes incorporating (CNHC^Npyridine^CNHC)-type ligands gratifyingly resulted in extension of the (3)MLCT lifetime by more than 2 orders of magnitude compared to the parental [Fe(tpy)2](2+) (tpy = 2,2':6',2″-terpyridine) complex. Quantum chemical (QC) studies also revealed that the (3)MC instead of the (5)MC state likely dictates the deactivation of the (3)MLCT state, a behavior distinct from traditional Fe(II)L6 complexes but rather resembling Ru analogues. A heteroleptic Fe(II) NHC complex featuring mesoionic bis(1,2,3-triazol-5-ylidene) (btz) ligands also delivered a 100-fold elongation of the (3)MLCT lifetime relative to its parental [Fe(bpy)3](2+) (bpy = 2,2'-bipyridine) complex. Again, a Ru-like deactivation mechanism of the (3)MLCT state was indicated by QC studies. With a COOH-functionalized homoleptic complex, a record (3)MLCT lifetime of 37 ps was recently observed on an Al2O3 nanofilm. As a proof of concept, it was further demonstrated that the significant improvement in the (3)MLCT lifetime indeed benefits efficient light harvesting with Fe(II) NHC complexes. For the first time, close-to-unity electron injection from the lowest-energy (3)MLCT state to a TiO2 nanofilm was achieved by a stable Fe(II) complex. This is in complete contrast to conventional Fe(II)L6-derived photosensitizers that could only make use of high-energy photons. These exciting results significantly broaden the understanding of the fundamental photophysics and photochemistry of d(6) Fe(II) complexes. They also open up new possibilities to develop solar energy-converting materials based on this abundant, inexpensive, and intrinsically nontoxic element.

Rationalization of the solvation effects on the AtO+ ground-state change.

PubMed

Ayed, Tahra; Réal, Florent; Montavon, Gilles; Galland, Nicolas

2013-09-12

(211)At radionuclide is of considerable interest as a radiotherapeutic agent for targeted alpha therapy in nuclear medicine, but major obstacles remain because the basic chemistry of astatine (At) is not well understood. The AtO(+) cationic form might be currently used for (211)At-labeling protocols in aqueous solution and has proved to readily react with inorganic/organic ligands. But AtO(+) reactivity must be hindered at first glance by spin restriction quantum rules: the ground state of the free cation has a dominant triplet character. Investigating AtO(+) clustered with an increasing number of water molecules and using various flavors of relativistic quantum methods, we found that AtO(+) adopts in solution a Kramers restricted closed-shell configuration resembling a scalar-relativistic singlet. The ground-state change was traced back to strong interactions, namely, attractive electrostatic interactions and charge transfer, with water molecules of the first solvation shell that lift up the degeneracy of the frontier π* molecular orbitals (MOs). This peculiarity brings an alternative explanation to the highly variable reproducibility reported for some astatine reactions: depending on the production protocols (with distillation in gas-phase or "wet chemistry" extraction), (211)At may or may not readily react.

Anchoring protein crystals to mounting loops with hydrogel using inkjet technology.

PubMed

Shinoda, Akira; Tanaka, Yoshikazu; Yao, Min; Tanaka, Isao

2014-11-01

X-ray crystallography is an important technique for structure-based drug discovery, mainly because it is the only technique that can reveal whether a ligand binds to the target protein as well as where and how it binds. However, ligand screening by X-ray crystallography involves a crystal-soaking experiment, which is usually performed manually. Thus, the throughput is not satisfactory for screening large numbers of candidate ligands. In this study, a technique to anchor protein crystals to mounting loops by using gel and inkjet technology has been developed; the method allows soaking of the mounted crystals in ligand-containing solution. This new technique may assist in the design of a fully automated drug-screening pipeline.

Microwave-assisted synthesis of water-soluble, fluorescent gold nanoclusters capped with small organic molecules and a revealing fluorescence and X-ray absorption study

NASA Astrophysics Data System (ADS)

Helmbrecht, C.; Lützenkirchen-Hecht, D.; Frank, W.

2015-03-01

Colourless solutions of blue light-emitting, water-soluble gold nanoclusters (AuNC) were synthesized from gold colloids under microwave irradiation using small organic molecules as ligands. Stabilized by 1,3,5-triaza-7-phosphaadamantane (TPA) or l-glutamine (GLU), fluorescence quantum yields up to 5% were obtained. AuNC are considered to be very promising for biological labelling, optoelectronic devices and light-emitting materials but the structure-property relationships have still not been fully clarified. To expand the knowledge about the AuNC apart from their fluorescent properties they were studied by X-ray absorption spectroscopy elucidating the oxidation state of the nanoclusters' gold atoms. Based on curve fitting of the XANES spectra in comparison to several gold references, optically transparent fluorescent AuNC are predicted to be ligand-stabilized Au5+ species. Additionally, their near edge structure compared with analogous results of polynuclear clusters known from the literature discloses an increasing intensity of the feature close to the absorption edge with decreasing cluster size. As a result, a linear relationship between the cluster size and the X-ray absorption coefficient can be established for the first time.Colourless solutions of blue light-emitting, water-soluble gold nanoclusters (AuNC) were synthesized from gold colloids under microwave irradiation using small organic molecules as ligands. Stabilized by 1,3,5-triaza-7-phosphaadamantane (TPA) or l-glutamine (GLU), fluorescence quantum yields up to 5% were obtained. AuNC are considered to be very promising for biological labelling, optoelectronic devices and light-emitting materials but the structure-property relationships have still not been fully clarified. To expand the knowledge about the AuNC apart from their fluorescent properties they were studied by X-ray absorption spectroscopy elucidating the oxidation state of the nanoclusters' gold atoms. Based on curve fitting of the XANES spectra in comparison to several gold references, optically transparent fluorescent AuNC are predicted to be ligand-stabilized Au5+ species. Additionally, their near edge structure compared with analogous results of polynuclear clusters known from the literature discloses an increasing intensity of the feature close to the absorption edge with decreasing cluster size. As a result, a linear relationship between the cluster size and the X-ray absorption coefficient can be established for the first time. Electronic supplementary information (ESI) available: The deconvoluted reference spectra are given in ESI Fig. 1-9. See DOI: 10.1039/c4nr07051h

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jay, Raphael M.; Norell, Jesper; Eckert, Sebastian

Soft X-ray spectroscopies are ideal probes of the local valence electronic structure of photocatalytically active metal sites. Here, we apply the selectivity of time-resolved resonant inelastic X-ray scattering at the iron L-edge to the transient charge distribution of an optically excited charge-transfer state in aqueous ferricyanide. Through comparison to steady-state spectra and quantum chemical calculations, the coupled effects of valence-shell closing and ligand-hole creation are experimentally and theoretically disentangled and described in terms of orbital occupancy, metal–ligand covalency, and ligand field splitting, thereby extending established steady-state concepts to the excited-state domain. π-Back-donation is found to be mainly determined by themore » metal site occupation, whereas the ligand hole instead influences σ-donation. Here, our results demonstrate how ultrafast resonant inelastic X-ray scattering can help characterize local charge distributions around catalytic metal centers in short-lived charge-transfer excited states, as a step toward future rationalization and tailoring of photocatalytic capabilities of transition-metal complexes.« less

Selective Precipitation and Purification of Monovalent Proteins Using Oligovalent Ligands and Ammonium Sulfate

PubMed Central

Mirica, Katherine A.; Lockett, Matthew R.; Snyder, Phillip W.; Shapiro, Nathan D.; Mack, Eric T.; Nam, Sarah; Whitesides, George M.

2012-01-01

This paper describes a method for the selective precipitation and purification of a monovalent protein (carbonic anhydrase is used as a demonstration) from cellular lysate using ammonium sulfate and oligovalent ligands. The oligovalent ligands induce the formation of protein-ligand aggregates, and at an appropriate concentration of dissolved ammonium sulfate, these complexes precipitate. The purification involves three steps: i) the removal of high-molecular weight impurities through the addition of ammonium sulfate to the crude cell lysate; ii) the introduction of an oligovalent ligand and the selective precipitation of the target protein-ligand aggregates from solution; and iii) the removal of the oligovalent ligand from the precipitate by dialysis to release the target protein. The increase of mass and volume of the proteins upon aggregate formation reduces their solubility, and results in the selective precipitation of these aggregates. We recovered human carbonic anhydrase, from crude cellular lysate, in 82% yield and 95% purity with a trivalent benzene sulfonamide ligand. This method provides a chromatography-free strategy of purifying monovalent proteins—for which appropriate oligovalent ligands can be synthesized—and combines the selectivity of affinity-based purification with the convenience of salt-induced precipitation. PMID:22188202

Selective precipitation and purification of monovalent proteins using oligovalent ligands and ammonium sulfate.

PubMed

Mirica, Katherine A; Lockett, Matthew R; Snyder, Phillip W; Shapiro, Nathan D; Mack, Eric T; Nam, Sarah; Whitesides, George M

2012-02-15

This paper describes a method for the selective precipitation and purification of a monovalent protein (carbonic anhydrase is used as a demonstration) from cellular lysate using ammonium sulfate and oligovalent ligands. The oligovalent ligands induce the formation of protein-ligand aggregates, and at an appropriate concentration of dissolved ammonium sulfate, these complexes precipitate. The purification involves three steps: (i) the removal of high-molecular-weight impurities through the addition of ammonium sulfate to the crude cell lysate; (ii) the introduction of an oligovalent ligand and the selective precipitation of the target protein-ligand aggregates from solution; and (iii) the removal of the oligovalent ligand from the precipitate by dialysis to release the target protein. The increase of mass and volume of the proteins upon aggregate formation reduces their solubility, and results in the selective precipitation of these aggregates. We recovered human carbonic anhydrase, from crude cellular lysate, in 82% yield and 95% purity with a trivalent benzene sulfonamide ligand. This method provides a chromatography-free strategy of purifying monovalent proteins--for which appropriate oligovalent ligands can be synthesized--and combines the selectivity of affinity-based purification with the convenience of salt-induced precipitation.

Ligand-Receptor Interaction Modulates the Energy Landscape of Enzyme-Instructed Self-Assembly of Small Molecules.

PubMed

Haburcak, Richard; Shi, Junfeng; Du, Xuewen; Yuan, Dan; Xu, Bing

2016-11-30

The concurrence of enzymatic reaction and ligand-receptor interactions is common for proteins, but rare for small molecules and has yet to be explored. Here we show that ligand-receptor interaction modulates the morphology of molecular assemblies formed by enzyme-instructed assembly of small molecules. While the absence of ligand-receptor interaction allows enzymatic dephosphorylation of a precursor to generate the hydrogelator that self-assembles to form long nanofibers, the presence of the ligand-receptor interaction biases the pathway to form precipitous aggregates containing short nanofibers. While the hydrogelators self-assemble to form nanofibers or nanoribbons that are unable to bind with the ligand (i.e., vancomycin), the addition of surfactant breaks up the assemblies to restore the ligand-receptor interaction. In addition, an excess amount of the ligands can disrupt the nanofibers and result in the precipitates. As the first example of the use of ligand-receptor interaction to modulate the kinetics of enzymatic self-assembly, this work not only provides a solution to evaluate the interaction between aggregates and target molecules but also offers new insight for understanding the emergent behavior of sophisticated molecular systems having multiple and parallel processes.

Excited States and Luminescent Properties of UO 2F 2 and Its Solvated Complexes in Aqueous Solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Su, Jing; Wang, Zheming; Pan, Duoqiang

2014-07-21

The electronic absorption and emission spectra of free UO 2F 2 and its water solvated complexes below 32 000 cm –1 are investigated at the levels of ab initio CASPT2 and CCSD(T) with inclusion of scalar relativistic and spin–orbit coupling effects. The influence of the water coordination on the electronic spectra of UO 2F 2 is explored by investigating the excited states of solvated complexes (H 2O) nUO 2F 2 (n = 1–3). In these uranyl complexes, water coordination is found to have appreciable influence on the 3Δ (Ω = 1 g) character of the luminescent state and on themore » electronic spectral shape. The simulated luminescence spectral curves based on the calculated spectral parameters of (H 2O) nUO 2F 2 from CCSD(T) approach agree well with experimental spectra in aqueous solution at both near-liquid-helium temperature and room temperature. The possible luminescence spectra of free UO 2F 2 in gas phase are predicted on the basis of CASPT2 and CCSD(T) results, respectively, by considering three symmetric vibration modes. Finally, the effect of competition between spin–orbit coupling and ligand field repulsion on the luminescent state properties is discussed.« less

Structure, Bonding, and Stability of Mercury Complexes with Thiolate and Thioether Ligands from High-Resolution XANES Spectroscopy and First-Principles Calculations.

PubMed

Manceau, Alain; Lemouchi, Cyprien; Rovezzi, Mauro; Lanson, Martine; Glatzel, Pieter; Nagy, Kathryn L; Gautier-Luneau, Isabelle; Joly, Yves; Enescu, Mironel

2015-12-21

We present results obtained from high energy-resolution L3-edge XANES spectroscopy and first-principles calculations for the structure, bonding, and stability of mercury(II) complexes with thiolate and thioether ligands in crystalline compounds, aqueous solution, and macromolecular natural organic matter (NOM). Core-to-valence XANES features that vary in intensity differentiate with unprecedented sensitivity the number and identity of Hg ligands and the geometry of the ligand environment. Post-Hartree-Fock XANES calculations, coupled with natural population analysis, performed on MP2-optimized Hg[(SR)2···(RSR)n] complexes show that the shape, position, and number of electronic transitions observed at high energy-resolution are directly correlated to the Hg and S (l,m)-projected empty densities of states and occupations of the hybridized Hg 6s and 5d valence orbitals. Linear two-coordination, the most common coordination geometry in mercury chemistry, yields a sharp 2p to 6s + 5d electronic transition. This transition varies in intensity for Hg bonded to thiol groups in macromolecular NOM. The intensity variation is explained by contributions from next-nearest, low-charge, thioether-type RSR ligands at 3.0-3.3 Å from Hg. Thus, Hg in NOM has two strong bonds to thiol S and k additional weak Hg···S contacts, or 2 + k coordination. The calculated stabilization energy is -5 kcal/mol per RSR ligand. Detection of distant ligands beyond the first coordination shell requires precise measurement of, and comparison to, spectra of reference compounds as well as accurate calculation of spectra for representative molecular models. The combined experimental and theoretical approaches described here for Hg can be applied to other closed-shell atoms, such as Ag(I) and Au(I). To facilitate further calculation of XANES spectra, experimental data, a new crystallographic structure of a key mercury thioether complex, Cartesian coordinates of the computed models, and examples of input files are provided as Supporting Information .

Ligand-Induced Conformational Change in the α7 Nicotinic Receptor Ligand Binding Domain

PubMed Central

Henchman, Richard H.; Wang, Hai-Long; Sine, Steven M.; Taylor, Palmer; McCammon, J. Andrew

2005-01-01

Molecular dynamics simulations of a homology model of the ligand binding domain of the α7 nicotinic receptor are conducted with a range of bound ligands to induce different conformational states. Four simulations of 15 ns each are run with no ligand, antagonist d-tubocurarine (dTC), agonist acetylcholine (ACh), and agonist ACh with potentiator Ca2+, to give insight into the conformations of the active and inactive states of the receptor and suggest the mechanism for conformational change. The main structural factor distinguishing the active and inactive states is that a more open, symmetric arrangement of the five subunits arises for the two agonist simulations, whereas a more closed and asymmetric arrangement results for the apo and dTC cases. Most of the difference arises in the lower portion of the ligand binding domain near its connection to the adjacent transmembrane domain. The transfer of the more open state to the transmembrane domain could then promote ion flow through the channel. Variation in how subunits pack together with no ligand bound appears to give rise to asymmetry in the apo case. The presence of dTC expands the receptor but induces rotations in alternate directions in adjacent subunits that lead to an asymmetric arrangement as in the apo case. Ca2+ appears to promote a slightly greater expansion in the subunits than ACh alone by stabilizing the C-loop and ACh positions. Although the simulations are unlikely to be long enough to view the full conformational changes between open and closed states, a collection of different motions at a range of length scales are observed that are likely to participate in the conformational change. PMID:15665135

Gallium(III) complexes of DOTA and DOTA-monoamide: kinetic and thermodynamic studies.

PubMed

Kubícek, Vojtech; Havlícková, Jana; Kotek, Jan; Tircsó, Gyula; Hermann, Petr; Tóth, Eva; Lukes, Ivan

2010-12-06

Given the practical advantages of the (68)Ga isotope in positron emission tomography applications, gallium complexes are gaining increasing importance in biomedical imaging. However, the strong tendency of Ga(3+) to hydrolyze and the slow formation and very high stability of macrocyclic complexes altogether render Ga(3+) coordination chemistry difficult and explain why stability and kinetic data on Ga(3+) complexes are rather scarce. Here we report solution and solid-state studies of Ga(3+) complexes formed with the macrocyclic ligand 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid, (DOTA)(4-), and its mono(n-butylamide) derivative, (DO3AM(Bu))(3-). Thermodynamic stability constants, log K(GaDOTA) = 26.05 and log K(GaDO3AM(Bu)) = 24.64, were determined by out-of-cell pH-potentiometric titrations. Due to the very slow formation and dissociation of the complexes, equilibration times of up to ∼4 weeks were necessary. The kinetics of complex dissociation were followed by (71)Ga NMR under both acidic and alkaline conditions. The GaDOTA complex is significantly more inert (τ(1/2) ∼12.2 d at pH = 0 and τ(1/2) ∼6.2 h at pH = 10) than the GaDO3AM(Bu) analogue (τ(1/2) ∼2.7 d at pH = 0 and τ(1/2) ∼0.7 h at pH = 10). Nevertheless, the kinetic inertness of both chelates is extremely high and approves the application of Ga(3+) complexes of such DOTA-like ligands in molecular imaging. The solid-state structure of the GaDOTA complex, crystallized from a strongly acidic solution (pH < 1), evidenced a diprotonated form with protons localized on the free carboxylate pendants.

Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases.

PubMed

Volbeda, Anne; Martin, Lydie; Cavazza, Christine; Matho, Michaël; Faber, Bart W; Roseboom, Winfried; Albracht, Simon P J; Garcin, Elsa; Rousset, Marc; Fontecilla-Camps, Juan C

2005-05-01

[NiFe] hydrogenases catalyze the reversible heterolytic cleavage of molecular hydrogen. Several oxidized, inactive states of these enzymes are known that are distinguishable by their very different activation properties. So far, the structural basis for this difference has not been understood because of lack of relevant crystallographic data. Here, we present the crystal structure of the ready Ni-B state of Desulfovibrio fructosovorans [NiFe] hydrogenase and show it to have a putative mu-hydroxo Ni-Fe bridging ligand at the active site. On the other hand, a new, improved refinement procedure of the X-ray diffraction data obtained for putative unready Ni-A/Ni-SU states resulted in a more elongated electron density for the bridging ligand, suggesting that it is a diatomic species. The slow activation of the Ni-A state, compared with the rapid activation of the Ni-B state, is therefore proposed to result from the different chemical nature of the ligands in the two oxidized species. Our results along with very recent electrochemical studies suggest that the diatomic ligand could be hydro-peroxide.

Mechanistic studies of hydrogen evolution in aqueous solution catalyzed by a tertpyridine-amine cobalt complex

DOE PAGES

Lewandowska-Andralojc, Anna; Baine, Teera; Zhao, Xuan; ...

2015-04-22

The ability of cobalt-based transition metal complexes to catalyze electrochemical proton reduction to produce molecular hydrogen has resulted in a large number of mechanistic studies involving various cobalt complexes. In addition, while the basic mechanism of proton reduction promoted by cobalt species is well understood, the reactivity of certain reaction intermediates, such as Co I and Co III–H, is still relatively unknown owing to their transient nature, especially in aqueous media. In this work we investigate the properties of intermediates produced during catalytic proton reduction in aqueous solutions promoted by the [(DPA-Bpy)Co(OH₂)] n+ (DPA-Bpy = N,N-bis(2-pyridinylmethyl)-2,20-bipyridine-6-methanamine) complex ([Co(L)(OH₂)] n+ wheremore » L is the pentadentate DPA-Bpy ligand or [ Co(OH₂)] n+ as a shorthand). Experimental results based on transient pulse radiolysis and laser flash photolysis methods, together with electrochemical studies and supported by DFT calculations indicate that, while the water ligand is strongly coordinated to the metal center in the oxidation state 3+, one-electron reduction of the complex to form a Co II species results in weakening the Co–O bond. The further reduction to a Co I species leads to the loss of the aqua ligand and the formation of [ CoI–VS)]⁺ (VS = vacant site). Interestingly, DFT calculations also predict the existence of a [Co I(κ⁴-L)(OH₂)]⁺ species at least transiently, and its formation is consistent with the experimental Pourbaix diagram. Both electrochemical and kinetics results indicate that the Co I species must undergo some structural change prior to accepting the proton, and this transformation represents the rate-determining step (RDS) in the overall formation of [ CoIII–H]⁺. We propose that this RDS may originate from the slow removal of a solvent ligand in the intermediate [Co I(κ⁴-L)(OH₂)]⁺ in addition to the significant structural reorganization of the metal complex and surrounding solvent resulting in a high free energy of activation.« less

The Behavior of the Ru-bda Water Oxidation Catalysts at Low Oxidation States.

PubMed

Matheu, Roc; Ghaderian, Abolfazl; Francas, Laia; Chernev, Petko; Ertem, Mehmed; Benet-Buchholz, Jordi; Batista, Victor; Haumann, Michael; Gimbert-Suriñach, Carolina; Sala, Xavier; Llobet, Antoni

2018-06-13

The Ru complex [RuII(bda-κ-N2O2)(N-NH2)2], 1, (bda2- = (2,2'-bipyridine)-6,6'-dicarboxylate; N-NH2 = 4-(pyridin-4-yl)aniline) is used as a synthetic intermediate to prepare Ru-bda complexes that contain the NO+, acetonitrile (MeCN) or H2O ligands at oxidation states II and III. Complex 1 reacts with excess NO+ to form a Ru complex where the aryl amine ligands N-NH2 in 1 are transformed into diazonium salts (N-N2+ = 4-(pyridin-4-yl)benzenediazonium)) together with the formation of a new Ru-NO group at the equatorial zone, to generate [RuII(bda-κ-N2O)(NO)(N-N2)2]3+, 23+. Similarly, complex 1 can also react with a coordinating solvent, such as MeCN, at room temperature leading to complex [RuII(bda-κ-N2O)(MeCN)(N-NH2)2], 3. Finally in acidic aqueous solutions solvent water coordinates the Ru center forming {[RuII(bda-κ-(NO)3)(H2O)(N-NH3)2](H2O)n}2+, 42+, that is strongly hydrogen bonded with additional water molecules at the second coordination sphere. We have additionally characterized the one electron oxidized complex {[RuIII(bda-κ-(NO)3.5)(H2O)(N-NH3)2](H2O)n}3+, 53+. The coordination mode of the complexes has been studied both in the solid state and in solution through single-crystal XRD, X-ray absorption spectroscopy, variable-temperature NMR and DFT calculations. While the κ-N2O is the main coordination mode for 23+ and 3, an equilibrium that involves isomers with κ-N2O and κ-NO2 coordination modes and neighboring hydrogen bonded water molecules is observed for 42+ and 53+. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Application of the principle of linked functions to ATP-driven ion pumps: kinetics of activation by ATP.

PubMed Central

Reynolds, J A; Johnson, E A; Tanford, C

1985-01-01

If a ligand binds with unequal affinity to two distinct states of a protein, then the equilibrium between the two states becomes a function of the concentration of the ligand. A necessary consequence is that the ligand must also affect the forward and/or reverse rate constants for transition between the two states. For an enzyme or transport protein with such a transition as a slow step in the catalytic cycle, the overall rate also becomes a function of ligand concentration. These conclusions are independent of whether or not the ligand is a direct participant in the reaction. If it is a direct participant, then the kinetic effect arising from the principle of linked functions is distinct from the direct catalytic effect. These principles suffice to account for the biphasic response of the hydrolytic activity of ATP-driven ion pumps to the concentration of ATP, without the need to invoke more than one ATP binding site per catalytic center. PMID:2987939

Synthesis, stabilization, and characterization of metal nanoparticles

NASA Astrophysics Data System (ADS)

White, Gregory Von, II

Wet chemical synthesis techniques offer the ability to control various nanoparticle characteristics including size, shape, dispersibility in both aqueous and organic solvents, and tailored surface chemistries appropriate for different applications. Large quantities of stabilizing ligands or surfactants are often required during synthesis to achieve these nanoparticle characteristics. Unfortunately, excess reaction byproducts, surfactants, and ligands remaining in solution after nanoparticle synthesis can impede application, and therefore post-synthesis purification must be employed. A liquid-liquid solvent/antisolvent pair (typically ethanol/toluene or ethanol/hexane for gold nanoparticles, GNPs) can be used to both purify and size-selectively fractionate hydrophobically modified nanoparticles. Alternatively, carbon dioxide may be used in place of a liquid antisolvent, a "green" approach, enabling both nanoparticle purification and size-selective fractionation while simultaneously eliminating mixed solvent waste and allowing solvent recycle. We have used small-angle neutron scattering (SANS) to investigate the ligand structure and composition response of alkanethiol modified gold and silver nanoparticles at varying anti-solvent conditions (CO2 or ethanol). The ligand lengths and ligand solvation for alkanethiol gold and silver NPs were found to decrease with increased antisolvent concentrations directly impacting their dispersibility in solution. Calculated Flory-Huggins interaction parameters support our SANS study for dodecanethiol dispersibility in the mixed organic solvents. This research has led to a greater understanding of the liquid-liquid precipitation process for metal nanoparticles, and provides critical results for future interaction energy modeling.

Controlled Redox Chemistry at Cerium within a Tripodal Nitroxide Ligand Framework

DOE PAGES

Bogart, Justin A.; Lippincott, Connor A.; Carroll, Patrick J.; ...

2015-10-27

Ligand reorganization has been shown to have a profound effect on the outcome of cerium redox chemistry. Through the use of a tethered, tripodal, trianionic nitroxide ligand, [((2-tBuNOH)C 6 H 4 CH 2 ) 3 N] 3- (TriNO x 3- ), controlled redox chemistry at cerium was accomplished, and typically reactive complexes of tetravalent cerium were isolated. These included rare cationic complexes [Ce(TriNO x )thf][BAr F 4 ], in which Ar F =3,5-(CF 3 ) 2 -C 6 H 3 , and [Ce(TriNO x )py][OTf] . A rare complete Ce-halide series, Ce(TriNO x )X, in which X=F - , Clmore » - , Br - , I - , was also synthesized. We explored the solution chemistry of these complexes through detailed solution-phase electrochemistry and 1 H NMR experiments and showed a unique shift in the ratio of species with inner- and outer-sphere anions with size of the anionic X - group. DFT calculations on the series of calculations corroborated the experimental findings. Also, the use of a bulky and strongly donating tethered tripodal nitroxide ligand allowed the controlled redox chemistry at cerium. As a result, rare examples of cationic Ce IV complexes were synthesized and fully characterized. The full Ce-halide series supported by the tripodal ligand framework is also reported (see scheme).« less

Exchangeability of N termini in the ligand-gated porins of Escherichia coli.

PubMed

Scott, D C; Cao, Z; Qi, Z; Bauler, M; Igo, J D; Newton, S M; Klebba, P E

2001-04-20

The ferric siderophore transporters of the Gram-negative bacterial outer membrane manifest a unique architecture: Their N termini fold into a globular domain that lodges within, and physically obstructs, a transmembrane porin beta-barrel formed by their C termini. We exchanged and deleted the N termini of two such siderophore receptors, FepA and FhuA, which recognize and transport ferric enterobactin and ferrichrome, respectively. The resultant chimeric proteins and empty beta-barrels avidly bound appropriate ligands, including iron complexes, protein toxins, and viruses. Thus, the ability to recognize and discriminate these molecules fully originates in the transmembrane beta-barrel domain. Both the hybrid and the deletion proteins also transported the ferric siderophore that they bound. The FepA constructs showed less transport activity than wild type receptor protein, but the FhuA constructs functioned with turnover numbers that were equivalent to wild type. The mutant proteins displayed the full range of transport functionalities, despite their aberrant or missing N termini, confirming (Braun, M., Killmann, H., and Braun, V. (1999) Mol. Microbiol. 33, 1037-1049) that the globular domain within the pore is dispensable to the siderophore internalization reaction, and when present, acts without specificity during solute uptake. These and other data suggest a transport process in which siderophore receptors undergo multiple conformational states that ultimately expel the N terminus from the channel concomitant with solute internalization.

Surface functionalization of titanium dioxide nanoparticles: Photo-stability and reactive oxygen species (ROS) generation

NASA Astrophysics Data System (ADS)

Louis, Kacie M.

Metal oxide nanoparticles are becoming increasingly prevalent in society for applications of sunscreens, cosmetics, paints, biomedical imaging, and photovoltaics. Due to the increased surface area to volume ratio of nanoparticles compared to bulk materials, it is important to know the health and safety impacts of these materials. One mechanism of toxicity of nominally "safe" materials such as TiO 2 is through the photocatalytic generation of reactive oxygen species (ROS). ROS production and ligand degradation can affect the bioavailability of these particles in aqueous organisms. We have investigated ROS generation by functionalized TiO2 nanoparticles and its influence on aggregation and bioavailability and toxicity to zebrafish embryos/larvae. For these studies we investigated anatase TiO2 nanoparticles. For application purposes and solution stability, the TiO2 nanoparticles were functionalized with a variety of ligands such as citrate, 3,4-dihydroxybenzaldehyde, and ascorbate. We quantitatively examined the amount of ROS produced in aqueous solution using fluorescent probes and see that more ROS is produced under UV light than in the dark control. Our measurements show that TiO2 toxicity reaches a maximum for nanoparticles with smaller diameters, and is correlated with surface area dependent changes in ROS generation. In an effort to reduce toxicity through control of the surface and surface ligands, we synthesized anatase nanoparticles of different sizes, functionalized them with different ligands, and examined the resulting ROS generation and ligand stability. Using a modular ligand containing a hydrophobic inner region and a hydrophilic outer region, we synthesized water-stable nanoparticles, via two different chemical reactions, having much-reduced ROS generation and thus reduced toxicity. These results suggest new strategies for making safer nanoparticles while still retaining their desired properties. We also examine the degradation of the different ligands on the surface of the particles using XPS and FTIR. The combination of ROS production and ligand degradation can affect the bioavailability of these particles in aqueous species.

Calix[4]arenes as selective extracting agents. An NMR dynamic and conformational investigation of the lanthanide(III) and thorium(IV) complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lambert, B.; Jacques, V.; Shivanyuk, A.

The lanthanide and Th{sup 4+} complexes with calix[4]arene ligands substituted either on the narrow or at the wide rim by four coordinating groups behave totally differently as shown by an NMR investigation of the dia- and paramagnetic complexes. Solutions of complexes were prepared by reacting anhydrous metal perchlorate salts with the ligands in dry acetonitrile (CAUTION). Relaxation time T{sub 1} titrations of acetonitrile solutions of Gd{sup 3+} by calixarenes indicate that ligands substituted on the narrow rim form stable 1:1 complexes whether they feature four amide groups (1) or four phosphine oxide functions. In contrast, a ligand substituted by fourmore » (carbamoylmethyl)-diphenylphosphine oxide moieties on the wide rim (3) and its derivatives form polymeric species even at a 1:1 ligand/metal concentration ratio. Nuclear magnetic relaxation dispersion (NMRD) curves (relaxation rates 1/T{sub 1} vs magnetic field strength) of Gd{sup 3+}, Gd{sup 3+}{center_dot}1 and Gd{sup 3+}{center_dot}3 perchlorates in acetonitrile are analyzed by an extended version of the Solomon-Bloembergen-Morgan equations. A comparison of the calculated rotational correlation times {tau}{sub r} shows that ligand 3 forms oligomeric Gd{sup 3+} species. The chelates of ligand 1 are axially symmetric (C{sub 4} symmetry), and the paramagnetic shifts induced by the Yb{sup 3+} ion are accounted for quantitatively. The addition of water or of nitrate ions does not modify the geometry of the complex. The metal chelates of 3 and its derivatives adopt a C{sub 2} symmetry, and the paramagnetic shifts are interpreted on a semiquantitative basis only. Water and NO{sub 3}{sup {minus}} ions completely labilize the complexes of the heavy lanthanides. The very high selectivity of ligand 3 through the lanthanide series stems from a complex interplay of factors.« less

Ligand-induced Epitope Masking: DISSOCIATION OF INTEGRIN α5β1-FIBRONECTIN COMPLEXES ONLY BY MONOCLONAL ANTIBODIES WITH AN ALLOSTERIC MODE OF ACTION.

PubMed

Mould, A Paul; Askari, Janet A; Byron, Adam; Takada, Yoshikazu; Jowitt, Thomas A; Humphries, Martin J

2016-09-30

We previously demonstrated that Arg-Gly-Asp (RGD)-containing ligand-mimetic inhibitors of integrins are unable to dissociate pre-formed integrin-fibronectin complexes (IFCs). These observations suggested that amino acid residues involved in integrin-fibronectin binding become obscured in the ligand-occupied state. Because the epitopes of some function-blocking anti-integrin monoclonal antibodies (mAbs) lie near the ligand-binding pocket, it follows that the epitopes of these mAbs may become shielded in the ligand-occupied state. Here, we tested whether function-blocking mAbs directed against α5β1 can interact with the integrin after it forms a complex with an RGD-containing fragment of fibronectin. We showed that the anti-α5 subunit mAbs JBS5, SNAKA52, 16, and P1D6 failed to disrupt IFCs and hence appeared unable to bind to the ligand-occupied state. In contrast, the allosteric anti-β1 subunit mAbs 13, 4B4, and AIIB2 could dissociate IFCs and therefore were able to interact with the ligand-bound state. However, another class of function-blocking anti-β1 mAbs, exemplified by Lia1/2, could not disrupt IFCs. This second class of mAbs was also distinguished from 13, 4B4, and AIIB2 by their ability to induce homotypic cell aggregation. Although the epitope of Lia1/2 was closely overlapping with those of 13, 4B4, and AIIB2, it appeared to lie closer to the ligand-binding pocket. A new model of the α5β1-fibronectin complex supports our hypothesis that the epitopes of mAbs that fail to bind to the ligand-occupied state lie within, or very close to, the integrin-fibronectin interface. Importantly, our findings imply that the efficacy of some therapeutic anti-integrin mAbs could be limited by epitope masking. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Synthesis and Base Hydrolysis of a Cobalt(III) Complex Coordinated by a Thioether Ligand

ERIC Educational Resources Information Center

Roecker, Lee

2008-01-01

A two-week laboratory experiment for students in advanced inorganic chemistry is described. Students prepare and characterize a cobalt(III) complex coordinated by a thioether ligand during the first week of the experiment and then study the kinetics of Co-S bond cleavage in basic solution during the second week. The synthetic portion of the…

Interactions of aromatic amino acids with heterocyclic ligand: An IR spectroscopic study

NASA Astrophysics Data System (ADS)

Tyunina, E. Yu.; Badelin, V. G.; Tarasova, G. N.

2015-09-01

The interactions of L-phenylalanine and L-tryptophan with nicotinic acid and uracyl in an aqueous buffer solution at pH 7.35 were studied by IR spectroscopy. The contributions of various functional groups to the complexation of aromatic amino acids with heterocyclic ligands were determined from the IR spectra of the starting substances and their mixtures.

Hydrogen peroxide and dioxygen activation by dinuclear copper complexes in aqueous solution: hydroxyl radical production initiated by internal electron transfer.

PubMed

Zhu, Qing; Lian, Yuxiang; Thyagarajan, Sunita; Rokita, Steven E; Karlin, Kenneth D; Blough, Neil V

2008-05-21

Dinuclear Cu(II) complexes, CuII2Nn (n = 4 or 5), were recently found to specifically cleave DNA in the presence of a reducing thiol and O2 or in the presence of H2O2 alone. However, CuII2N3 and a closely related mononuclear Cu(II) complex exhibited no selective reaction under either condition. Spectroscopic studies indicate an intermediate is generated from CuII2Nn (n = 4 or 5) and mononuclear Cu(II) solutions in the presence of H2O2 or from CuI2Nn (n = 4 or 5) in the presence of O2. This intermediate decays to generate OH radicals and ligand degradation products at room temperature. The lack of reactivity of the intermediate with a series of added electron donors suggests the intermediate discharges through a rate-limiting intramolecular electron transfer from the ligand to the metal peroxo center to produce an OH radical and a ligand-based radical. These results imply that DNA cleavage does not result from direct reaction with a metal-peroxo intermediate but instead arises from reaction with either OH radicals or ligand-based radicals.

Misuse of thermodynamics in the interpretation of isothermal titration calorimetry data for ligand binding to proteins.

PubMed

Pethica, Brian A

2015-03-01

Isothermal titration calorimetry (ITC) has given a mass of data on the binding of small molecules to proteins and other biopolymers, with particular interest in drug binding to proteins chosen as therapeutic indicators. Interpretation of the enthalpy data usually follows an unsound protocol that uses thermodynamic relations in circumstances where they do not apply. Errors of interpretation include incomplete definitions of ligand binding and equilibrium constants and neglect of the non-ideality of the solutions under study, leading to unreliable estimates of standard free energies and entropies of binding. The mass of reported thermodynamic functions for ligand binding to proteins estimated from ITC enthalpies alone is consequently of uncertain thermodynamic significance and utility. ITC and related experiments to test the protocol assumptions are indicated. A thermodynamic procedure avoiding equilibrium constants or other reaction models and not requiring protein activities is given. The discussion draws attention to the fundamental but neglected relation between the thermodynamic activity and bioactivity of drugs and to the generally unknown thermodynamic status of ligand solutions, which for drugs relates directly to effective therapeutic dosimetry. Copyright © 2014 Elsevier Inc. All rights reserved.

Tris-(hydroxyamino)triazines: high-affinity chelating tridentate O,N,O-hydroxylamine ligand for the cis-V(V)O2(+) cation.

PubMed

Nikolakis, Vladimiros A; Exarchou, Vassiliki; Jakusch, Tamás; Woolins, J Derek; Slawin, Alexandra M Z; Kiss, Tamás; Kabanos, Themistoklis A

2010-10-14

The treatment of the trichloro-1,3,5-triazine with N-methylhydroxylamine hydrochloride results in the replacement of the three chlorine atoms of the triazine ring with the function -N(OH)CH(3) yielding the symmetrical tris-(hydroxyamino)triazine ligand H(3)trihyat. Reaction of the ligand H(3)trihyat with NaV(V)O(3) in aqueous solution followed by addition of Ph(4)PCl gave the mononuclear vanadium(V) compound Ph(4)P[V(V)O(2)(Htrihyat)] (1). The structure of compound 1 was determined by X-ray crystallography and indicates that this compound has a distorted square-pyramidal arrangement around vanadium. The ligand Htrihyat(2-) is bonded to vanadium atom in a tridentate fashion at the triazine ring nitrogen atom and the two deprotonated hydroxylamido oxygen atoms. The high electron density of the triazine ring nitrogen atoms, which results from the resonative contribution of electrons of exocyclic nitrogen atoms, leads to a very strong V-N bond. The cis-[V(V)O(2)(Htrihyat)](-) species exhibits high hydrolytic stability in aqueous solution over a wide pH range, 2.5-11.5, as was evidenced by potentiometry.

A novel computational approach "BP-STOCH" to study ligand binding to finite lattice.

PubMed

Beshnova, Daria A; Bereznyak, Ekaterina G; Shestopalova, Anna V; Evstigneev, Maxim P

2011-03-01

We report a novel computational algorithm "BP-STOCH" to be used for studying single-type ligand binding with biopolymers of finite lengths, such as DNA oligonucleotides or oligopeptides. It is based on an idea to represent any type of ligand-biopolymer complex in a form of binary number, where "0" and "1" bits stand for vacant and engaged monomers of the biopolymer, respectively. Cycling over all binary numbers from the lowest 0 up to the highest 2(N) - 1 means a sequential generating of all possible configurations of vacant/engaged monomers, which, after proper filtering, results in a full set of possible types of complexes in solution between the ligand and the N-site lattice. The principal advantage of BP-STOCH algorithm is the possibility to incorporate into this cycle any conditions on computation of the concentrations and observed experimental parameters of the complexes in solution, and programmatic access to each monomer of the biopolymer within each binding site of every binding configuration. The latter is equivalent to unlimited extension of the basic reaction scheme and allows to use BP-STOCH algorithm as an alternative to conventional computational approaches.

Improved performance of colloidal CdSe quantum dot-sensitized solar cells by hybrid passivation.

PubMed

Huang, Jing; Xu, Bo; Yuan, Chunze; Chen, Hong; Sun, Junliang; Sun, Licheng; Agren, Hans

2014-11-12

A hybrid passivation strategy is employed to modify the surface of colloidal CdSe quantum dots (QDs) for quantum dot-sensitized solar cells (QDSCs), by using mercaptopropionic acid (MPA) and iodide anions through a ligand exchange reaction in solution. This is found to be an effective way to improve the performance of QDSCs based on colloidal QDs. The results show that MPA can increase the coverage of the QDs on TiO2 electrodes and facilitate the hole extraction from the photoxidized QDs, and simultaneously, that the iodide anions can remedy the surface defects of the CdSe QDs and thus reduce the recombination loss in the device. This hybrid passivation treatment leads to a significant enhancement of the power conversion efficiency of the QDSCs by 41%. Furthermore, an optimal ratio of iodide ions to MPA was determined for favorable hybrid passivation; results show that excessive iodine anions are detrimental to the loading of the QDs. This study demonstrates that the improvement in QDSC performance can be realized by using a combination of different functional ligands to passivate the QDs, and that ligand exchange in solution can be an effective approach to introduce different ligands.

Der p 5 Crystal Structure Provides Insight into the Group 5 Dust Mite Allergens

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mueller, G.; Gosavi, R; Krahn, J

2010-01-01

Group 5 allergens from house dust mites elicit strong IgE antibody binding in mite-allergic patients. The structure of Der p 5 was determined by x-ray crystallography to better understand the IgE epitopes, to investigate the biologic function in mites, and to compare with the conflicting published Blo t 5 structures, designated 2JMH and 2JRK in the Protein Data Bank. Der p 5 is a three-helical bundle similar to Blo t 5, but the interactions of the helices are more similar to 2JMH than 2JRK. The crystallographic asymmetric unit contains three dimers of Der p 5 that are not exactly alike.more » Solution scattering techniques were used to assess the multimeric state of Der p 5 in vitro and showed that the predominant state was monomeric, similar to Blo t 5, but larger multimeric species are also present. In the crystal, the formation of the Der p 5 dimer creates a large hydrophobic cavity of {approx}3000 {angstrom}{sup 3} that could be a ligand-binding site. Many allergens are known to bind hydrophobic ligands, which are thought to stimulate the innate immune system and have adjuvant-like effects on IgE-mediated inflammatory responses.« less

Ligand-Dependent Activation and Deactivation of the Human Adenosine A2A Receptor

PubMed Central

Li, Jianing; Jonsson, Amanda L.; Beuming, Thijs; Shelley, John C.; Voth, Gregory A.

2013-01-01

G protein-coupled receptors (GPCRs) are membrane proteins with critical functions in cellular signal transduction, representing a primary class of drug targets. Acting by direct binding, many drugs modulate GPCR activity and influence the signaling pathways associated with numerous diseases. However, complete details of ligand-dependent GPCR activation/deactivation are difficult to obtain from experiments. Therefore, it remains unclear how ligands modulate a GPCR’s activity. To elucidate the ligand-dependent activation/deactivation mechanism of the human adenosine A2A receptor (AA2AR), a member of the class A GPCRs, we performed large-scale unbiased molecular dynamics and metadynamics simulations of the receptor embedded in a membrane. At the atomic level, we have observed distinct structural states that resemble the active and inactive states. In particular we noted key structural elements changing in a highly concerted fashion during the conformational transitions, including six conformational states of a tryptophan (Trp2466.48). Our findings agree with a previously proposed view, that during activation, this tryptophan residue undergoes a rotameric transition that may be coupled to a series of coherent conformational changes, resulting in the opening of the G protein-binding site. Further, metadynamics simulations provide quantitative evidence for this mechanism, suggesting how ligand binding shifts the equilibrium between the active and inactive states. Our analysis also proposes that a few specific residues are associated with agonism/antagonism, affinity and selectivity, and suggests that the ligand-binding pocket can be thought of as having three distinct regions, providing dynamic features for structure-based design. Additional simulations with AA2AR bound to a novel ligand are consistent with our proposed mechanism. Generally, our study provides insights into the ligand-dependent AA2AR activation/deactivation in addition to what has been found in crystal structures. These results should aid in the discovery of more effective and selective GPCR ligands. PMID:23678995

Ligand-dependent activation and deactivation of the human adenosine A(2A) receptor.

PubMed

Li, Jianing; Jonsson, Amanda L; Beuming, Thijs; Shelley, John C; Voth, Gregory A

2013-06-12

G-protein-coupled receptors (GPCRs) are membrane proteins with critical functions in cellular signal transduction, representing a primary class of drug targets. Acting by direct binding, many drugs modulate GPCR activity and influence the signaling pathways associated with numerous diseases. However, complete details of ligand-dependent GPCR activation/deactivation are difficult to obtain from experiments. Therefore, it remains unclear how ligands modulate a GPCR's activity. To elucidate the ligand-dependent activation/deactivation mechanism of the human adenosine A2A receptor (AA2AR), a member of the class A GPCRs, we performed large-scale unbiased molecular dynamics and metadynamics simulations of the receptor embedded in a membrane. At the atomic level, we have observed distinct structural states that resemble the active and inactive states. In particular, we noted key structural elements changing in a highly concerted fashion during the conformational transitions, including six conformational states of a tryptophan (Trp246(6.48)). Our findings agree with a previously proposed view that, during activation, this tryptophan residue undergoes a rotameric transition that may be coupled to a series of coherent conformational changes, resulting in the opening of the G-protein binding site. Further, metadynamics simulations provide quantitative evidence for this mechanism, suggesting how ligand binding shifts the equilibrium between the active and inactive states. Our analysis also proposes that a few specific residues are associated with agonism/antagonism, affinity, and selectivity, and suggests that the ligand-binding pocket can be thought of as having three distinct regions, providing dynamic features for structure-based design. Additional simulations with AA2AR bound to a novel ligand are consistent with our proposed mechanism. Generally, our study provides insights into the ligand-dependent AA2AR activation/deactivation in addition to what has been found in crystal structures. These results should aid in the discovery of more effective and selective GPCR ligands.

The role of ligands on the equilibria between functional states of a G protein-coupled receptor.

PubMed

Kim, Tae Hun; Chung, Ka Young; Manglik, Aashish; Hansen, Alexandar L; Dror, Ron O; Mildorf, Thomas J; Shaw, David E; Kobilka, Brian K; Prosser, R Scott

2013-06-26

G protein-coupled receptors exhibit a wide variety of signaling behaviors in response to different ligands. When a small label was incorporated on the cytosolic interface of transmembrane helix 6 (Cys-265), (19)F NMR spectra of the β2 adrenergic receptor (β2AR) reconstituted in maltose/neopentyl glycol detergent micelles revealed two distinct inactive states, an activation intermediate state en route to activation, and, in the presence of a G protein mimic, a predominant active state. Analysis of the spectra as a function of temperature revealed that for all ligands, the activation intermediate is entropically favored and enthalpically disfavored. β2AR enthalpy changes toward activation are notably lower than those observed with rhodopsin, a likely consequence of basal activity and the fact that the ionic lock and other interactions stabilizing the inactive state of β2AR are weaker. Positive entropy changes toward activation likely reflect greater mobility (configurational entropy) in the cytoplasmic domain, as confirmed through an order parameter analysis. Ligands greatly influence the overall changes in enthalpy and entropy of the system and the corresponding changes in population and amplitude of motion of given states, suggesting a complex landscape of states and substates.

New superhindered polydentate polyphosphine ligands P(CH2CH2P(t)Bu2)3, PhP(CH2CH2P(t)Bu2)2, P(CH2CH2CH2P(t)Bu2)3, and their ruthenium(II) chloride complexes.

PubMed

Gilbert-Wilson, Ryan; Field, Leslie D; Bhadbhade, Mohan M

2012-03-05

The synthesis and characterization of the extremely hindered phosphine ligands, P(CH(2)CH(2)P(t)Bu(2))(3) (P(2)P(3)(tBu), 1), PhP(CH(2)CH(2)P(t)Bu(2))(2) (PhP(2)P(2)(tBu), 2), and P(CH(2)CH(2)CH(2)P(t)Bu(2))(3) (P(3)P(3)(tBu), 3) are reported, along with the synthesis and characterization of ruthenium chloro complexes RuCl(2)(P(2)P(3)(tBu)) (4), RuCl(2)(PhP(2)P(2)(tBu)) (5), and RuCl(2)(P(3)P(3)(tBu)) (6). The bulky P(2)P(3)(tBu) (1) and P(3)P(3)(tBu) (3) ligands are the most sterically encumbered PP(3)-type ligands so far synthesized, and in all cases, only three phosphorus donors are able to bind to the metal center. Complexes RuCl(2)(PhP(2)P(2)(tBu)) (5) and RuCl(2)(P(3)P(3)(tBu)) (6) were characterized by crystallography. Low temperature solution and solid state (31)P{(1)H} NMR were used to demonstrate that the structure of RuCl(2)(P(2)P(3)(tBu)) (4) is probably analogous to that of RuCl(2)(PhP(2)P(2)(tBu)) (5) which had been structurally characterized.

Tuning Confinement in Colloidal Silicon Nanocrystals with Saturated Surface Ligands.

PubMed

Carroll, Gerard M; Limpens, Rens; Neale, Nathan R

2018-05-09

The optical properties of silicon nanocrystals (Si NCs) are a subject of intense study and continued debate. In particular, Si NC photoluminescence (PL) properties are known to depend strongly on the surface chemistry, resulting in electron-hole recombination pathways derived from the Si NC band-edge, surface-state defects, or combined NC-conjugated ligand hybrid states. In this Letter, we perform a comparison of three different saturated surface functional groups-alkyls, amides, and alkoxides-on nonthermal plasma-synthesized Si NCs. We find a systematic and size-dependent high-energy (blue) shift in the PL spectrum of Si NCs with amide and alkoxy functionalization relative to alkyl. Time-resolved photoluminescence and transient absorption spectroscopies reveal no change in the excited-state dynamics between Si NCs functionalized with alkyl, amide, or alkoxide ligands, showing for the first time that saturated ligands-not only surface-derived charge-transfer states or hybridization between NC and low-lying ligand orbitals-are responsible for tuning the Si NC optical properties. To explain these PL shifts we propose that the atom bound to the Si NC surface strongly interacts with the Si NC electronic wave function and modulates the Si NC quantum confinement. These results reveal a potentially broadly applicable correlation between the optoelectronic properties of Si NCs and related quantum-confined structures based on the interaction between NC surfaces and the ligand binding group.

Tuning Confinement in Colloidal Silicon Nanocrystals with Saturated Surface Ligands

DOE PAGES

Carroll, Gerard M.; Limpens, Rens; Neale, Nathan R.

2018-04-16

The optical properties of silicon nanocrystals (Si NCs) are a subject of intense study and continued debate. In particular, Si NC photoluminescence (PL) properties are known to depend strongly on the surface chemistry, resulting in electron-hole recombination pathways derived from the Si NC band-edge, surface-state defects, or combined NC-conjugated ligand hybrid states. In this Letter, we perform a comparison of three different saturated surface functional groups - alkyls, amides, and alkoxides - on nonthermal plasma-synthesized Si NCs. We find a systematic and size-dependent high-energy (blue) shift in the PL spectrum of Si NCs with amide and alkoxy functionalization relative tomore » alkyl. Time-resolved photoluminescence and transient absorption spectroscopies reveal no change in the excited-state dynamics between Si NCs functionalized with alkyl, amide, or alkoxide ligands, showing for the first time that saturated ligands - not only surface-derived charge-transfer states or hybridization between NC and low-lying ligand orbitals - are responsible for tuning the Si NC optical properties. To explain these PL shifts we propose that the atom bound to the Si NC surface strongly interacts with the Si NC electronic wave function and modulates the Si NC quantum confinement. Furthermore, these results reveal a potentially broadly applicable correlation between the optoelectronic properties of Si NCs and related quantum-confined structures based on the interaction between NC surfaces and the ligand binding group.« less

Modulation of protein function by exogenous ligands in protein cavities: CO binding to a myoglobin cavity mutant containing unnatural proximal ligands.

PubMed

Decatur, S M; DePillis, G D; Boxer, S G

1996-04-02

A variety of heterocyclic ligands can be exchanged into the proximal cavity of sperm whale myoglobin mutant H93G, providing a simple method for introduction of the equivalent of unnatural amino acid side chains into a functionally critical location in this protein. These modified proteins bind CO on the distal side. 1H NMR data on H93G(Im)CO, where Im is imidazole, demonstrate that the structure of the distal heme pocket in H93G(Im)CO is very similar to that of wild type; thus, the effects of the proximal ligand's properties on CO binding can be studied with minimal perturbation of distal pocket structure. The exogenous proximal ligands used in this study include imidazole (Im), 4-methylimidazole (4-MeIm), 4-bromoimidazole (4-BrIm), N-methylimidazole (N-MeIm), pyridine (Pyr), and 3-fluoropyridine (3-FPyr). Substitution of the proximal ligand is found to produce substantial changes in the CO on and off rates, the equilibrium binding constant, and the vibrational stretch frequency of CO. Many of the changes are as large as those reported for distal pocket mutants prepared by site-directed mutagenesis. The ability to systematically vary the nature of the proximal ligand is exploited to test the effects of particular properties of the proximal ligand on CO binding. For example, 4-MeIm and 4-BrIm are similar in size and shape but differ significantly in pKa. The same relationship is true for Pyr and 3-FPyr. By comparison of the IR spectra and CO recombination kinetics of these complexes, the effects of proximal ligand pKa on the CO binding are assessed. Likewise, N-MeIm and 4-MeIm are similar in size and pKa but differ in their ability to hydrogen bond to amino acid residues in the proximal cavity. Comparisons of IR spectra and CO binding kinetics in these complexes reveal that proximal ligand conformation and hydrogen bonding affect the kinetics of CO binding. The mechanism of proximal ligand exchange between solution and the proximal cavity in CO complexes was investigated by obtaining the 19F NMR spectrum of H93G(3-FPyr)CO, whose 19F signal can be observed without interference from resonances of the protein. The proximal ligand is found to exchange within a few seconds by saturation transfer. This exchange rate is about 2 orders of magniture faster than what is observed for the isoelectronic metcyano complex [Decatur, S. M., & Boxer, S. G. (1995) Biochemistry 34, 2122-2129]; in both the ferrous CO and ferric cyano complexes, the proximal ligand exchange rate is independent of ligand concentration. These results suggest that the rate-limiting step in proximal ligand exchange is breakage of the iron-ligand bond, followed by rapid diffusion of the ligand through the protein to bulk solution.

Chemodynamics of aquatic metal complexes: from small ligands to colloids.

PubMed

Van Leeuwen, Herman P; Buffle, Jacques

2009-10-01

Recent progress in understanding the formation/dissociation kinetics of aquatic metal complexes with complexants in different size ranges is evaluated and put in perspective, with suggestions for further studies. The elementary steps in the Eigen mechanism, i.e., diffusion and dehydration of the metal ion, are reviewed and further developed. The (de)protonation of both the ligand and the coordinating metal ion is reconsidered in terms of the consequences for dehydration rates and stabilities of the various outer-sphere complexes. In the nanoparticulate size range, special attention is given to the case of fulvic ligands, for which the impact of electrostatic interactions is especially large. In complexation with colloidal ligands (hard, soft, and combination thereof) the diffusive transport of metal ions is generally a slower step than in the case of complexation with small ligands in a homogeneous solution. The ensuing consequences for the chemodynamics of colloidal complexes are discussed in detail and placed in a generic framework, encompassing the complete range of ligand sizes.

The use of supramolecular structures as protein ligands.

PubMed

Stopa, Barbara; Jagusiak, Anna; Konieczny, Leszek; Piekarska, Barbara; Rybarska, Janina; Zemanek, Grzegorz; Król, Marcin; Piwowar, Piotr; Roterman, Irena

2013-11-01

Congo red dye as well as other eagerly self-assembling organic molecules which form rod-like or ribbon-like supramolecular structures in water solutions, appears to represent a new class of protein ligands with possible wide-ranging medical applications. Such molecules associate with proteins as integral clusters and preferentially penetrate into areas of low molecular stability. Abnormal, partly unfolded proteins are the main binding target for such ligands, while well packed molecules are generally inaccessible. Of particular interest is the observation that local susceptibility for binding supramolecular ligands may be promoted in some proteins as a consequence of function-derived structural changes, and that such complexation may alter the activity profile of target proteins. Examples are presented in this paper.

Ligand-Substitution Reactions of the Tellurium Compound AS-101 in Physiological Aqueous and Alcoholic Solutions.

PubMed

Silberman, Alon; Albeck, Michael; Sredni, Benjamin; Albeck, Amnon

2016-11-07

Since its first crystallization, the aqueous structure of the tellurium-containing experimental drug AS-101 has never been studied. We show that, under the aqueous conditions in which it is administered, AS-101 is subjected to an immediate ligand-substitution reaction with water, yielding a stable hydrolyzed oxide anion product that is identified, for the first time, to be TeOCl 3 - . Studying the structure of AS-101 in propylene glycol (PG), an alcoholic solvent often used for the topical and oral administration of AS-101, revealed the same phenomenon of ligand-substitution reaction between the alcoholic ligands. Upon exposure to water, the PG-substituted product is also hydrolyzed to the same tellurium(IV) oxide form, TeOCl 3 - .

On the binding determinants of the glutamate agonist with the glutamate receptor ligand binding domain.

PubMed

Speranskiy, Kirill; Kurnikova, Maria

2005-08-30

Ionotropic glutamate receptors (GluRs) are ligand-gated membrane channel proteins found in the central neural system that mediate a fast excitatory response of neurons. In this paper, we report theoretical analysis of the ligand-protein interactions in the binding pocket of the S1S2 (ligand binding) domain of the GluR2 receptor in the closed conformation. By utilizing several theoretical methods ranging from continuum electrostatics to all-atom molecular dynamics simulations and quantum chemical calculations, we were able to characterize in detail glutamate agonist binding to the wild-type and E705D mutant proteins. A theoretical model of the protein-ligand interactions is validated via direct comparison of theoretical and Fourier transform infrared spectroscopy (FTIR) measured frequency shifts of the ligand's carboxylate group vibrations [Jayaraman et al. (2000) Biochemistry 39, 8693-8697; Cheng et al. (2002) Biochemistry 41, 1602-1608]. A detailed picture of the interactions in the binding site is inferred by analyzing contributions to vibrational frequencies produced by protein residues forming the ligand-binding pocket. The role of mobility and hydrogen-bonding network of water in the ligand-binding pocket and the contribution of protein residues exposed in the binding pocket to the binding and selectivity of the ligand are discussed. It is demonstrated that the molecular surface of the protein in the ligand-free state has mainly positive electrostatic potential attractive to the negatively charged ligand, and the potential produced by the protein in the ligand-binding pocket in the closed state is complementary to the distribution of the electrostatic potential produced by the ligand itself. Such charge complementarity ensures specificity to the unique charge distribution of the ligand.

Ab initio metadynamics simulations of oxygen/ligand interactions in organoaluminum clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alnemrat, Sufian; Hooper, Joseph P., E-mail: jphooper@nps.edu

2014-10-14

Car-Parrinello molecular dynamics combined with a metadynamics algorithm is used to study the initial interaction of O{sub 2} with the low-valence organoaluminum clusters Al{sub 4}Cp{sub 4} (Cp=C{sub 5}H{sub 5}) and Al{sub 4}Cp{sub 4}{sup *} (Cp{sup *}=C{sub 5}[CH{sub 3}]{sub 5}). Prior to reaction with the aluminum core, simulations suggest that the oxygen undergoes a hindered crossing of the steric barrier presented by the outer ligand monolayer. A combination of two collective variables based on aluminum/oxygen distance and lateral oxygen displacement was found to produce distinct reactant, product, and transition states for this process. In the methylated cluster with Cp{sup *} ligands,more » a broad transition state of 45 kJ/mol was observed due to direct steric interactions with the ligand groups and considerable oxygen reorientation. In the non-methylated cluster the ligands distort away from the oxidizer, resulting in a barrier of roughly 34 kJ/mol with minimal O{sub 2} reorientation. A study of the oxygen/cluster system fixed in a triplet multiplicity suggests that the spin state does not affect the initial steric interaction with the ligands. The metadynamics approach appears to be a promising means of analyzing the initial steps of such oxidation reactions for ligand-protected clusters.« less

Giant Spherical Cluster with I-C140 Fullerene Topology**

PubMed Central

Heinl, Sebastian; Peresypkina, Eugenia; Sutter, Jörg; Scheer, Manfred

2015-01-01

We report on an effective cluster expansion of CuBr-linked aggregates by the increase of the steric bulk of the CpR ligand in the pentatopic molecules [CpRFe(η5-P5)]. Using [CpBIGFe(η5-P5)] (CpBIG=C5(4-nBuC6H4)5), the novel multishell aggregate [{CpBIGFe(η5:2:1:1:1:1:1-P5)}12(CuBr)92] is obtained. It shows topological analogy to the theoretically predicted I-C140 fullerene molecule. The spherical cluster was comprehensively characterized by various methods in solution and in the solid state. PMID:26411255

A binuclear Mn(III) complex of a scorpiand-like ligand displaying a single unsupported Mn(III)-O-Mn(III) bridge.

PubMed

Blasco, Salvador; Cano, Joan; Clares, M Paz; García-Granda, Santiago; Doménech, Antonio; Jiménez, Hermas R; Verdejo, Begoña; Lloret, Francesc; García-España, Enrique

2012-11-05

The crystal structure of a binuclear Mn(III) complex of a scorpiand-like ligand (L) displays an unsupported single oxo bridging ligand with a Mn(III)-O-Mn(III) angle of 174.7°. Magnetic susceptibility measurements indicate strong antiferromagnetic coupling between the two metal centers. DFT calculations have been carried out to understand the magnetic behavior and to analyze the nature of the observed Jahn-Teller distortion. Paramagnetic (1)H NMR has been applied to rationalize the formation and magnetic features of the complexes formed in solution.

Photophysical Properties of Pt(II) Polypyridines with Five- versus Six-Membered Chelate Rings: Trade-Offs in Angle Strain.

PubMed

Natoli, Sean N; Hight, Lauren M; Zeller, Matthias; McMillin, David R

2018-06-04

This report describes the synthesis and characterization of a series of eight [Pt(NNN)X] + complexes where the tridentate NNN ligand is (2,2'-bipyrid-6-yl)(pyrid-2-yl)sulfide (btp) or methyl(2,2'-bipyrid-6-yl)(pyrid-2-yl)amine (bmap) and X is OMe, Cl, phenylethynyl (C 2 Ph), or cyclohexylethynyl (C 2 Cy). The expectation was that inserting a heteroatom into the backbone of 2,2':6',2″-terpyridine (trpy) would expand the overall intraligand bite angle, introduce ILCT character into the excited states, and improve the photophysical properties. Crystal structures of [Pt(bmap)C 2 Ph] + and [Pt(btp)Cl] + reveal that atom insertion into the trpy backbone successfully expands the bite angle of the ligand by 8-10°. However, the impact on the photophysics is minimal. Indeed, of the eight systems investigated, only the [Pt(bmap)C 2 Ph] + and [Pt(btp)C 2 Ph] + complexes display appreciable emission in fluid solution, and they exhibit shorter emission lifetimes than [Pt(trpy)C 2 Ph] + . One reason is that the bond angle preferences of platinum and the inserted heteroatom induce the six-membered rings to deviate from planarity and adopt a boat-like conformation, impairing charge delocalization within the ligand. In addition, angle strain induces the donor atoms about platinum to assume a pseudotetrahedral arrangement, which offsets any benefit due to the increase in overall bite angle by promoting deactivation via d-d excited states. The results reveal that, in order to improve the luminescence of a [Pt(NNN)X] + system, one must take care to avoid trading one kind of angle strain for another.

Exquisite Modulation of the Active Site of Methanocaldococcus jannaschii Adenylosuccinate Synthetase in Forward Reaction Complexes.

PubMed

Karnawat, Vishakha; Mehrotra, Sonali; Balaram, Hemalatha; Puranik, Mrinalini

2016-05-03

In enzymes that conduct complex reactions involving several substrates and chemical transformations, the active site must reorganize at each step to complement the transition state of that chemical step. Adenylosuccinate synthetase (ADSS) utilizes a molecule each of guanosine 5'-monophosphate (GTP) and aspartate to convert inosine 5'-monophosphate (IMP) into succinyl adenosine 5'-monophosphate (sAMP) through several kinetic intermediates. Here we followed catalysis by ADSS through high-resolution vibrational spectral fingerprints of each substrate and intermediate involved in the forward reaction. Vibrational spectra show differential ligand distortion at each step of catalysis, and band positions of substrates are influenced by binding of cosubstrates. We found that the bound IMP is distorted toward its N1-deprotonated form even in the absence of any other ligands. Several specific interactions between GTP and active-site amino acid residues result in large Raman shifts and contribute substantially to intrinsic binding energy. When both IMP and GTP are simultaneously bound to ADSS, IMP is converted into an intermediate 6-phosphoryl inosine 5'-monophosphate (6-pIMP). The 6-pIMP·ADSS complex was found to be stable upon binding of the third ligand, hadacidin (HDA), an analogue of l-aspartate. We find that in the absence of HDA, 6-pIMP is quickly released from ADSS, is unstable in solution, and converts back into IMP. HDA allosterically stabilizes ADSS through local conformational rearrangements. We captured this complex and determined the spectra and structure of 6-pIMP in its enzyme-bound state. These results provide important insights into the exquisite tuning of active-site interactions with changing substrate at each kinetic step of catalysis.

Spectroscopic and electrochemical properties of organic framework of macrocylic OONNOO-donor ligand with its metal organic framework: host/guest stability measurements.

PubMed

Kumar, Rajiv; Singh, R P; Singh, R P

2008-11-15

In this study, we synthesized 1,2-di(o-aminophenoxy)ethane, as the starting material, used in the preparation of a novel hexadentate OONNOO-donor macrocyclic ligand-1,4,11,14-tetraoxo-7,8-diaza-5,6:9,10;15,16:19,20-terabezocyclododeca-8,17-iene. It has twenty membered organic framework (OF), which has been designed, synthesized and characterized. Our main findings of this paper are related to the organic framework of ligand, its capacity to digest the metal ions and the stability of metal organic framework (MOFs) with cobalt(II), nickel(II) and manganese(II). The authenticity of the used organic framework and its metal complexes have been detected and observed in solid state as well as in aqueous solutions. The main observations were made on the basis of physiochemical measurements viz.: elemental analyses, molar conductance measurements, magnetic susceptibility measurements, IR, 1H NMR, 13C NMR, mass spectroscopy, electronic, ESR spectroscopy. In addition, the magnetic susceptibility and electrochemistry measurements have been made. The 1H NMR spectra suggest stereochemistry and proton movement interaction. Considering the used organic framework there are a lot of carbon atoms in the molecule reflected by the 13C NMR spectrum. All these observations gave a clear view to confirming the encapsulation; arrive at the composition, structure and geometry of encapsulated complexes. In simple words, it confirms the host/guest coordination and its stability. Electrochemical properties of the complexes have been investigated to confirm the various changes in oxidation state of metals with change in potentials with respect to current at different scan rate.

Multiparameter flow cytometry of a pH sensitive ligand bound to receptors and inside cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fay, S.P.; Habbersett, R.; Posner, R.G.

1993-01-01

Because fluoresceinated ligands of the neutrophil formyl peptide receptor can be protonated either upon binding to the receptor on the cell surface or in acidified intracellular compartments, the authors synthesized a ligand conjugated to the pH sensitive fluorescent probe SNAFL (CHO-Met-Leu-Phe-Phe-Lys-SNAFL). In the three laser flow cytometer at LANL, protonated dye is excited at 488 nm and emits at 530 nm; unprotonated dye is excited at 568 nm and emits at 650 nm. Detection at the isobestic and isoemissive points at 528 and 600 nm is used to keep track of variations in ligand concentration from sample to sample. Themore » SNAFL-ligand bound to HL-60 cells (which overexpress the formyl peptide receptor) was compared to the free ligand in solution over a pH range from 6.5 to 9.0. The results suggest that the ligand bound to cell surface receptors was protonated in the binding pocket, possibly by virtue of its proximity to His 90, based on sequence data. When the cells were raised from 4[degrees] to 37[degrees], they also observed a time-dependent acidification of the ligand, indicative of ligand-receptor processing beginning 3-4 minutes after internalization.« less

The coordination chemistry of group 15 element ligand complexes--a developing area.

PubMed

Scheer, Manfred

2008-09-07

A survey of the contemporary challenges of the field of unsubstituted group 15 element ligand complexes (excluding N) is given. The focus of the article is on the coordination chemistry behaviour of such E(n) ligand complexes. This field is subdivided into two areas of reactivity: E(n) ligand complexes with (i) noncoordinated Lewis-acidic cations and (ii) Lewis-acidic coordination compounds containing at least one permanently coordinating ligand. In the latter case, insoluble 1D and 2D polymers respectively are obtained; however, under special conditions soluble, spherical, fullerene-like giant molecules are formed. These nano-sized molecules are up to 2.4 nm in diameter and are able to encapsulate small molecules in their holes. In contrast, the first-mentioned field uses weakly coordinating anions to obtain readily soluble di- and polycationic products. These show depolymerisation tendencies in solution under the formation of oligomer-monomer equilibria and thus reveal dynamic supramolecular aggregation processes.

Inorganic resins for clinical use of .sup.213Bi generators

DOEpatents

DePaoli, David W [Knoxville, TN; Hu, Michael Z [Knoxville, TN; Mirzadeh, Saed [Knoxville, TN; Clavier, John W [Elizabethton, TN

2011-03-29

Applicant's invention is a radionuclide generator resin material for radiochemical separation of daughter radionuclides, particularly .sup.213Bi, from a solution of parental radionuclides, the resin material capable of providing clinical quantities of .sup.213Bi of at least 20-mCi, wherein the resin material comprises a silica-based structure having at least one bifunctional ligand covalently attached to the surface of the silica-based structure. The bifunctional ligand comprises a chemical group having desirable surface functionality to enable the covalent attachment of the bifunctional ligand thereon the surface of the structure and the bifunctional ligand further comprises a second chemical group capable of binding and holding the parental radionuclides on the resin material while allowing the daughter radionuclides to elute off the resin material. The bifunctional ligand has a carbon chain with a limited number of carbons to maintain radiation stability of the resin material.

Challenges and solutions for the analysis of in situ , in crystallo micro-spectrophotometric data

DOE PAGES

Dworkowski, Florian S. N.; Hough, Michael A.; Pompidor, Guillaume; ...

2015-01-01

Combining macromolecular crystallography with in crystallo micro-spectrophotometry yields valuable complementary information on the sample, including the redox states of metal cofactors, the identification of bound ligands and the onset and strength of undesired photochemistry, also known as radiation damage. However, the analysis and processing of the resulting data differs significantly from the approaches used for solution spectrophotometric data. The varying size and shape of the sample, together with the suboptimal sample environment, the lack of proper reference signals and the general influence of the X-ray beam on the sample have to be considered and carefully corrected for. In the presentmore » article, we discuss how to characterize and treat these sample-dependent artefacts in a reproducible manner and we demonstrate the SLS-APE in situ, in crystallo optical spectroscopy data-analysis toolbox.« less

Role of Buffers in Protein Formulations.

PubMed

Zbacnik, Teddy J; Holcomb, Ryan E; Katayama, Derrick S; Murphy, Brian M; Payne, Robert W; Coccaro, Richard C; Evans, Gabriel J; Matsuura, James E; Henry, Charles S; Manning, Mark Cornell

2017-03-01

Buffers comprise an integral component of protein formulations. Not only do they function to regulate shifts in pH, they also can stabilize proteins by a variety of mechanisms. The ability of buffers to stabilize therapeutic proteins whether in liquid formulations, frozen solutions, or the solid state is highlighted in this review. Addition of buffers can result in increased conformational stability of proteins, whether by ligand binding or by an excluded solute mechanism. In addition, they can alter the colloidal stability of proteins and modulate interfacial damage. Buffers can also lead to destabilization of proteins, and the stability of buffers themselves is presented. Furthermore, the potential safety and toxicity issues of buffers are discussed, with a special emphasis on the influence of buffers on the perceived pain upon injection. Finally, the interaction of buffers with other excipients is examined. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Replica Exchange with Solute Tempering: Efficiency in Large Scale Systems

PubMed Central

Huang, Xuhui; Hagen, Morten; Kim, Byungchan; Friesner, Richard A.; Zhou, Ruhong; Berne, B. J.

2009-01-01

We apply the recently developed replica exchange with solute tempering (REST) to three large solvated peptide systems: an α-helix, a β-hairpin, and a TrpCage, with these peptides defined as the “central group”. We find that our original implementation of REST is not always more efficient than the replica exchange method (REM). Specifically, we find that exchanges between folded (F) and unfolded (U) conformations with vastly different structural energies are greatly reduced by the nonappearance of the water self-interaction energy in the replica exchange acceptance probabilities. REST, however, is expected to remain useful for a large class of systems for which the energy gap between the two states is not large, such as weakly bound protein–ligand complexes. Alternatively, a shell of water molecules can be incorporated into the central group, as discussed in the original paper. PMID:17439169

Interactions of solvent with the heme region of methemoglobin and fluoro-methemoglobin.

PubMed

Koenig, S H; Brown, R D; Lindstrom, T R

1981-06-01

It is now more than 20 years since Davidson and collaborators (1957, Biochim. Biophys, Acta. 26:370-373; J. Mol. Biol. 1:190-191) applied the theoretical ideas of Bloembergen et al. (1948. Phys. Rev. 73:679-712) on outer sphere magnetic relaxation of solvent protons to studies of solutions of methemoglobin. From then on, there has been debate regarding the relative contributions to paramagnetic solvent proton relaxation by inner sphere (ligand-exchange) effects and by outer sphere (diffusional) effects in methemoglobin solutions. Gupta and Mildvan (1975. J. Biol. Chem 250:146-253) extended the early measurements, attributed the relatively small paramagnetic effects to exchange with solvent of the water ligand of the heme-Fe3+ ion, and interpreted their data to indicate cooperativity and an alkaline Bohr effect in the presence of inositol hexaphosphate. They neglected the earlier discussions entirely, and made no reference to outer sphere effects. We have measured the relaxation rate of solvent protons as a function of magnetic field for solutions of methemoglobin, under a variety of conditions of pH and temperature, and have given careful consideration to the relatively large diamagnetic corrections that are necessary by making analogous measurements on oxyhemoglobin, carbonmonoxyhemoglobin, and cyano- and azide-methemoglobin. (The latter two, because of their short electronic relaxation times, behave as though diamagnetic). We show that the paramagnetic contribution to solvent relaxation can be dominated by outer sphere effects, a result implying that many conclusions, including those of Gupta and Mildvan, require reexamination. Finally, we present data for fluoro-methemoglobin, which relaxes solvent protons an order of magnitude better than does methemoglobin. Here one has a startling breakdown of the dogma that has been the basis for interpreting many ligand-replacement studies; in contrast to the prevailing view that replacement of a water ligand of a protein-bound paramagnetic ion by another ligand should decrease relaxation rates, replacement of H2O by F- increases the relaxation rate drastically. The data can all be reconciled, however, with what is anticipated from knowledge of ligand interactions in the heme region.

Changing paradigm from one target one ligand towards multi target directed ligand design for key drug targets of Alzheimer disease: An important role of Insilco methods in multi target directed ligands design.

PubMed

Kumar, Akhil; Tiwari, Ashish; Sharma, Ashok

2018-03-15

Alzheimer disease (AD) is now considered as a multifactorial neurodegenerative disorder and rapidly increasing to an alarming situation and causing higher death rate. One target one ligand hypothesis is not able to provide complete solution of AD due to multifactorial nature of disease and one target one drug seems to fail to provide better treatment against AD. Moreover, current available treatments are limited and most of the upcoming treatments under clinical trials are based on modulating single target. So the current AD drug discovery research shifting towards new approach for better solution that simultaneously modulate more than one targets in the neurodegenerative cascade. This can be achieved by network pharmacology, multi-modal therapies, multifaceted, and/or the more recently proposed term "multi-targeted designed drugs. Drug discovery project is tedious, costly and long term project. Moreover, multi target AD drug discovery added extra challenges such as good binding affinity of ligands for multiple targets, optimal ADME/T properties, no/less off target side effect and crossing of the blood brain barrier. These hurdles may be addressed by insilico methods for efficient solution in less time and cost as computational methods successfully applied to single target drug discovery project. Here we are summarizing some of the most prominent and computationally explored single target against AD and further we discussed successful example of dual or multiple inhibitors for same targets. Moreover we focused on ligand and structure based computational approach to design MTDL against AD. However is not an easy task to balance dual activity in a single molecule but computational approach such as virtual screening docking, QSAR, simulation and free energy are useful in future MTDLs drug discovery alone or in combination with fragment based method. However, rational and logical implementations of computational drug designing methods are capable of assisting AD drug discovery and play an important role in optimizing multi-target drug discovery. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Protein–ligand interactions investigated by thermal shift assays (TSA) and dual polarization interferometry (DPI)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grøftehauge, Morten K., E-mail: m.k.groftehauge@durham.ac.uk; Hajizadeh, Nelly R.; Swann, Marcus J.

2015-01-01

The biophysical characterization of protein–ligand interactions in solution using techniques such as thermal shift assay, or on surfaces using, for example, dual polarization interferometry, plays an increasingly important role in complementing crystal structure determinations. Over the last decades, a wide range of biophysical techniques investigating protein–ligand interactions have become indispensable tools to complement high-resolution crystal structure determinations. Current approaches in solution range from high-throughput-capable methods such as thermal shift assays (TSA) to highly accurate techniques including microscale thermophoresis (MST) and isothermal titration calorimetry (ITC) that can provide a full thermodynamic description of binding events. Surface-based methods such as surface plasmonmore » resonance (SPR) and dual polarization interferometry (DPI) allow real-time measurements and can provide kinetic parameters as well as binding constants. DPI provides additional spatial information about the binding event. Here, an account is presented of new developments and recent applications of TSA and DPI connected to crystallography.« less

Superbasic amidine monodentate ligands in fac-[Re(CO)3(5,5'-Me2bipy)(amidine)]BF4 complexes: dependence of amidine configuration on the remote nitrogen substituents.

PubMed

Perera, Theshini; Fronczek, Frank R; Marzilli, Patricia A; Marzilli, Luigi G

2010-08-02

Addition of various RNH(2) to fac-[Re(CO)(3)(5,5'-Me(2)bipy)(CH(3)CN)]BF(4) (1) converts the acetonitrile ligand to the amidine ligand (a superbase) in fac-[Re(CO)(3)(5,5'-Me(2)bipy)(HNC(CH(3))NHR)]BF(4) products. Each complex has four conceivable isomers (E, E', Z, and Z') because the amidine CN bonds have double-bond character, and the two remote NHR group substituents are different. The reaction of 1 in acetonitrile is complete in 6 to 96 h (25 degrees C) and forms fac-[Re(CO)(3)(5,5'-Me(2)bipy)(HNC(CH(3))NHR)]BF(4) E' and Z isomers. Only the E' isomer formed crystals (R = methyl, isopropyl, isobutyl, tert-butyl, and benzyl). Upon dissolution of such crystals in acetonitrile-d(3), NMR spectra with highly dominant E' signals gradually changed (approximately 15 min at room temperature) to spectra with signals for an equilibrium mixture of E' and Z isomers. Such slow E'-to-Z isomer interchange is also indicated by 2D ROESY NMR data used primarily to assign solution structure. Equilibrium ratios (E':Z) of approximately 65:35 for R = methyl, isopropyl, and isobutyl and 83:17 for R = tert-butyl demonstrate that increasing the remote NHR group steric bulk above a threshold size favors the E' isomer. Consistent with this trend, fac-[Re(CO)(3)(5,5'-Me(2)bipy)(HNC(CH(3))NH(2))]BF(4), with a remote NH(2) (low bulk) group, favors the Z isomer. In contrast, although the remote NH(benzyl) group in fac-[Re(CO)(3)(5,5'-Me(2)bipy)(HNC(CH(3))NH(CH(2)C(6)H(5))]BF(4) has only moderate bulk, the E' isomer has high abundance as a result of favorable 5,5'-Me(2)bipy/benzyl stacking, evidence for which is present in both solid and solution states. The fac-[Re(CO)(3)(5,5'-Me(2)bipy)(HNC(CH(3))NHR)]BF(4) E isomer can be detected in solvents of low polarity. However, the Z' isomer was not observed, undoubtedly because unfavorable remote-group clashes with the equatorial ligands destabilize this isomer. Challenge studies with a 5-fold excess of 4-dimethylaminopyridine in acetonitrile-d(3) establish that fac-[Re(CO)(3)(5,5'-Me(2)bipy)(HNC(CH(3))NHCH(CH(3))(2))]BF(4) is robust because the isopropylamidine ligand was not displaced, consistent with the superbase character of amidine ligands.

[Study on synthesis and matching degree of energy level of terbium complexes using o-fluoro-benzoic acid as ligand].

PubMed

Tao, Dong-Liang; Zhang, Kun; Zhang, Hong; Cui, Yu-Min; Xu, Yi-Zhuang; Liu, Yu-Hai

2014-04-01

Tb(2-FBA)3 x 2H2O and Tb(2-FBA)3 phen were synthesized using o-fluoro-benzoic acid (2-FBA) as the first ligand, and 1,10-phenanthroline (phen) as the second ligand. Elemental analysis and IR spectra were employed to characterize the molecular composition of the two kinds of lanthanide complexes. The UV absorption spectra with same concentration show that the second ligand phen of Tb(2-FBA)3 phen absorbs the portion of the UV light instead of the first ligand 2-FBA. Liquid fluorescence spectra with same concentration show that the fluorescence intensity of Tb(2-FBA)3 x 2H2O is higher than that of Tb (2-FBA)3 phen. The analytical results show that the energy level of 2-FBA matches the lowest excited state energy level of Tb3+ (5D4) better than that of phen. The O-H oscillation of the crystal water in Tb(2-FBA)3 x 2H2O will greatly consume the absorbed energy by ligands, and cause the fluorescence intensity of Tb(2-FBA)3 x 2H2O significantly decline. The energy level of triplet state of the first ligand 2-FBA corresponding to the absorption peak 273 nm has poor matching degree with the 5D4 energy level of Tb3+. In this case, the emission intensity of Tb(2-FBA)3 x 2H2O is still stronger than that of Tb(2-FBA)3 phen. It illustrates that the energy level of the triplet state of the first ligand 2-FBA corresponding to 252 nm has much better matching degree with the lowest excited state of 5D4 energy level of Tb3+ than that of phen. It is the only way to compensate for energy loss by thermal vibration of water molecules and low energy transfer efficiency for poor matching degree between the energy level of corresponding to 273 nm of the first ligand 2-FBA and 5D4 energy level of Tb3+. By combining UV absorption spectra with fluorescence spectra of lanthanide complexes to qualitatively analyze energy level of ligands, the contribution of different types of ligands to the fluorescence properties can be preliminarily understood.

Impact of protein and ligand impurities on ITC-derived protein-ligand thermodynamics.

PubMed

Grüner, Stefan; Neeb, Manuel; Barandun, Luzi Jakob; Sielaff, Frank; Hohn, Christoph; Kojima, Shun; Steinmetzer, Torsten; Diederich, François; Klebe, Gerhard

2014-09-01

The thermodynamic characterization of protein-ligand interactions by isothermal titration calorimetry (ITC) is a powerful tool in drug design, giving valuable insight into the interaction driving forces. ITC is thought to require protein and ligand solutions of high quality, meaning both the absence of contaminants as well as accurately determined concentrations. Ligands synthesized to deviating purity and protein of different pureness were titrated by ITC. Data curation was attempted also considering information from analytical techniques to correct stoichiometry. We used trypsin and tRNA-guanine transglycosylase (TGT), together with high affinity ligands to investigate the effect of errors in protein concentration as well as the impact of ligand impurities on the apparent thermodynamics. We found that errors in protein concentration did not change the thermodynamic properties obtained significantly. However, most ligand impurities led to pronounced changes in binding enthalpy. If protein binding of the respective impurity is not expected, the actual ligand concentration was corrected for and the thus revised data compared to thermodynamic properties obtained with the respective pure ligand. Even in these cases, we observed differences in binding enthalpy of about 4kJ⋅mol(-1), which is considered significant. Our results indicate that ligand purity is the critical parameter to monitor if accurate thermodynamic data of a protein-ligand complex are to be recorded. Furthermore, artificially changing fitting parameters to obtain a sound interaction stoichiometry in the presence of uncharacterized ligand impurities may lead to thermodynamic parameters significantly deviating from the accurate thermodynamic signature. Copyright © 2014 Elsevier B.V. All rights reserved.

Valence tautomerism in synthetic models of cytochrome P450

PubMed Central

Das, Pradip Kumar; Samanta, Subhra; McQuarters, Ashley B.; Lehnert, Nicolai

2016-01-01

CytP450s have a cysteine-bound heme cofactor that, in its as-isolated resting (oxidized) form, can be conclusively described as a ferric thiolate species. Unlike the native enzyme, most synthetic thiolate-bound ferric porphyrins are unstable in air unless the axial thiolate ligand is sterically protected. Spectroscopic investigations on a series of synthetic mimics of cytP450 indicate that a thiolate-bound ferric porphyrin coexists in organic solutions at room temperature (RT) with a thiyl-radical bound ferrous porphyrin, i.e., its valence tautomer. The ferric thiolate state is favored by greater enthalpy and is air stable. The ferrous thiyl state is favored by entropy, populates at RT, and degrades in air. These ground states can be reversibly interchanged at RT by the addition or removal of water to the apolar medium. It is concluded that hydrogen bonding and local electrostatics protect the resting oxidized cytP450 active site from degradation in air by stabilizing the ferric thiolate ground state in contrast to its synthetic analogs. PMID:27302948

Photophysics of self-assembled zinc porphyrin-bidentate diamine ligand complexes.

PubMed

Danger, Brook R; Bedient, Krysta; Maiti, Manisankar; Burgess, Ian J; Steer, Ronald P

2010-10-21

The effects of complexation--by bidentate nitrogen-containing ligands such as pyrazine and 4,4'-bipyridine commonly used for porphyrin self-assembly--on the photophysics of the model metalloporphyrin, ZnTPP, are reported. Ligation to form the 5-coordinate species introduces an intramolecular charge transfer (ITC) state that, depending on the oxidation and reduction potentials of the electron donor and acceptor, can become involved in the excited state relaxation processes. For ZnTPP, ligation with pyridine has little effect on excited state relaxation following either Q-band or Soret band excitation. However, coordination of ZnTPP with pyrazine and bipyridine causes the S(2) (Soret) state of the ligated species to decay almost exclusively via an S(2)-ICT-S(1) pathway, while affecting the S(1) decay route only slightly. In these 5-coordinate species the S(2)-ICT-S(1) decay route is ultrafast and nearly quantitative. Literature redox data for other bidentate ligands such as DABCO and multidentate ligands commonly used for pophyrin assembly suggest that the ITC states introduced by them could also modify the excited state relaxation dynamics of a wide variety of multiporphyrin arrays.

Complete Reversible Refolding of a G-Protein Coupled Receptor on a Solid Support

PubMed Central

Di Bartolo, Natalie; Compton, Emma L. R.; Warne, Tony; Edwards, Patricia C.; Tate, Christopher G.; Schertler, Gebhard F. X.; Booth, Paula J.

2016-01-01

The factors defining the correct folding and stability of integral membrane proteins are poorly understood. Folding of only a few select membrane proteins has been scrutinised, leaving considerable deficiencies in knowledge for large protein families, such as G protein coupled receptors (GPCRs). Complete reversible folding, which is problematic for any membrane protein, has eluded this dominant receptor family. Moreover, attempts to recover receptors from denatured states are inefficient, yielding at best 40–70% functional protein. We present a method for the reversible unfolding of an archetypal family member, the β1-adrenergic receptor, and attain 100% recovery of the folded, functional state, in terms of ligand binding, compared to receptor which has not been subject to any unfolding and retains its original, folded structure. We exploit refolding on a solid support, which could avoid unwanted interactions and aggregation that occur in bulk solution. We determine the changes in structure and function upon unfolding and refolding. Additionally, we employ a method that is relatively new to membrane protein folding; pulse proteolysis. Complete refolding of β1-adrenergic receptor occurs in n-decyl-β-D-maltoside (DM) micelles from a urea-denatured state, as shown by regain of its original helical structure, ligand binding and protein fluorescence. The successful refolding strategy on a solid support offers a defined method for the controlled refolding and recovery of functional GPCRs and other membrane proteins that suffer from instability and irreversible denaturation once isolated from their native membranes. PMID:26982879

Identification of the dominant photochemical pathways and mechanistic insights to the ultrafast ligand exchange of Fe(CO) 5 to Fe(CO) 4EtOH

DOE PAGES

Kunnus, K.; Josefsson, I.; Rajkovic, I.; ...

2016-02-09

We utilized femtosecond time-resolved resonant inelastic X-ray scattering and ab initio theory to study the transient electronic structure and the photoinduced molecular dynamics of a model metal carbonyl photocatalyst Fe(CO) 5 in ethanol solution. We propose mechanistic explanation for the parallel ultrafast intra-molecular spin crossover and ligation of the Fe(CO) 4 which are observed following a charge transfer photoexcitation of Fe(CO) 5 as reported in our previous study [Wernet et al., Nature 520, 78 (2015)]. We find that branching of the reaction pathway likely happens in the 1A 1 state of Fe(CO) 4. A sub-picosecond time constant of themore » spin crossover from 1B 2 to 3B 2 is rationalized by the proposed 1B 2 → 1A 1 → 3B 2 mechanism. Ultrafast ligation of the 1B 2 Fe(CO) 4 state is significantly faster than the spin-forbidden and diffusion limited ligation process occurring from the 3B 2 Fe(CO) 4 ground state that has been observed in the previous studies. We propose that the ultrafast ligation occurs via 1B 2 → 1A 1 → 1A' Fe(CO) 4EtOH pathway and the time scale of the 1A 1 Fe(CO) 4 state ligation is governed by the solute-solvent collision frequency. In conclusion, our study emphasizes the importance of understanding the interaction of molecular excited states with the surrounding environment to explain the relaxation pathways of photoexcited metal carbonyls in solution.« less

Crystal structures of two Bordetella pertussis periplasmic receptors contribute to defining a novel pyroglutamic acid binding DctP subfamily.

PubMed

Rucktooa, Prakash; Antoine, Rudy; Herrou, Julien; Huvent, Isabelle; Locht, Camille; Jacob-Dubuisson, Françoise; Villeret, Vincent; Bompard, Coralie

2007-06-29

Gram-negative bacteria have developed several different transport systems for solute uptake. One of these, the tripartite ATP independent periplasmic transport system (TRAP-T), makes use of an extracytoplasmic solute receptor (ESR) which captures specific solutes with high affinity and transfers them to their partner permease complex located in the bacterial inner membrane. We hereby report the structures of DctP6 and DctP7, two such ESRs from Bordetella pertussis. These two proteins display a high degree of sequence and structural similarity and possess the "Venus flytrap" fold characteristic of ESRs, comprising two globular alpha/beta domains hinged together to form a ligand binding cleft. DctP6 and DctP7 both show a closed conformation due to the presence of one pyroglutamic acid molecule bound by highly conserved residues in their respective ligand binding sites. BLAST analyses have revealed that the DctP6 and DctP7 residues involved in ligand binding are strictly present in a number of predicted TRAP-T ESRs from other bacteria. In most cases, the genes encoding these TRAP-T systems are located in the vicinity of a gene coding for a pyroglutamic acid metabolising enzyme. Both the high degree of conservation of these ligand binding residues and the genomic context of these TRAP-T-coding operons in a number of bacterial species, suggest that DctP6 and DctP7 constitute the prototypes of a novel TRAP-T DctP subfamily involved in pyroglutamic acid transport.

Molecular structure and biological studies on Cr(III), Mn(II) and Fe(III) complexes of heterocyclic carbohydrazone ligand.

PubMed

Abu El-Reash, G M; El-Gammal, O A; Radwan, A H

2014-01-01

The chelating behavior of the ligand (H2APC) based on carbohydrazone core modified with pyridine end towards Cr(III), Mn(II) and Fe(III) ions have been examined. The (1)H NMR and IR data for H2APC revealed the presence of two stereoisomers syn and anti in both solid state and in solution in addition to the tautomeric versatility based on the flexible nature of the hydrazone linkage leading to varied coordination modes. The spectroscopic data confirmed that the ligand behaves as a monobasic tridentate in Cr(III) and Fe(III) complexes and as neutral tetradentate in Mn(II) complex. The electronic spectra as well as the magnetic measurements confirmed the octahedral geometry for all complexes. The bond length and angles were evaluated by DFT method using material studio program for all complexes. The thermal behavior and the kinetic parameters of degradation were determined using Coats-Redfern and Horowitz-Metzger methods. The antioxidant (DDPH and ABTS methods), anti-hemolytic and cytotoxic activities of the compounds have been screened. Cr(III) complex and H2APC showed the highest antioxidant activity using ABTS and DPPH methods. With respect to in vitro Ehrlich ascites assay, H2APC exhibited the potent activity followed by Fe(III) and Cr(III)complexes. Copyright © 2013 Elsevier B.V. All rights reserved.

DOTA analogues with a phosphinate-iminodiacetate pendant arm: modification of the complex formation rate with a strongly chelating pendant.

PubMed

Procházková, Soňa; Kubíček, Vojtěch; Böhmová, Zuzana; Holá, Kateřina; Kotek, Jan; Hermann, Petr

2017-08-08

The new ligand H 6 do3aP ida combines the macrocyclic DOTA-like cavity and the open-chain iminodiacetate group connected through a coordinating phosphinate spacer. Its acid-base and coordination properties in solution were studied by potentiometry. Thermodynamic coordination characteristics of both chelating units are similar to those reported for H 4 dota and iminodiacetic acid themselves, respectively, so, macrocyclic and iminodiacetate units behave independently. The formation kinetics of the Ce(iii)-H 6 do3aP ida complex was studied by UV-Vis spectrophotometry. Various out-of-cage intermediates were identified with 1 : 1, 1 : 2 and 2 : 1 ligand-to-metal ratios. The presence of the strongly coordinating iminodiacetate group significantly slows down the metal ion transfer into the macrocyclic cavity and, so, the formation of the in-cage complex is two orders of magnitude slower than that reported for the Ce(iii)-H 4 dota system. The kinetic inertness of the [Ce(do3aP ida )] 3- complex towards acid-assisted dissociation is comparable to that of the [Ce(dota)] - complex. The coordination modes of the ligand are demonstrated in the solid-state structure of [Cu 4 (do3aP ida )(OH)(H 2 O) 4 ]Cl·7.5H 2 O.

Reactivity of tris(acetylacetonato) iron(III) with tridentate [ONO] donor Schiff base as an access to newer mixed-ligand iron(III) complexes

NASA Astrophysics Data System (ADS)

Bhattacharjee, Chira R.; Goswami, Pankaj; Pramanik, Harun A. R.; Paul, Pradip C.; Mondal, Paritosh

2011-05-01

Two new mixed-ligand iron(III) complexes, [Fe(L n)(acac)(C 2H 5OH)] incorporating coordinated ethanol from the reaction solvent were accessed from the reaction of [Fe(acac) 3] with [ONO] donor dibasic tridentate unsymmetrical Schiff base ligands derived from condensation of 2-hydroxy-1-napthaldehyde with 2-aminophenol (H 2L 1) or 2-aminobenzoic acid (H 2L 2). The thermal study (TGA-DTA) provided evidence for weakly bound ethanol which is readily substituted by neutral N-donor molecule imidazole, benzimidazole or pyridine to produce an array of newer complexes, [Fe(L n)(acac)X] ( n = 1, 2; X = Im, Bim, Py). The compounds were characterized by elemental analyses, FT-IR, UV-vis, solution electrical conductivity, FAB mass, 1H and 13C NMR spectroscopy. Room temperature magnetic susceptibility measurements ( μeff ˜ 5.8 B.M.) are consistent with spin-free octahedral iron(III) complexes. Cyclic voltammetry of ethanol complexes revealed a quasi-reversible one electron redox response (Δ Ep > 100 mV) for the Fe(III)/Fe(II) couple. Low half wave redox potential ( E1/2) values suggested easy redox susceptibility. The ground state geometries of the ethanol and imidazole complexes have been ascertained to be distorted octahedral by density functional theory using DMol3 program at BLYP/DNP level.

Reactivity and effectiveness of traditional and novel ligands for multi-micronutrient fertilization in a calcareous soil

PubMed Central

López-Rayo, Sandra; Nadal, Paloma; Lucena, Juan J.

2015-01-01

This study compares the effectiveness of multi-micronutrient formulations containing iron (Fe), manganese (Mn), and zinc (Zn) with traditional (EDTA, DTPA, HEEDTA, and EDDHAm) or novel chelates (o,p-EDDHA, S,S-EDDS, and IDHA) and natural complexing agents (gluconate and lignosulfonate). The stability and reactivity of the formulations were studied on batch experiments with calcareous soil and by speciation modeling. Formulations containing traditional ligands maintained higher Mn but lower Zn concentration in soil solution than the novel ligands. The gluconate and lignosulfonate maintained low concentrations of both Mn and Zn in soil solution. Selected formulations were applied into calcareous soil and their efficacy was evaluated in a pot experiment with soybean. The formulation containing DTPA led to the highest Zn concentration in plants, as well as the formulation containing S,S-EDDS in the short-term, which correlated with its biodegradability. The application of traditional or novel ligands in formulations did not result in sufficient plant Mn concentrations, which was related to the low Mn stability observed for all formulations under moderate oxidation conditions. The results highlight the need to consider the effect of metals and ligands interactions in multi-nutrient fertilization and the potential of S,S-EDDS to be used for Zn fertilization. Furthermore, it is necessary to explore new sources of Mn fertilization for calcareous soils that have greater stability and efficiency, or instead to use foliar fertilization. PMID:26442065

Reactivity and effectiveness of traditional and novel ligands for multi-micronutrient fertilization in a calcareous soil.

PubMed

López-Rayo, Sandra; Nadal, Paloma; Lucena, Juan J

2015-01-01

This study compares the effectiveness of multi-micronutrient formulations containing iron (Fe), manganese (Mn), and zinc (Zn) with traditional (EDTA, DTPA, HEEDTA, and EDDHAm) or novel chelates (o,p-EDDHA, S,S-EDDS, and IDHA) and natural complexing agents (gluconate and lignosulfonate). The stability and reactivity of the formulations were studied on batch experiments with calcareous soil and by speciation modeling. Formulations containing traditional ligands maintained higher Mn but lower Zn concentration in soil solution than the novel ligands. The gluconate and lignosulfonate maintained low concentrations of both Mn and Zn in soil solution. Selected formulations were applied into calcareous soil and their efficacy was evaluated in a pot experiment with soybean. The formulation containing DTPA led to the highest Zn concentration in plants, as well as the formulation containing S,S-EDDS in the short-term, which correlated with its biodegradability. The application of traditional or novel ligands in formulations did not result in sufficient plant Mn concentrations, which was related to the low Mn stability observed for all formulations under moderate oxidation conditions. The results highlight the need to consider the effect of metals and ligands interactions in multi-nutrient fertilization and the potential of S,S-EDDS to be used for Zn fertilization. Furthermore, it is necessary to explore new sources of Mn fertilization for calcareous soils that have greater stability and efficiency, or instead to use foliar fertilization.

Solution NMR characterization of magnetic/electronic properties of azide and cyanide-inhibited substrate complexes of human heme oxygenase: implications for steric ligand tilt.

PubMed

Peng, Dungeng; Ogura, Hiroshi; Ma, Li-Hua; Evans, John P; de Montellano, Paul R Ortiz; La Mar, Gerd N

2013-04-01

Solution 2D (1)H NMR was carried out on the azide-ligated substrate complex of human heme oxygenase, hHO, to provide information on the active site molecular structure, chromophore electronic/magnetic properties, and the distal H-bond network linked to the exogenous ligand by catalytically relevant oriented water molecules. While 2D NMR exhibited very similar patterns of two-dimensional nuclear Overhauser spectroscopy cross peaks of residues with substrate and among residues as the previously characterized cyanide complex, significant, broadly distributed chemical shift differences were observed for both labile and non-labile protons. The anisotropy and orientation of the paramagnetic susceptibility tensor, χ, were determined for both the azide and cyanide complexes. The most significant difference observed is the tilt of the major magnetic axes from the heme normal, which is only half as large for the azide than cyanide ligand, with each ligand tilted toward the catalytically cleaved α-meso position. The difference in chemical shifts is quantitatively correlated with differences in dipolar shifts in the respective complexes for all but the distal helix. The necessity of considering dipolar shifts, and hence determination of the orientation/anisotropy of χ, in comparing chemical shifts involving paramagnetic complexes, is emphasized. The analysis shows that the H-bond network cannot detect significant differences in H-bond acceptor properties of cyanide versus azide ligands. Lastly, significant retardation of distal helix labile proton exchange upon replacing cyanide with azide indicates that the dynamic stability of the distal helix is increased upon decreasing the steric interaction of the ligand with the distal helix. Copyright © 2013. Published by Elsevier Inc.

Design of a Hole Trapping Ligand

DOE PAGES

La Croix, Andrew D.; O’Hara, Andrew; Reid, Kemar R.; ...

2017-01-18

A new ligand that covalently attaches to the surface of colloidal CdSe/ CdS nanorods and can simultaneously chelate a molecular metal center is described. The dithiocarbamate$-$bipyridine ligand system facilitates hole transfer through energetic overlap at the inorganic$-$organic interface and conjugation through the organic ligand to a chelated metal center. Density functional theory calculations show that the coordination of the free ligand to a CdS surface causes the formation of two hybridized molecular states that lie in the band gap of CdS. The further chelation of Fe(II) to the bipyridine moiety causes the presence of seven midgap states. Hole transfer frommore » the CdS valence band to the midgap states is dipole allowed and occurs at a faster rate than what is experimentally known for the CdSe/CdS band-edge radiative recombination. In the case of the ligand bound with iron, a two-step process emerges that places the hole on the iron, again at rates much faster than band gap recombination. The system was experimentally assembled and characterized via UV$-$vis absorbance spectroscopy, fluorescence spectroscopy, time-resolved photoluminescence spectroscopy, and energy dispersive X-ray spectroscopy. Lastly, theoretically predicted red shifts in absorbance were observed experimentally, as well as the expected quench in photoluminescence and lifetimes in time-resolved photoluminescence« less

Design of a Hole Trapping Ligand

DOE Office of Scientific and Technical Information (OSTI.GOV)

La Croix, Andrew D.; O’Hara, Andrew; Reid, Kemar R.

A new ligand that covalently attaches to the surface of colloidal CdSe/ CdS nanorods and can simultaneously chelate a molecular metal center is described. The dithiocarbamate$-$bipyridine ligand system facilitates hole transfer through energetic overlap at the inorganic$-$organic interface and conjugation through the organic ligand to a chelated metal center. Density functional theory calculations show that the coordination of the free ligand to a CdS surface causes the formation of two hybridized molecular states that lie in the band gap of CdS. The further chelation of Fe(II) to the bipyridine moiety causes the presence of seven midgap states. Hole transfer frommore » the CdS valence band to the midgap states is dipole allowed and occurs at a faster rate than what is experimentally known for the CdSe/CdS band-edge radiative recombination. In the case of the ligand bound with iron, a two-step process emerges that places the hole on the iron, again at rates much faster than band gap recombination. The system was experimentally assembled and characterized via UV$-$vis absorbance spectroscopy, fluorescence spectroscopy, time-resolved photoluminescence spectroscopy, and energy dispersive X-ray spectroscopy. Lastly, theoretically predicted red shifts in absorbance were observed experimentally, as well as the expected quench in photoluminescence and lifetimes in time-resolved photoluminescence« less

Using the Antenna Effect as a Spectroscopic Tool; Photophysics and Solution Thermodynamics of the Model Luminescent Hydroxypyridonate Complex [EuIII(3,4,3-LI(1,2-HOPO))]-

PubMed Central

Abergel, Rebecca J.; D'Aléo, Anthony; Leung, Clara Ng Pak; Shuh, David K.; Raymond, Kenneth N.

2009-01-01

While widely used in bioassays, the spectrofluorimetric method described here uses the antenna effect as a tool to probe the thermodynamic parameters of ligands that sensitize lanthanide luminescence. The Eu3+ coordination chemistry, solution thermodynamic stability and photophysical properties of the spermine-based hydroxypyridonate octadentate chelator 3,4,3-LI(1,2-HOPO) are reported. The complex [EuIII(3,4,3-LI(1,2-HOPO))]- luminesces with a long lifetime (805 μs) and a quantum yield of 7.0% in aqueous solution, at pH 7.4. These remarkable optical properties were exploited to determine the high (and proton-independent) stability of the complex (log β110 = 20.2(2)) and to define the influence of the ligand scaffold on the stability and photophysical properties. PMID:19902920

Structural and photophysical studies on gallium(III) 8-hydroxyquinoline-5-sulfonates. Does excited state decay involve ligand photolabilisation?

PubMed

Ramos, M Luísa; de Sousa, Andreia R E; Justino, Licínia L G; Fonseca, Sofia M; Geraldes, Carlos F G C; Burrows, Hugh D

2013-03-14

Multinuclear ((1)H, (13)C and (71)Ga) magnetic resonance spectroscopy (1D and 2D), DFT calculations and luminescence techniques have been used to study 8-hydroxyquinoline-5-sulfonate (8-HQS) and its complexes with Ga(III) in aqueous solutions. The study combines the high sensitivity of luminescence techniques and the selectivity of multinuclear NMR spectroscopy with the structural details accessible through DFT calculations, and aims to obtain a complete understanding of the complexation between the Ga(3+) ion and 8-HQS, and how this influences the luminescence behaviour. A full speciation study has been performed on this system and three complexes detected, with (metal : ligand) 1 : 1, 1 : 2 and 1 : 3 stoichiometries, the results being consistent with those previously found for the system Al(III)-8-HQS. Complexation in these systems is relevant to their potential biomedical, sensing and optoelectronic applications. On binding to Ga(III), a marked increase is seen in the intensity of the 8-HQS fluorescence band, which is accompanied by changes in the absorption spectra. These support the use of 8-HQS as a sensitive fluorescent sensor to detect Ga(3+) metal ions in surface waters, biological fluids, etc., and its metal complexes as an emitting or charge transport layer in light emitting devices. However, the fluorescence quantum yield of the Ga(III)-8-HQS 1 : 3 complex is about 35% of that of the corresponding system with Al(III). Although this may be due in part to a heavy atom effect favouring S(1)→ T(1) intersystem crossing with Ga(3+), this does not agree with transient absorption measurements on the triplet state yield, which is lower with the Ga(III) system than with Al(III). Instead, it is suggested that photolabilisation of ligand exchange plays a major role in nonradiative decay of the excited state and that this is more efficient with the Ga(3+) complex. Based on these results, suggestions are made of ways of enhancing fluorescence intensity in metal complexes with 8-HQS by inhibiting ligand exchange using surfactant complexation for applications in either sensing or optoelectronics.

Trans influence on the rate of reductive elimination. Reductive elimination of amines from isomeric arylpalladium amides with unsymmetrical coordination spheres.

PubMed

Yamashita, Makoto; Cuevas Vicario, Jose V; Hartwig, John F

2003-12-31

To determine the trans effect on the rates of reductive eliminations from arylpalladium(II) amido complexes, the reactions of arylpalladium amido complexes bearing symmetrical and unsymmetrical DPPF (DPPF = bis(diphenylphosphino)ferrocene) derivatives were studied. THF solutions of LPd(Ar)(NMeAr') (L = DPPF, DPPF-OMe, DPPF-CF3, DPPF-OMe,Ph, DPPF-Ph,CF3, and DPPF-OMe,CF3; Ar = C6H4-4-CF3; Ar' = C6H4-4-CH3, Ph, and C6H4-4-OMe) underwent C-N bond forming reductive elimination at -15 C to form the corresponding N-methyldiarylamine in high yield. Complexes ligated by symmetrical DPPF derivatives with electron-withdrawing substituents on the DPPF aryl groups underwent reductive elimination faster than complexes ligated by symmetrical DPPF derivatives with electron-donating substituents on the ligand aryl groups. Studies of arylpalladium amido complexes containing unsymmetrical DPPF ligands revealed several trends. First, the complex with the weaker donor trans to nitrogen and the stronger donor trans to the palladium-bound aryl group underwent reductive elimination faster than the regioisomeric complex with the stronger donor trans to nitrogen and the weaker donor trans to the palladium-bound aryl group. Second, the effect of varying the substituents on the phosphorus donor trans to the nitrogen was larger than the effect of varying the substituents on the phosphorus donor trans to the palladium-bound aryl group. Third, the difference in rate between the isomeric arylpalladium amido complexes was similar in magnitude to the differences in rates resulting from conventional variation of substituents on the symmetric phosphine ligands. This result suggests that the geometry of the complex is equal in importance to the donating ability of the dative ligands. The ratio of the differences in rates of reaction of the isomeric complexes was similar to the relative populations of the two geometric isomers. This result and consideration of transition state geometries suggest that the reaction rates are controlled more by substituent effects on ground state stability than on transition state energies. In addition, variation of the aryl group at the amido nitrogen showed systematically that complexes with more electron-donating groups at nitrogen undergo faster reductive elimination than those with less electron-donating groups at nitrogen.

Synthesis and redox properties of fac-BrRe(CO)3[1,2-(PPh2)2-closo-1,2-C2B10H10]: The first structurally characterized rhenium carbonyl containing a carboranyl-based diphosphine ligand

NASA Astrophysics Data System (ADS)

Lin, Chen-Hao; Nesterov, Vladimir N.; Richmond, Michael G.

2018-03-01

The diphosphine 1,2-(PPh2)2-closo-1,2-C2B10H10 reacts with BrRe(CO)5 and fac-BrRe(CO)3(THF)2 to give fac-BrRe(CO)3[1,2-(PPh2)2-closo-1,2-C2B10H10] (1) in high yields (>80%). Compound 1 is the first structurally characterized rhenium carbonyl that contains an ancillary carborane-based diphosphine ligand. 1 has been characterized in solution by IR and NMR spectroscopies (1H and 31P), and the solid-state structure has been determined by X-ray diffraction analysis. The electrochemical properties of 1 have been investigated by cyclic voltammetry, and the composition of the DFT-computed HOMO and LUMO levels are discussed relative to the electrochemical data. The thermodynamics for the formation of 1 from the rhenium precursors BrRe(CO)5 and fac-BrRe(CO)3(THF)2 have been evaluated by DFT calculations.

A flexible 1,8-naphthyridyl derivative and its Zn(II) complexes: synthesis, structures, spectroscopic properties and recognition of Cd(II).

PubMed

Zhang, Hui-Miao; Fu, Wen-Fu; Gan, Xin; Xu, Yan-Qing; Wang, Jun; Xu, Quan-Qing; Chi, Shao-Ming

2008-12-21

A flexible ligand bis(7-methyl-1,8-naphthyridine-2-ylamino)methane (), having kappa(4)-chelating and kappa(2)-bridging modes, and its intriguing structural complexes of Zn(II) with mu-OH, kappa(1)-OAc, mu-kappa(1)-OAc and mu-kappa(2)-OAc ligands, [Zn(2)()(2)(OH)](ClO(4))(3) (), [Zn(4)()(2)(OAc)(6)(OH)(2)].CH(2)Cl(2) (.CH(2)Cl(2)) and [Zn(5)()(2)(OAc)(10)](n).4nH(2)O (.4H(2)O) were synthesized and their structures were determined by X-ray crystallography. These compounds exhibited intense blue fluorescent emissions with a lambda(max) in the range of 380-410 nm in CH(2)Cl(2), CH(3)CN and CH(3)OH solutions, and solid-state emissions centered at 416, 463, 490 and 451 nm were observed for the compounds , , and at room temperature, respectively. The investigated fluorescence properties of associated with various metal ions showed that the fluorescence enhancement of with Cd(II) was more sensitive than with other interfering cations.

Syntheses, structures, photoluminescence of four dicarboxylate-controlled Zn(II) coordination complexes incorporating flexible 1-(4-pyridylmethyl)-benzimidazole ligand

NASA Astrophysics Data System (ADS)

Hao, Hong-Jun; Du, Ming-Yue; Wang, Dan-Feng; Sun, Cheng-Jie; Wang, Zhan-Hui; Huang, Rong-Bin; Zheng, Lan-Sun

2013-09-01

Four Zn(II) coordination complexes, namely {[Zn(pmbm)2(tpa)]·H2O}n (1), {[Zn(pmbm)(phda)]·2(H2O)}n (2), [Zn(pmbm)(aze)]n (3), {[Zn(pmbm)(1,4-ndc)]·2(CH3OH)}n (4) [pmbm = 1-(4-pyridylmethyl)-benzimidazole, H2tpa = terephthalic acid, H2phda = phenylenediacetic acid, H2aze = azelaic acid, 1,4-ndcH2 = 1,4-naphthalenedicarboxylic acid] have been synthesized by solution phase ultrasonic reactions of Zn(AC)2·2H2O with pmbm and various dicarboxylates ligands under the ammoniacal condition. All the complexes have been characterized by elemental analyses, IR spectra and X-ray diffraction. Complexes 1 and 2 exhibit one-dimensional chains structure and complex 3 and 4 are two-dimensional sheets structure with (4,4) topology. Complexes 1-4 spanning from one-dimensional chains to two-dimensional sheets suggest that dicarboxylates play significant roles in the formation of such coordination architectures. The photoluminescences of the complexes were also investigated in the solid state at room temperature.

Metal-ion interactions with carbohydrates. Crystal structure and FT-IR study of the SmCl3-ribose complex.

PubMed

Lu, Yan; Guo, Jianyu

2006-04-10

A single-crystal of SmCl3.C5H10O5.5H2O was obtained from methanol-water solution and its structure determined by X-ray. Two forms of the complex as a pair of anomers and related conformers were found in the single-crystal in a disordered state. One ligand is alpha-D-ribopyranose in the 4C1 conformation and the other one is beta-D-ribopyranose. The anomeric ratio is 1:1. Both ligands provide three hydroxyl groups in ax-eq-ax orientation for coordination. The Sm3+ ion is nine-coordinated with five Sm-O bonds from water molecules, three Sm-O bonds from hydroxyl groups of the D-ribopyranose and one Sm-Cl bond. The hydroxyl groups, water molecules and chloride ions form an extensive hydrogen-bond network. The IR spectral C-C, O-H, C-O, and C-O-H vibrations were observed to be shifted in the complex and the IR results are in accord with those of X-ray diffraction.

Near-infrared-emitting colloidal Ag2S quantum dots exhibiting upconversion luminescence

NASA Astrophysics Data System (ADS)

Zhang, Yanyan; Jiang, Danyu; Yang, Wei; Wang, Dandan; Zheng, Huiping; Du, Yuansheng; Li, Xi; Li, Qiang

2017-02-01

Ag2S quantum dots (QDs) coated with thioglycolic acid (Ag2S QDs-TGA) have been synthesized in an organic solvent via a stepwise addition of reagents. When excited by a 980 nm laser, the near-infrared-emitting colloidal Ag2S QDs-TGA exhibit upconversion luminescence (UCL). The observed photoluminescence (PL) was attributed to the presence of ligand-modified Ag2S on the QD surfaces. Hence, upon dilution of the solution, the PL intensity initially increased before subsequently decreasing, accompanied by a blue shift in the PL spectra. The PL phenomena can be attributed to the increase in the amount of ligand-modified Ag2S on the QD surfaces upon dilution, which in turn affected the fluorescence resonance energy transfer (FRET) and re-emission of the surface energy level. The relations between the emission intensity of Ag2S QDs-TGA and the excitation power are investigated, and the results confirm that the UCL in Ag2S QDs-TGA can be ascribed to a two-photon-assisted absorption process via a real energy state.

Alkali metal cation complexation by 1,3-alternate, mono-ionisable calix[4]arene-benzocrown-6 compounds

DOE PAGES

Surowiec, Malgorzata A.; Custelcean, Radu; Surowiec, Kazimierz; ...

2014-04-23

Alkali metal cation extraction behavior for two series of 1,3-alternate, mono-ionizable calix[4]arene-benzocrown-6 compounds is examined. In Series 1, the proton-ionizable group is a substituent on the benzo group of the polyether ring that directs it away from the crown ether cavity. In Series 2, the proton-ionizable group is attached to one para position in the calixarene framework, thus positioning it over the crown ether ring. Competitive solvent extraction of alkali metal cations from aqueous solutions into chloroform shows high Cs+ efficiency and selectivity. Single-species extraction pH profiles of Cs+ for Series 1 and 2 ligands with the same proton-ionizable groupmore » are very similar. Thus, association of Cs+ with the calixcrown ring is more important than the the proton-ionizable group’s position in relation to the crown ether cavity. Solid-state structures are presented for two unionized ligands from Series 2, as is a crystal containing two different ionized ligand–Cs+ complexes.« less

Highly stable biocompatible inorganic nanoparticles by self-assembly of triblock-copolymer ligands.

PubMed

Pöselt, Elmar; Fischer, Steffen; Foerster, Stephan; Weller, Horst

2009-12-15

A novel type of ligand for biofunctionalization of nanoparticles is presented that comprises tailor-made triblock-copolymers consisting of a polyethylene imine binding block, a hydrophobic polycaprolactone and a terminal functionalized polyethelene oxide block. Phase transfer to water occurs simply by ligand and water addition and removal of the organic solvents. It is shown that the intermediate polycaprolacton block favors the attachment to the particle surface and shields the binding groups effectively from the solution. As a consequence, the particles exhibit an outstanding stability in various aqueous media for biological studies and give easy access to specific coupling reactions at the terminal end groups of the polyethylene oxide block. Controlling the ligand exchange parameters leads to self-assembly to either individual encapsulated nanoparticles or to multifunctional nanobeads.

Effect of urea on protein-ligand association.

PubMed

Stepanian, Lora; Son, Ikbae; Chalikian, Tigran V

2017-12-01

We combine experimental and theoretical approaches to investigate the influence of a cosolvent on a ligand-protein association event. We apply fluorescence measurements to determining the affinity of the inhibitor tri-N-acetylglucosamine [(GlcNAc) 3 ] for lysozyme at urea concentrations ranging from 0 to 8M. Notwithstanding that, at room temperature and neutral pH, lysozyme retains its native conformation up to the solubility limit of urea, the affinity of (GlcNAc) 3 for the protein steadily decreases as the concentration of urea increases. We analyze the urea dependence of the binding free energy within the framework of a simplified statistical thermodynamics-based model that accounts for the excluded volume effect and direct solute-solvent interactions. The analysis reveals that the detrimental action of urea on the inhibitor-lysozyme binding originates from competition between the free energy contributions of the excluded volume effect and direct solute-solvent interactions. The free energy contribution of direct urea-solute interactions narrowly overcomes the excluded volume contribution thereby resulting in urea weakening the protein-ligand association. More broadly, the successful application of the simple model employed in this work points to the possibility of its use in quantifying the stabilizing/destabilizing action of individual cosolvents on biochemical folding and binding reactions. Copyright © 2016 Elsevier B.V. All rights reserved.

Direct Determination of Vibrational Density of States Change on Ligand Binding to a Protein

NASA Astrophysics Data System (ADS)

Balog, Erika; Becker, Torsten; Oettl, Martin; Lechner, Ruep; Daniel, Roy; Finney, John; Smith, Jeremy C.

2004-07-01

The change in the vibrational density of states of a protein (dihydrofolate reductase) on binding a ligand (methotrexate) is determined using inelastic neutron scattering. The vibrations of the complex soften significantly relative to the unbound protein. The resulting free-energy change, which is directly determined by the density of states change, is found to contribute significantly to the binding equilibrium.

NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers.

PubMed

Sekhar, Ashok; Kay, Lewis E

2013-08-06

The importance of dynamics to biomolecular function is becoming increasingly clear. A description of the structure-function relationship must, therefore, include the role of motion, requiring a shift in paradigm from focus on a single static 3D picture to one where a given biomolecule is considered in terms of an ensemble of interconverting conformers, each with potentially diverse activities. In this Perspective, we describe how recent developments in solution NMR spectroscopy facilitate atomic resolution studies of sparsely populated, transiently formed biomolecular conformations that exchange with the native state. Examples of how this methodology is applied to protein folding and misfolding, ligand binding, and molecular recognition are provided as a means of illustrating both the power of the new techniques and the significant roles that conformationally excited protein states play in biology.

Lanthanide Fluorobenzoates as Bio-Probes: a Quest for the Optimal Ligand Fluorination Degree.

PubMed

Kalyakina, Alena S; Utochnikova, Valentina V; Bushmarinov, Ivan S; Le-Deygen, Irina M; Volz, Daniel; Weis, Patrick; Schepers, Ute; Kuzmina, Natalia P; Bräse, Stefan

2017-10-20

The thorough study of fluorinated benzoates of lanthanides (Eu, Tb, Nd, Er, Yb, Gd, La, Lu) is reported. Their composition in single crystal and powder state revealed two predominant structural motifs. An in-depth luminescence study has been performed on the reported fluorobenzoates, showing, that terbium and europium complexes in solid state possess high luminescence intensity with the quantum yield of up to 69 %. High solubility in most organic solvents, as well as in water, combined with the high luminescence intensity in water solution and non-toxicity allowed the testing of europium complexes as bioprobes in cellulo. Among all tested fluorobenzoates, europium 2-fluorobenzoate dihydrate combined the best luminescent properties, thermodynamic stability, aqueous solubility, and non-toxicity, and was shown to be a viable bio-marker. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Solid-state polymerisation via [2+2] cycloaddition reaction involving coordination polymers.

PubMed

Medishetty, Raghavender; Park, In-Hyeok; Lee, Shim Sung; Vittal, Jagadese J

2016-03-14

Highly crystalline metal ions containing organic polymers are potentially useful to manipulate the magnetic and optical properties to make advanced multifunctional materials. However, it is challenging to synthesise monocrystalline metal complexes of organic polymers and single-phase hybrid materials made up of both coordination and organic polymers by traditional solution crystallisation. This requires an entirely different approach in the solid-state by thermal or photo polymerisation of the ligands. Among the photochemical methods available, [2+2] cycloaddition reaction has been recently employed to generate cyclobutane based coordination polymers from the metal complexes. Cyclobutane polymers have also been integrated into coordination polymers in this way. Recent advancements in the construction of polymeric chains of cyclobutane rings through photo-dimerisation reaction in the monocrystalline solids containing metal complexes, coordination polymers and metal-organic framework structures are discussed here.

Ligand Extraction Properties of the GM2 Activator Protein and Its Interactions with Lipid Vesicles

PubMed Central

Ran, Yong; Fanucci, Gail E.

2009-01-01

Abstract The GM2 activator protein (GM2AP) is an accessory protein required for the enzymatic conversion of GM2 to GM3 by hydrolases in the lysosomal compartments of cells. Here, GM2AP interactions with lipid vesicles are investigated by sucrose-loaded vesicle sedimentation and gel filtration assays, and the effects of pH and lipid composition on membrane binding and lipid extraction are characterized. The sedimentation experiments allow for facile quantification of the percentage of protein in solution and on the bilayer surface, with detailed analysis of the protein:lipid complex that remains in solution. Optimum binding and ligand extraction is found for pH 4.8 where <15% of the protein remains surface associated regardless of the lipid composition. In addition to extracting GM2, we find that GM2AP readily extracts dansyl-headgroup-labeled lipids as well as other phospholipids from vesicles. The ability of GM2AP to extract dansyl-DHPE from vesicles is altered by pH and the specific ligand GM2. Although the unique endosomal lipid, bis(monoacylglycero)phosphate, is not required for ligand extraction, it does enhance the extraction efficiency of GM2 when cholesterol is present in the vesicles. PMID:19580763

Ligand extraction properties of the GM2 activator protein and its interactions with lipid vesicles.

PubMed

Ran, Yong; Fanucci, Gail E

2009-07-08

The GM2 activator protein (GM2AP) is an accessory protein required for the enzymatic conversion of GM2 to GM3 by hydrolases in the lysosomal compartments of cells. Here, GM2AP interactions with lipid vesicles are investigated by sucrose-loaded vesicle sedimentation and gel filtration assays, and the effects of pH and lipid composition on membrane binding and lipid extraction are characterized. The sedimentation experiments allow for facile quantification of the percentage of protein in solution and on the bilayer surface, with detailed analysis of the protein:lipid complex that remains in solution. Optimum binding and ligand extraction is found for pH 4.8 where <15% of the protein remains surface associated regardless of the lipid composition. In addition to extracting GM2, we find that GM2AP readily extracts dansyl-headgroup-labeled lipids as well as other phospholipids from vesicles. The ability of GM2AP to extract dansyl-DHPE from vesicles is altered by pH and the specific ligand GM2. Although the unique endosomal lipid, bis(monoacylglycero)phosphate, is not required for ligand extraction, it does enhance the extraction efficiency of GM2 when cholesterol is present in the vesicles.

Functional Stability of the Human Kappa Opioid Receptor Reconstituted in Nanodiscs Revealed by a Time-Resolved Scintillation Proximity Assay

PubMed Central

Hansen, Randi Westh; Wang, Xiaole; Golab, Agnieszka; Bornert, Olivier; Oswald, Christine; Wagner, Renaud; Martinez, Karen Laurence

2016-01-01

Long-term functional stability of isolated membrane proteins is crucial for many in vitro applications used to elucidate molecular mechanisms, and used for drug screening platforms in modern pharmaceutical industry. Compared to soluble proteins, the understanding at the molecular level of membrane proteins remains a challenge. This is partly due to the difficulty to isolate and simultaneously maintain their structural and functional stability, because of their hydrophobic nature. Here we show, how scintillation proximity assay can be used to analyze time-resolved high-affinity ligand binding to membrane proteins solubilized in various environments. The assay was used to establish conditions that preserved the biological function of isolated human kappa opioid receptor. In detergent solution the receptor lost high-affinity ligand binding to a radiolabelled ligand within minutes at room temperature. After reconstitution in Nanodiscs made of phospholipid bilayer the half-life of high-affinity ligand binding to the majority of receptors increased 70-fold compared to detergent solubilized receptors—a level of stability that is appropriate for further downstream applications. Time-resolved scintillation proximity assay has the potential to screen numerous conditions in parallel to obtain high levels of stable and active membrane proteins, which are intrinsically unstable in detergent solution, and with minimum material consumption. PMID:27035823

Solution NMR studies provide structural basis for endotoxin pattern recognition by the innate immune receptor CD14

DOE Office of Scientific and Technical Information (OSTI.GOV)

Albright, Seth; Chen Bin; Holbrook, Kristen

CD14 functions as a key pattern recognition receptor for a diverse array of Gram-negative and Gram-positive cell-wall components in the host innate immune response by binding to pathogen-associated molecular patterns (PAMPs) at partially overlapping binding site(s). To determine the potential contribution of CD14 residues in this pattern recognition, we have examined using solution NMR spectroscopy, the binding of three different endotoxin ligands, lipopolysaccharide, lipoteichoic acid, and a PGN-derived compound, muramyl dipeptide to a {sup 15}N isotopically labeled 152-residue N-terminal fragment of sCD14 expressed in Pichia pastoris. Mapping of NMR spectral changes upon addition of ligands revealed that the pattern ofmore » residues affected by binding of each ligand is partially similar and partially different. This first direct structural observation of the ability of specific residue combinations of CD14 to differentially affect endotoxin binding may help explain the broad specificity of CD14 in ligand recognition and provide a structural basis for pattern recognition. Another interesting finding from the observed spectral changes is that the mode of binding may be dynamically modulated and could provide a mechanism for binding endotoxins with structural diversity through a common binding site.« less

Extracellular enzymes in sensing environmental nutrients and ecosystem changes: Ligand mediation in organic phosphorus cycling

USDA-ARS?s Scientific Manuscript database

Inorganic and organic phosphates react strongly with soil constituents, resulting in relatively low concentrations of soluble P in the soil solution. Multiple competing reactions are operating to regulate the solution-phase concentration of P-containing organic substrates and the released phosphate...

Influence of surface states of CuInS2 quantum dots in quantum dots sensitized photo-electrodes

NASA Astrophysics Data System (ADS)

Peng, Zhuoyin; Liu, Yueli; Wu, Lei; Zhao, Yinghan; Chen, Keqiang; Chen, Wen

2016-12-01

Surface states are significant factor for the enhancement of electrochemical performance in CuInS2 quantum dot sensitized photo-electrodes. DDT, OLA, MPA, and S2- ligand capped CuInS2 quantum dot sensitized photo-electrodes are prepared by thermolysis, solvethermal and ligand-exchange processes, respectively, and their optical properties and photoelectrochemical properties are investigated. The S2- ligand enhances the UV-vis absorption and electron-hole separation property as well as the excellent charge transfer performance of the photo-electrodes, which is attributed to the fact that the atomic S2- ligand for the interfacial region of quantum dots may improve the electron transfer rate. These S2--capped CuInS2 quantum dot sensitized photo-electrodes exhibit the excellent photoelectrochemical efficiency and IPCE peak value, which is higher than that of the samples with DDT, OLA and MPA ligands.

Cobalt(II) and Cobalt(III) Coordination Compounds.

ERIC Educational Resources Information Center

Thomas, Nicholas C.; And Others

1989-01-01

Presents a laboratory experiment which illustrates the formation of tris(phenanthroline)cobalt complexes in the 2+ and 3+ oxidation states, the effect of coordination on reactions of the ligand, and the use of a ligand displacement reaction in recovering the transformed ligand. Uses IR, UV-VIS, conductivity, and NMR. (MVL)

Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015

NASA Astrophysics Data System (ADS)

Slynko, Inna; Da Silva, Franck; Bret, Guillaume; Rognan, Didier

2016-09-01

High affinity ligands for a given target tend to share key molecular interactions with important anchoring amino acids and therefore often present quite conserved interaction patterns. This simple concept was formalized in a topological knowledge-based scoring function (GRIM) for selecting the most appropriate docking poses from previously X-rayed interaction patterns. GRIM first converts protein-ligand atomic coordinates (docking poses) into a simple 3D graph describing the corresponding interaction pattern. In a second step, proposed graphs are compared to that found from template structures in the Protein Data Bank. Last, all docking poses are rescored according to an empirical score (GRIMscore) accounting for overlap of maximum common subgraphs. Taking the opportunity of the public D3R Grand Challenge 2015, GRIM was used to rescore docking poses for 36 ligands (6 HSP90α inhibitors, 30 MAP4K4 inhibitors) prior to the release of the corresponding protein-ligand X-ray structures. When applied to the HSP90α dataset, for which many protein-ligand X-ray structures are already available, GRIM provided very high quality solutions (mean rmsd = 1.06 Å, n = 6) as top-ranked poses, and significantly outperformed a state-of-the-art scoring function. In the case of MAP4K4 inhibitors, for which preexisting 3D knowledge is scarce and chemical diversity is much larger, the accuracy of GRIM poses decays (mean rmsd = 3.18 Å, n = 30) although GRIM still outperforms an energy-based scoring function. GRIM rescoring appears to be quite robust with comparison to the other approaches competing for the same challenge (42 submissions for the HSP90 dataset, 27 for the MAP4K4 dataset) as it ranked 3rd and 2nd respectively, for the two investigated datasets. The rescoring method is quite simple to implement, independent on a docking engine, and applicable to any target for which at least one holo X-ray structure is available.

Paramagnetic oxotungsten(V) complexes containing the hydrotris(3,5-dimethylpyrazol-1-yl)borate ligand.

PubMed

Sproules, Stephen; Eagle, Aston A; Taylor, Michelle K; Gable, Robert W; White, Jonathan M; Young, Charles G

2011-05-16

Sky-blue Tp*WOCl(2) has been synthesized from the high-yielding reaction of Tp*WO(2)Cl with boron trichloride in refluxing toluene. Dark-red Tp*WOI(2) was prepared via thermal decarbonylation followed by aerial oxidation of Tp*WI(CO)(3) in acetonitrile. From these precursors, an extensive series of mononuclear tungstenyl complexes, Tp*WOXY [X = Cl(-), Y = OPh(-), SPh(-); X = Y = OPh(-), 2-(n-propyl)phenolate (PP(-)), SPh(-), SePh(-); XY = toluene-3,4-dithiolate (tdt(2-)), quinoxaline-2,3-dithiolate (qdt(2-)), benzene-1,2-diselenolate (bds(2-)); Tp* = hydrotris(3,5-dimethylpyrazol-1-yl)borate], was prepared by metathesis with the respective alkali-metal salt of X(-)/XY(2-) or (NHEt(3))(2)(qdt). The complexes were characterized by microanalysis, mass spectrometry, electrochemistry, IR, electron paramagnetic resonance (EPR), and electronic absorption spectroscopies, and X-ray crystallography (for X = Y = OPh(-), PP(-), SPh(-); XY = bds(2-)). The six-coordinate, distorted-octahedral tungsten centers are coordinated by terminal oxo [W≡O = 1.689(6)-1.704(3) Å], tridentate Tp*, and monodentate or bidentate O/S/Se-donor ligands. Spin Hamiltonian parameters derived from the simulation of fluid-solution X-band EPR spectra revealed that the soft-donor S/Se ligand complexes had larger g values and smaller (183)W hyperfine coupling constants than the less covalent hard-donor O/Cl species. The former showed low-energy ligand-to-metal charge-transfer bands in the near-IR region of their electronic absorption spectra. These oxotungsten(V) complexes display lower reduction potentials than their molybdenum counterparts, underscoring the preference of tungsten for higher oxidation states. Furthermore, the protonation of the pyrazine nitrogen atoms of the qdt(2-) ligand has been examined by spectroelectrochemistry; the product of the one-electron reduction of [Tp*WO(qdtH)](+) revealed usually intense low-energy bands.

Tuning optoelectronic properties of small semiconductor nanocrystals through surface ligand chemistry

NASA Astrophysics Data System (ADS)

Lawrence, Katie N.

Semiconductor nanocrystals (SNCs) are a class of material with one dimension <100 nm, which display size, shape, and composition dependent photophysical (absorption and emission) properties. Ultrasmall SNCs are a special class of SNCs whose diameter is <3.0 nm and are strongly quantum confined leading to a high surface to volume ratio. Therefore, their electronic and photophysical properties are fundamentally dictated by their surface chemistry, and as such, even a minute variation of the surface ligation can have a colossal impact on these properties. Since the development of the hot injection-method by Bawendi et al., the synthetic methods of SNCs have evolved from high-temperature, highly toxic precursors to low-temperature, relatively benign precursors over the last 25 years. Unfortunately, optimization of their synthetic methods by appropriate surface ligation is still deficient. The deficiency lies in the incomplete or inappropriate surface passivation during the synthesis and/or post-synthetic modification procedure, which due to the high surface to volume ratio of ultrasmall SNCs, is a significant problem. Currently, direct synthetic methods produce SNCs that are either soluble in an aqueous media or soluble in organic solvents therefore limiting their applicability. In addition, use of insulating ligands hinder SNCs' transport properties and thus their potential application in solid state devices. Appropriate choice of surface ligation can provide 1) solubility, 2) stability, and 3) facilitate exciton delocalization. In this dissertation, the effects of appropriate surface ligation on strongly quantum confined ultrasmall SNCs was investigated. Due to their high surface to volume ratio, we are able to highly control their optical and electronic properties through surface ligand modification. Throughout this dissertation, we utilized a variety of ligands (e.g. oleylamine, cadmium benzoate, and PEGn-thiolate) in order to change the solubility of the SNC as well as investigate their optical and electronic properties. First delocalization of the excitonic wave function 1) into the ligand monolayer using metal carboxylates and 2) beyond the ligand monolayer to provide strong inter-SNC electronic coupling using poly(ethylene) glycol (PEG)-thiolate was explored. Passivation of the Se sites of metal chalcogenide SNCs by metal carboxylates provided a two-fold outcome: (1) facilitating the delocalization of exciton wave functions into ligand monolayers (through appropriate symmetry matching and energy alignment) and (2) increasing fluorescence quantum yield (through passivation of midgap trap states). An ˜240 meV red-shift in absorbance was observed upon addition of Cd(O2CPh)2, as well as a ˜260 meV shift in emission with an increase in PL-QY to 73%. Through a series of control experiments, as well as full reversibility of our system, we were able to conclude that the observed bathochromic shifts were the sole consequence of delocalization, not a change in size or relaxation of the inorganic core, as previously reported. Furthermore, the outstanding increase in PL-QY was found to be a product of both passivation and delocalization effects. Next we used poly(ethylene) glycol (PEG)-thiolate ligands to passivate the SNC and provide unique solubility properties in both aqueous and organic solvents as well as utilized their highly conductive nature to explore inter-SNC electronic coupling. The electronic coupling was studied: 1) as a function of SNC size where the smallest SNC exhibited the largest coupling energy (170 meV) and 2) as a function of annealing temperature, where an exceptionally large (˜400 meV) coupling energy was observed. This strong electronic coupling in self-organized films could facilitate the large-scale production of highly efficient electronic materials for advanced optoelectronic device applications. Strong inter-SNC electronic coupling together with high solubility, such as that provided by PEG-thiolate-coated CdSe SNCs, can increase the stability of SNCs during solution-phase electrochemical characterization. Therefore, we utilized these properties to characterize solution-state electrochemical properties and photocatalytic activity of ternary copper indium diselenide (CuInSe2) SNCs as a function of their size and surface ligand chemistry. Electrochemical characterization of our PEG-thiolate-coated SNCs showed that the thermodynamic driving force (-?G) for oxygen reduction, which increased with decreasing bandgap, was a major contributor to the overall photocatalytic reaction. Additionally, phenol degradation efficiency was monitored in which the smallest diameter SNC and shortest chain length of PEG provided the highest efficiency. The information provided herein could be used to produce superior SNC photocatalysts for a variety of applications including oxidation of organic contaminants, conversion of water to hydrogen gas, and decomposition of crude oil or pesticides. Therefore, we believe our work will significantly advance quantitative electrochemical characterization of SNCs and allow for the design of highly efficient, sustainable photocatalysts resulting in economic and environmental benefits.

Second-Sphere Effects in Dinuclear FeIIIZnII Hydrolase Biomimetics: Tuning Binding and Reactivity Properties.

PubMed

Camargo, Tiago Pacheco; Neves, Ademir; Peralta, Rosely A; Chaves, Cláudia; Maia, Elene C P; Lizarazo-Jaimes, Edgar H; Gomes, Dawidson A; Bortolotto, Tiago; Norberto, Douglas R; Terenzi, Hernán; Tierney, David L; Schenk, Gerhard

2018-01-02

Herein, we report the synthesis and characterization of two dinuclear Fe III Zn II complexes [Fe III Zn II LP1] (1) and [Fe III Zn II LP2] (2), in which LP1 and LP2 are conjugated systems containing one and two pyrene groups, respectively, connected via the diamine -HN(CH 2 ) 4 NH- spacer to the well-known N 5 O 2 -donor H 2 L ligand (H 2 L = 2-bis{[(2-pyridylmethyl)aminomethyl]-6-[(2-hydroxybenzyl)(2-pyridylmethyl)]aminomethyl}-4-methylphenol). The complex [Fe III Zn II L1] (3), in which H 2 L was modified to H 2 L1, with a carbonyl group attached to the terminal phenol group, was included in this study for comparison purposes. 1 Both complexes 1 and 2 were satisfactorily characterized in the solid state and in solution. Extended X-ray absorption fine structure data for 1 and 3 in an acetonitrile solution show that the multiply bridged structure seen in the solid state of 3 is retained in solution. Potentiometric and UV-vis titration of 1 and 2 show that electrostatic interaction between the protonated amino groups and coordinated water molecules significantly decreases the pK a of the iron(III)-bound water compared to those of 3. On the other hand, catalytic activity studies using 1 and 2 in the hydrolysis of the activated substrate bis(2,4-dinitrophenyl)phosphate (BDNPP) resulted in a significant increase in the association of the substrate (K ass ≅ 1/K M ) compared to that of 3 because of electrostatic and hydrophobic interactions between BDNPP and the side-chain diaminopyrene of the ligands H 2 LP1 and H 2 LP2. In addition, the introduction of the pyrene motifs in 1 and 2 enhanced their activity toward DNA and as effective antitumor drugs, although the biochemical mechanism of the latter effect is currently under investigation. These complexes represent interesting examples of how to promote an increase in the activity of traditional artificial metal nucleases by introducing second-coordination-sphere effects.

Solution thermodynamic stability of complexes formed with the octadentate hydroxypyridinonate ligand 3,4,3-LI(1,2-HOPO): A critical feature for efficient chelation of lanthanide(IV) and actinide(IV) ions

PubMed Central

Deblonde, Gauthier J-P.; Sturzbecher-Hoehne, Manuel; Abergel, Rebecca J.

2013-01-01

The solution thermodynamics of water soluble complexes formed between Ce(III), Ce(IV), Th(IV) and the octadentate chelating agent 3,4,3-LI(1,2-HOPO) were investigated. Several techniques including spectrofluorimetric and automated spectrophotometric titrations were used to overcome the slow spontaneous oxidation of Ce(III) complexes yielding to stability constants of log β110 = 17.4 ± 0.5, log β11-1 = 8.3 ± 0.4 and log β111 = 21.2 ± 0.4 for [Ce(III)(3,4,3-LI(1,2-HOPO))]−, [Ce(III)(3,4,3-LI(1,2-HOPO)(OH)]2− and [Ce(III)(3,4,3-LI(1,2-HOPO)H], respectively. Using the spectral properties of the hydroxypyridinonate chelator in ligand competition titrations against nitrilotriacetic acid, the stability constant log β110 = 41.5 ± 0.5 was determined for [Ce(IV)(3,4,3-LI(1,2-HOPO))]. Finally, the extraordinarily stable complex [Ce(IV)(3,4,3-LI(1,2-HOPO))] was used in Th(IV) competition titrations, resulting in a stability constant of log β110 = 40.1 ± 0.5 for [Th(IV)3,4,3-LI(1,2-HOPO))]. These experimental values are in excellent agreement with previous estimates, they are discussed with respect to the ionic radius and oxidation state of each cationic metal and allow predictions on the stability of other actinide complexes including [U(IV)(3,4,3-LI(1,2-HOPO))], [Np(IV)(3,4,3-LI(1,2-HOPO))] and [Pu(IV)(3,4,3-LI(1,2-HOPO))]. Comparisons with the standard ligand diethylenetriamine pentaacetic acid (DTPA) provide a thermodynamic basis for the observed significantly higher efficacy of 3,4,3-LI(1,2-HOPO) as an in vivo actinide decorporation agent. PMID:23855806

Ligand interaction with the purified serotonin transporter in solution and at the air/water interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Faivre, V.; Manivet, P.; Callaway, J.C.

2000-06-01

The purified serotonin transporter (SERT) was spread at the air/water interface and the effects both of its surface density and of the temperature on its interfacial behavior were studied. The recorded isotherms evidenced the existence of a stable monolayer undergoing a lengthy rearrangement. SERT/ligand interactions appeared to be dependent on the nature of the studied molecules. Whereas an unrelated drug (chlorcyclizine) did not bind to the spread SERT, it interacted with its specific ligands. Compared to heterocyclic drugs, for which binding appeared to be concentration-dependent, a 'two-site' mechanism was evidenced for pinoline and imipramine.

Surface control of blastospore attachment and ligand-mediated hyphae adhesion of Candida albicans.

PubMed

Varghese, Nisha; Yang, Sijie; Sejwal, Preeti; Luk, Yan-Yeung

2013-11-14

Adhesion on a surface via nonspecific attachment or multiple ligand-receptor interactions is a critical event for fungal infection by Candida albicans. Here, we find that the tri(ethylene glycol)- and d-mannitol-terminated monolayers do not resist the blastospore attachment, but prevent the hyphae adhesion of C. albicans. The hyphae adhesion can be facilitated by tripeptide sequences of arginine-glycine-aspartic acid (RGD) covalently decorated on a background of tri(ethylene glycol)-terminated monolayers. This adhesion mediated by selected ligands is sensitive to the scrambling of peptide sequences, and is inhibited by the presence of cyclic RGD peptides in the solution.

Non-nucleoside building blocks for copper-assisted and copper-free click chemistry for the efficient synthesis of RNA conjugates.

PubMed

Jayaprakash, K N; Peng, Chang Geng; Butler, David; Varghese, Jos P; Maier, Martin A; Rajeev, Kallanthottathil G; Manoharan, Muthiah

2010-12-03

Novel non-nucleoside alkyne monomers compatible with oligonucleotide synthesis were designed, synthesized, and efficiently incorporated into RNA and RNA analogues during solid-phase synthesis. These modifications allowed site-specific conjugation of ligands to the RNA oligonucleotides through copper-assisted (CuAAC) and copper-free strain-promoted azide-alkyne cycloaddition (SPAAC) reactions. The SPAAC click reactions of cyclooctyne-oligonucleotides with various classes of azido-functionalized ligands in solution phase and on solid phase were efficient and quantitative and occurred under mild reaction conditions. The SPAAC reaction provides a method for the synthesis of oligonucleotide-ligand conjugates uncontaminated with copper ions.

The separation of lanthanides and actinides in supercritical fluid carbon dioxide

DOE PAGES

Mincher, Bruce J.; Wai, Chien M.; Fox, Robert V.; ...

2015-10-28

Supercritical fluid carbon dioxide presents an attractive alternative to conventional solvents for recovery of the actinides and lanthanides. Carbon dioxide is a good solvent for fluorine and phosphate-containing ligands, including the traditional tributylphosphate ligand used in process-scale uranium separations. Actinide and lanthanide oxides may even be directly dissolved in carbon dioxide containing the complexes formed between these ligands and mineral acids, obviating the need for large volumes of acids for leaching and dissolution, and the corresponding organic liquid–liquid solvent extraction solutions. As a result, examples of the application of this novel technology for actinide and lanthanide separations are presented.

AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility

PubMed Central

Ravindranath, Pradeep Anand; Forli, Stefano; Goodsell, David S.; Olson, Arthur J.; Sanner, Michel F.

2015-01-01

Automated docking of drug-like molecules into receptors is an essential tool in structure-based drug design. While modeling receptor flexibility is important for correctly predicting ligand binding, it still remains challenging. This work focuses on an approach in which receptor flexibility is modeled by explicitly specifying a set of receptor side-chains a-priori. The challenges of this approach include the: 1) exponential growth of the search space, demanding more efficient search methods; and 2) increased number of false positives, calling for scoring functions tailored for flexible receptor docking. We present AutoDockFR–AutoDock for Flexible Receptors (ADFR), a new docking engine based on the AutoDock4 scoring function, which addresses the aforementioned challenges with a new Genetic Algorithm (GA) and customized scoring function. We validate ADFR using the Astex Diverse Set, demonstrating an increase in efficiency and reliability of its GA over the one implemented in AutoDock4. We demonstrate greatly increased success rates when cross-docking ligands into apo receptors that require side-chain conformational changes for ligand binding. These cross-docking experiments are based on two datasets: 1) SEQ17 –a receptor diversity set containing 17 pairs of apo-holo structures; and 2) CDK2 –a ligand diversity set composed of one CDK2 apo structure and 52 known bound inhibitors. We show that, when cross-docking ligands into the apo conformation of the receptors with up to 14 flexible side-chains, ADFR reports more correctly cross-docked ligands than AutoDock Vina on both datasets with solutions found for 70.6% vs. 35.3% systems on SEQ17, and 76.9% vs. 61.5% on CDK2. ADFR also outperforms AutoDock Vina in number of top ranking solutions on both datasets. Furthermore, we show that correctly docked CDK2 complexes re-create on average 79.8% of all pairwise atomic interactions between the ligand and moving receptor atoms in the holo complexes. Finally, we show that down-weighting the receptor internal energy improves the ranking of correctly docked poses and that runtime for AutoDockFR scales linearly when side-chain flexibility is added. PMID:26629955

X-ray Absorption Spectroscopy Systematics at the Tungsten L-Edge

PubMed Central

2015-01-01

A series of mononuclear six-coordinate tungsten compounds spanning formal oxidation states from 0 to +VI, largely in a ligand environment of inert chloride and/or phosphine, was interrogated by tungsten L-edge X-ray absorption spectroscopy. The L-edge spectra of this compound set, comprised of [W0(PMe3)6], [WIICl2(PMePh2)4], [WIIICl2(dppe)2][PF6] (dppe = 1,2-bis(diphenylphosphino)ethane), [WIVCl4(PMePh2)2], [WV(NPh)Cl3(PMe3)2], and [WVICl6], correlate with formal oxidation state and have usefulness as references for the interpretation of the L-edge spectra of tungsten compounds with redox-active ligands and ambiguous electronic structure descriptions. The utility of these spectra arises from the combined correlation of the estimated branching ratio of the L3,2-edges and the L1 rising-edge energy with metal Zeff, thereby permitting an assessment of effective metal oxidation state. An application of these reference spectra is illustrated by their use as backdrop for the L-edge X-ray absorption spectra of [WIV(mdt)2(CO)2] and [WIV(mdt)2(CN)2]2– (mdt2– = 1,2-dimethylethene-1,2-dithiolate), which shows that both compounds are effectively WIV species even though the mdt ligands exist at different redox levels in the two compounds. Use of metal L-edge XAS to assess a compound of uncertain formulation requires: (1) Placement of that data within the context of spectra offered by unambiguous calibrant compounds, preferably with the same coordination number and similar metal ligand distances. Such spectra assist in defining upper and/or lower limits for metal Zeff in the species of interest. (2) Evaluation of that data in conjunction with information from other physical methods, especially ligand K-edge XAS. (3) Increased care in interpretation if strong π-acceptor ligands, particularly CO, or π-donor ligands are present. The electron-withdrawing/donating nature of these ligand types, combined with relatively short metal–ligand distances, exaggerate the difference between formal oxidation state and metal Zeff or, as in the case of [WIV(mdt)2(CO)2], exert the subtle effect of modulating the redox level of other ligands in the coordination sphere. PMID:25068843

X-ray absorption spectroscopy systematics at the tungsten L-edge.

PubMed

Jayarathne, Upul; Chandrasekaran, Perumalreddy; Greene, Angelique F; Mague, Joel T; DeBeer, Serena; Lancaster, Kyle M; Sproules, Stephen; Donahue, James P

2014-08-18

A series of mononuclear six-coordinate tungsten compounds spanning formal oxidation states from 0 to +VI, largely in a ligand environment of inert chloride and/or phosphine, was interrogated by tungsten L-edge X-ray absorption spectroscopy. The L-edge spectra of this compound set, comprised of [W(0)(PMe3)6], [W(II)Cl2(PMePh2)4], [W(III)Cl2(dppe)2][PF6] (dppe = 1,2-bis(diphenylphosphino)ethane), [W(IV)Cl4(PMePh2)2], [W(V)(NPh)Cl3(PMe3)2], and [W(VI)Cl6], correlate with formal oxidation state and have usefulness as references for the interpretation of the L-edge spectra of tungsten compounds with redox-active ligands and ambiguous electronic structure descriptions. The utility of these spectra arises from the combined correlation of the estimated branching ratio of the L3,2-edges and the L1 rising-edge energy with metal Zeff, thereby permitting an assessment of effective metal oxidation state. An application of these reference spectra is illustrated by their use as backdrop for the L-edge X-ray absorption spectra of [W(IV)(mdt)2(CO)2] and [W(IV)(mdt)2(CN)2](2-) (mdt(2-) = 1,2-dimethylethene-1,2-dithiolate), which shows that both compounds are effectively W(IV) species even though the mdt ligands exist at different redox levels in the two compounds. Use of metal L-edge XAS to assess a compound of uncertain formulation requires: (1) Placement of that data within the context of spectra offered by unambiguous calibrant compounds, preferably with the same coordination number and similar metal ligand distances. Such spectra assist in defining upper and/or lower limits for metal Zeff in the species of interest. (2) Evaluation of that data in conjunction with information from other physical methods, especially ligand K-edge XAS. (3) Increased care in interpretation if strong π-acceptor ligands, particularly CO, or π-donor ligands are present. The electron-withdrawing/donating nature of these ligand types, combined with relatively short metal-ligand distances, exaggerate the difference between formal oxidation state and metal Zeff or, as in the case of [W(IV)(mdt)2(CO)2], exert the subtle effect of modulating the redox level of other ligands in the coordination sphere.

Control of intramolecular π-π stacking interaction in cationic iridium complexes via fluorination of pendant phenyl rings.

PubMed

He, Lei; Ma, Dongxin; Duan, Lian; Wei, Yongge; Qiao, Juan; Zhang, Deqiang; Dong, Guifang; Wang, Liduo; Qiu, Yong

2012-04-16

Intramolecular π-π stacking interaction in one kind of phosphorescent cationic iridium complexes has been controlled through fluorination of the pendant phenyl rings on the ancillary ligands. Two blue-green-emitting cationic iridium complexes, [Ir(ppy)(2)(F2phpzpy)]PF(6) (2) and [Ir(ppy)(2)(F5phpzpy)]PF(6) (3), with the pendant phenyl rings on the ancillary ligands substituted with two and five fluorine atoms, respectively, have been synthesized and compared to the parent complex, [Ir(ppy)(2)(phpzpy)]PF(6) (1). Here Hppy is 2-phenylpyridine, F2phpzpy is 2-(1-(3,5-difluorophenyl)-1H-pyrazol-3-yl)pyridine, F5phpzpy is 2-(1-pentafluorophenyl-1H-pyrazol-3-yl)-pyridine, and phpzpy is 2-(1-phenyl-1H-pyrazol-3-yl)pyridine. Single crystal structures reveal that the pendant phenyl rings on the ancillary ligands stack to the phenyl rings of the ppy ligands, with dihedral angles of 21°, 18°, and 5.0° between least-squares planes for complexes 1, 2, and 3, respectively, and centroid-centroid distances of 3.75, 3.65, and 3.52 Å for complexes 1, 2, and 3, respectively, indicating progressively reinforced intramolecular π-π stacking interactions from complexes 1 to 2 and 3. Compared to complex 1, complex 3 with a significantly reinforced intramolecular face-to-face π-π stacking interaction exhibits a significantly enhanced (by 1 order of magnitude) photoluminescent efficiency in solution. Theoretical calculations reveal that in complex 3 it is unfavorable in energy for the pentafluorophenyl ring to swing by a large degree and the intramolecular π-π stacking interaction remains on the lowest triplet state. © 2012 American Chemical Society

New half sandwich-type Ru(II) coordination compounds characterized by the fac-Ru(dmso-S)3 fragment: influence of the face-capping group on the chemical behavior and in vitro anticancer activity.

PubMed

Bratsos, Ioannis; Simonin, Camilla; Zangrando, Ennio; Gianferrara, Teresa; Bergamo, Alberta; Alessio, Enzo

2011-10-07

The Ru(II) complex fac-[RuCl(dmso-S)(3)(dmso-O)(2)][PF(6)] (P2) was found to be an excellent precursor for the facile preparation in high yield of half sandwich-type compounds of the general formula fac-[RuCl(dmso-S)(3)(N)(2)][PF(6)] (e.g. (N)(2) = 1,2-diaminoethane (en, 4), trans-1,2-diaminocyclohexane (dach, 5), or 2 NH(3) (6)). Neutral half sandwich-type compounds of the general formula fac-[RuCl(dmso-S)(3)(N-O)] where N-O is an anionic chelating ligand (e.g. N-O = picolinate (pic, 7)) are best prepared from the universal Ru(II)-dmso precursor cis-[RuCl(2)(dmso)(4)] (P1). These complexes, that were fully characterized in solution and in the solid state, are structurally similar to the anticancer organometallic compounds [Ru(η(6)-arene)(chel)Cl][PF(6)](n) but, in place of a face-capping arene, have the fac-Ru(dmso-S)(3) fragment. In contrast to what observed for the corresponding arene compounds, that rapidly hydrolyze the Cl ligand upon dissolution in water, compounds 4-6 are very stable and inert in aqueous solution. Probably their inertness is the reason why they showed no significant cytotoxicity against the MDA-MB-231 cancer cell line.

Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography

NASA Astrophysics Data System (ADS)

Stagno, J. R.; Liu, Y.; Bhandari, Y. R.; Conrad, C. E.; Panja, S.; Swain, M.; Fan, L.; Nelson, G.; Li, C.; Wendel, D. R.; White, T. A.; Coe, J. D.; Wiedorn, M. O.; Knoska, J.; Oberthuer, D.; Tuckey, R. A.; Yu, P.; Dyba, M.; Tarasov, S. G.; Weierstall, U.; Grant, T. D.; Schwieters, C. D.; Zhang, J.; Ferré-D'Amaré, A. R.; Fromme, P.; Draper, D. E.; Liang, M.; Hunter, M. S.; Boutet, S.; Tan, K.; Zuo, X.; Ji, X.; Barty, A.; Zatsepin, N. A.; Chapman, H. N.; Spence, J. C. H.; Woodson, S. A.; Wang, Y.-X.

2017-01-01

Riboswitches are structural RNA elements that are generally located in the 5‧ untranslated region of messenger RNA. During regulation of gene expression, ligand binding to the aptamer domain of a riboswitch triggers a signal to the downstream expression platform. A complete understanding of the structural basis of this mechanism requires the ability to study structural changes over time. Here we use femtosecond X-ray free electron laser (XFEL) pulses to obtain structural measurements from crystals so small that diffusion of a ligand can be timed to initiate a reaction before diffraction. We demonstrate this approach by determining four structures of the adenine riboswitch aptamer domain during the course of a reaction, involving two unbound apo structures, one ligand-bound intermediate, and the final ligand-bound conformation. These structures support a reaction mechanism model with at least four states and illustrate the structural basis of signal transmission. The three-way junction and the P1 switch helix of the two apo conformers are notably different from those in the ligand-bound conformation. Our time-resolved crystallographic measurements with a 10-second delay captured the structure of an intermediate with changes in the binding pocket that accommodate the ligand. With at least a 10-minute delay, the RNA molecules were fully converted to the ligand-bound state, in which the substantial conformational changes resulted in conversion of the space group. Such notable changes in crystallo highlight the important opportunities that micro- and nanocrystals may offer in these and similar time-resolved diffraction studies. Together, these results demonstrate the potential of ‘mix-and-inject’ time-resolved serial crystallography to study biochemically important interactions between biomacromolecules and ligands, including those that involve large conformational changes.

Tuning the Electronic Structure of Fe(II) Polypyridines via Donor Atom and Ligand Scaffold Modifications: A Computational Study.

PubMed

Bowman, David N; Bondarev, Alexey; Mukherjee, Sriparna; Jakubikova, Elena

2015-09-08

Fe(II) polypyridines are an important class of pseudo-octahedral metal complexes known for their potential applications in molecular electronic switches, data storage and display devices, sensors, and dye-sensitized solar cells. Fe(II) polypyridines have a d(6) electronic configuration and pseudo-octahedral geometry and can therefore possess either a high-spin (quintet) or a low-spin (singlet) ground state. In this study, we investigate a series of complexes based on [Fe(tpy)2](2+) (tpy = 2,2';6',2″-terpyridine) and [Fe(dcpp)2](2+) (dcpp = 2,6-bis(2-carboxypyridyl)pyridine). The ligand field strength in these complexes is systematically tuned by replacing the central pyridine with five-membered (N-heterocyclic carbene, pyrrole, furan) or six-membered (aryl, thiazine-1,1-dioxide, 4-pyrone) moieties. To determine the impact of ligand substitutions on the relative energies of metal-centered states, the singlet, triplet, and quintet states of the Fe(II) complexes were optimized in water (PCM) using density functional theory at the B3LYP+D2 level with 6-311G* (nonmetals) and SDD (Fe) basis sets. It was found that the dcpp ligand scaffold allows for a more ideal octahedral coordination environment in comparison to the tpy ligand scaffold. The presence of six-membered central rings also allows for a more ideally octahedral coordination environment relative to five-membered central rings, regardless of the ligand scaffold. We find that the ligand field strength in the Fe(II) polypyridines can be tuned by altering the donor atom identity, with C donor atoms providing the strongest ligand field.

Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography

PubMed Central

Stagno, J. R.; Liu, Y.; Bhandari, Y. R.; Conrad, C. E.; Panja, S.; Swain, M.; Fan, L.; Nelson, G.; Li, C.; Wendel, D. R.; White, T. A.; Coe, J. D.; Wiedorn, M. O.; Knoska, J.; Oberthuer, D.; Tuckey, R. A.; Yu, P.; Dyba, M.; Tarasov, S. G.; Weierstall, U.; Grant, T. D.; Schwieters, C. D.; Zhang, J.; Ferré-D’Amaré, A. R.; Fromme, P.; Draper, D. E.; Liang, M.; Hunter, M. S.; Boutet, S.; Tan, K.; Zuo, X.; Ji, X.; Barty, A.; Zatsepin, N. A.; Chapman, H. N.; Spence, J. C. H.; Woodson, S. A.; Wang, Y.-X.

2017-01-01

Riboswitches are structural RNA elements that are generally located in the 5′ untranslated region of messenger RNA. During regulation of gene expression, ligand binding to the aptamer domain of a riboswitch triggers a signal to the downstream expression platform1–3. A complete understanding of the structural basis of this mechanism requires the ability to study structural changes over time4. Here we use femtosecond X-ray free electron laser (XFEL) pulses5,6 to obtain structural measurements from crystals so small that diffusion of a ligand can be timed to initiate a reaction before diffraction. We demonstrate this approach by determining four structures of the adenine riboswitch aptamer domain during the course of a reaction, involving two unbound apo structures, one ligand-bound intermediate, and the final ligand-bound conformation. These structures support a reaction mechanism model with at least four states and illustrate the structural basis of signal transmission. The three-way junction and the P1 switch helix of the two apo conformers are notably different from those in the ligand-bound conformation. Our time-resolved crystallographic measurements with a 10-second delay captured the structure of an intermediate with changes in the binding pocket that accommodate the ligand. With at least a 10-minute delay, the RNA molecules were fully converted to the ligand-bound state, in which the substantial conformational changes resulted in conversion of the space group. Such notable changes in crystallo highlight the important opportunities that micro- and nanocrystals may offer in these and similar time-resolved diffraction studies. Together, these results demonstrate the potential of ‘mix-and-inject’ time-resolved serial crystallography to study biochemically important interactions between biomacromolecules and ligands, including those that involve large conformational changes. PMID:27841871

Stable coordination of the inhibitory Ca2+ ion at MIDAS in integrin CD11b/CD18 by an antibody-derived ligand aspartate: Implications for integrin regulation and structure-based drug design

PubMed Central

Mahalingam, Bhuvaneshwari; Ajroud, Kaouther; Alonso, Jose Luis; Anand, Saurabh; Adair, Brian; Horenstein, Alberto L; Malavasi, Fabio; Xiong, Jian-Ping; Arnaout, M. Amin

2011-01-01

A central feature of integrin interaction with physiologic ligands is the monodentate binding of a ligand carboxylate to a Mg2+ ion hexacoordinated at the metal-ion-dependent-adhesion site (MIDAS) in the integrin A-domain. This interaction stabilizes the A-domain in the high-affinity state, which is distinguished from the default low-affinity state by tertiary changes in the domain that culminate in cell adhesion. Small molecule ligand-mimetic integrin antagonists act as partial agonists, eliciting similar activating conformational changes in the A-domain, which has contributed to paradoxical adhesion and increased patient mortality in large clinical trials. As with other ligand-mimetic integrin antagonists, the function-blocking monoclonal antibody (mAb) 107 binds MIDAS of integrin CD11b/CD18 A-domain (CD11bA), but in contrast, it favors the inhibitory Ca2+ ion over Mg2+ at MIDAS. We determined the crystal structures of the Fab fragment of mAb 107 complexed to the low- and high-affinity states of CD11bA. Favored binding of Ca2+ at MIDAS is caused by the unusual symmetric bidentate ligation of a Fab-derived ligand Asp to a heptacoordinated MIDAS Ca2+. Binding of Fab 107 to CD11bA did not trigger the activating tertiary changes in the domain or in the full-length integrin. These data show that denticity of the ligand Asp/Glu can modify divalent cation selectivity at MIDAS and hence integrin function. Stabilizing the Ca2+ ion at MIDAS by bidentate ligation to a ligand Asp/Glu may provide one approach for designing pure integrin antagonists. PMID:22095715

Dual Lifetimes for Complexes between Glutathione-S-transferase (hGSTA1-1) and Product-like Ligands Detected by Single-Molecule Fluorescence Imaging.

PubMed

Pettersson, John R; Lanni, Frederick; Rule, Gordon S

2017-08-08

Single-molecule fluorescence techniques were used to characterize the binding of products and inhibitors to human glutathione S-transferase A1-1 (hGSTA1-1). The identification of at least two different bound states for the wild-type enzyme suggests that there are at least two conformations of the protein, consistent with the model that ligand binding promotes closure of the carboxy-terminal helix over the active site. Ligand induced changes in ensemble fluorescence energy transfer support this proposed structural change. The more predominant state in the ensemble of single molecules shows a significantly faster off-rate, suggesting that the carboxy-terminal helix is delocalized in this state, permitting faster exit of the bound ligand. A point mutation (I219A), which is known to interfere with the association of the carboxy-terminal helix with the enzyme, shows increased rates of interconversion between the open and closed state. Kinematic traces of fluorescence from single molecules show that a single molecule readily samples a number of different conformations, each with a characteristic off-rate.

Synthesis, Properties, and Light-Emitting Electrochemical Cell (LEEC) Device Fabrication of Cationic Ir(III) Complexes Bearing Electron-Withdrawing Groups on the Cyclometallating Ligands

PubMed Central

2016-01-01

The structure–property relationship study of a series of cationic Ir(III) complexes in the form of [Ir(C^N)2(dtBubpy)]PF6 [where dtBubpy = 4,4′-di-tert-butyl-2,2′-bipyridine and C^N = cyclometallating ligand bearing an electron-withdrawing group (EWG) at C4 of the phenyl substituent, i.e., −CF3 (1), −OCF3 (2), −SCF3 (3), −SO2CF3 (4)] has been investigated. The physical and optoelectronic properties of the four complexes were comprehensively characterized, including by X-ray diffraction analysis. All the complexes exhibit quasireversible dtBubpy-based reductions from −1.29 to −1.34 V (vs SCE). The oxidation processes are likewise quasireversible (metal + C^N ligand) and are between 1.54 and 1.72 V (vs SCE). The relative oxidation potentials follow a general trend associated with the Hammett parameter (σ) of the EWGs. Surprisingly, complex 4 bearing the strongest EWG does not adhere to the expected Hammett behavior and was found to exhibit red-shifted absorption and emission maxima. Nevertheless, the concept of introducing EWGs was found to be generally useful in blue-shifting the emission maxima of the complexes (λem = 484–545 nm) compared to that of the prototype complex [Ir(ppy)2(dtBubpy)]PF6 (where ppy = 2-phenylpyridinato) (λem = 591 nm). The complexes were found to be bright emitters in solution at room temperature (ΦPL = 45–66%) with microsecond excited-state lifetimes (τe = 1.14–4.28 μs). The photophysical properties along with density functional theory (DFT) calculations suggest that the emission of these complexes originates from mixed contributions from ligand-centered (LC) transitions and mixed metal-to-ligand and ligand-to-ligand charge transfer (LLCT/MLCT) transitions, depending on the EWG. In complexes 1, 3, and 4 the 3LC character is prominent over the mixed 3CT character, while in complex 2, the mixed 3CT character is much more pronounced, as demonstrated by DFT calculations and the observed positive solvatochromism effect. Due to the quasireversible nature of the oxidation and reduction waves, fabrication of light-emitting electrochemical cells (LEECs) using these complexes as emitters was possible with the LEECs showing moderate efficiencies. PMID:27681985

Dynamical pairwise entanglement and two-point correlations in the three-ligand spin-star structure

NASA Astrophysics Data System (ADS)

Motamedifar, M.

2017-10-01

We consider the three-ligand spin-star structure through homogeneous Heisenberg interactions (XXX-3LSSS) in the framework of dynamical pairwise entanglement. It is shown that the time evolution of the central qubit ;one-particle; state (COPS) brings about the generation of quantum W states at periodical time instants. On the contrary, W states cannot be generated from the time evolution of a ligand ;one-particle; state (LOPS). We also investigate the dynamical behavior of two-point quantum correlations as well as the expectation values of the different spin-components for each element in the XXX-3LSSS. It is found that when a W state is generated, the same value of the concurrence between any two arbitrary qubits arises from the xx and yy two-point quantum correlations. On the opposite, zz quantum correlation between any two qubits vanishes at these time instants.

The crystal structure of NAD(P)H oxidase from Lactobacillus sanfranciscensis: insights into the conversion of O2 into two water molecules by the flavoenzyme.

PubMed

Lountos, George T; Jiang, Rongrong; Wellborn, William B; Thaler, Tracey L; Bommarius, Andreas S; Orville, Allen M

2006-08-15

The FAD-dependent NAD(P)H oxidase from Lactobacillus sanfrancisensis (L.san-Nox2) catalyzes the oxidation of 2 equivalents of either NADH or NADPH and reduces 1 equivalent of O(2) to yield 2 equivalents of water. During steady-state turnover only 0.5% of the reducing equivalents are detected in solution as hydrogen peroxide, suggesting that it is not released from the enzyme after the oxidation of the first equivalent of NAD(P)H and reaction with O(2). Here we report the crystal structure of L.san-Nox2 to 1.8 A resolution. The enzyme crystallizes as a dimer with each monomer consisting of a FAD binding domain (residues 1-120), a NAD(P)H binding domain (residues 150-250), and a dimerization domain (residues 325-451). The electron density for the redox-active Cys42 residue located adjacent to the si-face FAD is consistent with oxidation to the sulfenic acid (Cys-SOH) state. The side chain of Cys42 is also observed in two conformations; in one the sulfenic acid is hydrogen bonded to His10 and in the other it hydrogen bonds with the FAD O2' atom. Surprisingly, the NAD(P)H binding domains each contain an ADP ligand as established by electron density maps and MALDI-TOF analysis of the ligands released from heat-denatured enzyme. The ADP ligand copurifies with the enzyme, and its presence does not inhibit enzyme activity. Consequently, we hypothesize that either NADPH or NADH substrates bind via a long channel that extends from the enzyme exterior and terminates at the FAD re-face. A homology model of the NADH oxidase from Lactococcus lactis (L.lac-Nox2) was also generated using the crystal structure of L.san-Nox2, which reveals several important similarities and differences between the two enzymes. HPLC analysis of ligands released from denatured L.lac-Nox2 indicates that it does not bind ADP, which correlates with the specificity of the enzyme for oxidation of NADH.

High Valent Manganese and Cobalt Complexes of Oxidatively Robust Nitrogen and Oxygen Donor Ligands.

NASA Astrophysics Data System (ADS)

Gordon-Wylie, Scott Wallace

1995-01-01

The focus of this thesis is to extend the range of ligands that satisfy the Collins criteria through a program of organic synthesis, and to apply the resulting high valent metal ligand complexes to the solution of current problems in structural inorganic chemistry, solid state chemistry (with a particular emphasis on magnetic interactions in solids) and to homogeneous and heterogeneous catalysis. Notable achievements along these directions to date are: (i) A streamlined synthesis of diamide dialkoxide and diamide diphenoxide acyclic ligands which allows for a wide range of both electron withdrawing and electron donating substituents to be incorporated into the ligand framework. (ii) The first example of a LMn(V)O species stable enough to be crystallographically characterized was obtained, utilizing the acyclic ligands of (i). (iii) Catalytic O-atom transfer oxidations utilizing acyclic ligands from (i) have been performed. Planar Co(III) complexes of these ligands can catalyze O-atom transfers, ^1 with 30-50 turnovers, including enantioselective ones,^2 implicating that the ligands remain at least partially intact during the catalytic process. (iv) Unusual magnetic ordering has been observed in an infinite linear chain of S = 2 LMn(III) centers, in collaboration with Edmund P. Day. (v) Ferromagnetic exchange has been obtained in a ((LCo(III)) _3Co(II)) ^{-} complex^4 Magnetic model building in collaboration with Gordon Yee and Emile Bominaar has led to an understanding of the magnetic data suitable for publication.^5 (vi) Adaptation of a range of electronic substituents (see (i)) into a macrocyclic framework^7 allows for the preparation of hydrolytically and oxidatively stable high valent metal complexes. The presence of a range of electronic substituents further allows redox potentials for a single (LM) ^{rm n+}/(LM) ^{(rm n+1)+ } oxidation process to be tuned over a range that spans ca. 1 V. (vii) Initial linear syntheses for these macrocycles involved the use of organic azide intermediates. (viii) A new macrocyclic switching ligand has been synthesized utilizing (vii), that allows H^{+} or other lewis acids to act at the secondary site as electron withdrawing groups from the metal. In the structurally characterized switching (Co(III)( kappa^4-L)) ^{ -} complex, there is a bidentate switching site consisting of a pyridine-N and an adjacent amide-O donor. It has been found that the cobalt(II) derivative (CO(II)(kappa^4-L)) ^{-} readily reduces O _2 by an outer sphere (presumably by 1 e ^{-}) process. (ix) Robust homogeneous metalloredox-active oxidants are an important strategic goal for primary pollution prevention, or what is often called "green chemistry". Use of (vii) provides access to quantities of a macrocyclic ligand, that is derivatized in such a way that it can be attached to a solid polymer support. (x) C-H bond activation has been observed in iron systems^{15} in collaboration with Mike Bartos (the principal investigator) where use of (vii) has allowed quantities of ligand to be synthesized and burned in reaction chemistry with nitriles and oxidants. (xi) Macrocyclic ligands with organic solubilizing groups have been prepared utilizing (vii) and metal complexes with substantial alkane solubility result. (Abstract shortened by UMI.).

The Shine-Dalgarno sequence of riboswitch-regulated single mRNAs shows ligand-dependent accessibility bursts

NASA Astrophysics Data System (ADS)

Rinaldi, Arlie J.; Lund, Paul E.; Blanco, Mario R.; Walter, Nils G.

2016-01-01

In response to intracellular signals in Gram-negative bacteria, translational riboswitches--commonly embedded in messenger RNAs (mRNAs)--regulate gene expression through inhibition of translation initiation. It is generally thought that this regulation originates from occlusion of the Shine-Dalgarno (SD) sequence upon ligand binding; however, little direct evidence exists. Here we develop Single Molecule Kinetic Analysis of RNA Transient Structure (SiM-KARTS) to investigate the ligand-dependent accessibility of the SD sequence of an mRNA hosting the 7-aminomethyl-7-deazaguanine (preQ1)-sensing riboswitch. Spike train analysis reveals that individual mRNA molecules alternate between two conformational states, distinguished by `bursts' of probe binding associated with increased SD sequence accessibility. Addition of preQ1 decreases the lifetime of the SD's high-accessibility (bursting) state and prolongs the time between bursts. In addition, ligand-jump experiments reveal imperfect riboswitching of single mRNA molecules. Such complex ligand sensing by individual mRNA molecules rationalizes the nuanced ligand response observed during bulk mRNA translation.

Characterization of the Raf kinase inhibitory protein (RKIP) binding pocket: NMR-based screening identifies small-molecule ligands.

PubMed

Shemon, Anne N; Heil, Gary L; Granovsky, Alexey E; Clark, Mathew M; McElheny, Dan; Chimon, Alexander; Rosner, Marsha R; Koide, Shohei

2010-05-05

Raf kinase inhibitory protein (RKIP), also known as phoshaptidylethanolamine binding protein (PEBP), has been shown to inhibit Raf and thereby negatively regulate growth factor signaling by the Raf/MAP kinase pathway. RKIP has also been shown to suppress metastasis. We have previously demonstrated that RKIP/Raf interaction is regulated by two mechanisms: phosphorylation of RKIP at Ser-153, and occupation of RKIP's conserved ligand binding domain with a phospholipid (2-dihexanoyl-sn-glycero-3-phosphoethanolamine; DHPE). In addition to phospholipids, other ligands have been reported to bind this domain; however their binding properties remain uncharacterized. In this study, we used high-resolution heteronuclear NMR spectroscopy to screen a chemical library and assay a number of potential RKIP ligands for binding to the protein. Surprisingly, many compounds previously postulated as RKIP ligands showed no detectable binding in near-physiological solution conditions even at millimolar concentrations. In contrast, we found three novel ligands for RKIP that specifically bind to the RKIP pocket. Interestingly, unlike the phospholipid, DHPE, these newly identified ligands did not affect RKIP binding to Raf-1 or RKIP phosphorylation. One out of the three ligands displayed off target biological effects, impairing EGF-induced MAPK and metabolic activity. This work defines the binding properties of RKIP ligands under near physiological conditions, establishing RKIP's affinity for hydrophobic ligands and the importance of bulky aliphatic chains for inhibiting its function. The common structural elements of these compounds defines a minimal requirement for RKIP binding and thus they can be used as lead compounds for future design of RKIP ligands with therapeutic potential.

Proteolysis of EphA2 converts it from a tumor suppressor to an oncoprotein

PubMed Central

KOSHIKAWA, Naohiko; HOSHINO, Daisuke; TANIGUCHI, Hiroaki; MINEGISHI, Tomoko; TOMARI, Taizo; NAM, Sung-Ouk; AOKI, Mikiko; SUETA, Takayuki; NAKAGAWA, Takashi; MIYAMOTO, Shingo; NABESHIMA, Kazuki; WEAVER, Alissa M.; SEIKI, Motoharu

2015-01-01

Eph receptor tyrosine kinases are considered candidate therapeutic targets in cancer, but they can exert opposing effects on cell growth. In presence of its ligands, Eph receptor EphA2 suppresses signaling by other growth factor receptors, including ErbB, whereas ligand-independent activation of EphA2 augments ErbB signaling. To deploy EphA2-targeting drugs effectively in tumors, the anti-oncogenic ligand-dependent activation state of EphA2 must be discriminated from its oncogenic ligand-independent state. Since the molecular basis for the latter is little understood, we investigated how the activation state of EphA2 can be switched in tumor tissue. We found that ligand-binding domain of EphA2 is cleaved frequently by the membrane metalloproteinase MT1-MMP, a powerful modulator of the pericellular environment in tumor cells. EphA2 immunostaining revealed a significant loss of the N-terminal portion of EphA2 in areas of tumor tissue that expressed MT1-MMP. Moreover, EphA2 phosphorylation patterns that signify ligand-independent activation were observed specifically in these areas of tumor tissue. Mechanistic experiments revealed that processing of EphA2 by MT1-MMP promoted ErbB signaling, anchorage-independent growth, and cell migration. Conversely, expression of a proteolysis-resistant mutant of EphA2 prevented tumorigenesis and metastasis of human tumor xenografts in mice. Overall, our results showed how the proteolytic state of EphA2 in tumors determines its effector function and influences its status as a candidate biomarker for targeted therapy. PMID:26130649

Theoretical study on mechanism of the photochemical ligand substitution of fac-[Re(I)(bpy)(CO)3(PR3)](+) complex.

PubMed

Saita, Kenichiro; Harabuchi, Yu; Taketsugu, Tetsuya; Ishitani, Osamu; Maeda, Satoshi

2016-07-14

The mechanism of the CO ligand dissociation of fac-[Re(I)(bpy)(CO)3P(OMe)3](+) has theoretically been investigated, as the dominant process of the photochemical ligand substitution (PLS) reactions of fac-[Re(I)(bpy)(CO)3PR3](+), by using the (TD-)DFT method. The PLS reactivity can be determined by the topology of the T1 potential energy surface because the photoexcited complex is able to decay into the T1 state by internal conversions (through conical intersections) and intersystem crossings (via crossing seams) with sufficiently low energy barriers. The T1 state has a character of the metal-to-ligand charge-transfer ((3)MLCT) around the Franck-Condon region, and it changes to the metal-centered ((3)MC) state as the Re-CO bond is elongated and bent. The equatorial CO ligand has a much higher energy barrier to leave than that of the axial CO, so that the axial CO ligand selectively dissociates in the PLS reaction. The single-component artificial force induced reaction (SC-AFIR) search reveals the CO dissociation pathway in photostable fac-[Re(I)(bpy)(CO)3Cl]; however, the dissociation barrier on the T1 state is substantially higher than that in fac-[Re(I)(bpy)(CO)3PR3](+) and the minimum-energy seams of crossings (MESXs) are located before and below the barrier. The MESXs have also been searched in fac-[Re(I)(bpy)(CO)3PR3](+) and no MESXs were found before and below the barrier.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, D.; Ladipo, F.T.; Braddock-Wilking, J.

Low temperature crystal structures of (DABCO)H{sup +}Co(CO){sub 4}{sup -} (1) and (DABCO)H{sup +}Co(CO){sub 3}PPh{sub 3}{sup -} (2) (DABCO = 1,4-diazabicyclooctane) indicate that both salts exhibit N-H...Co hydrogen bonding. IR and NMR data indicate that these hydrogen bonded species persist in nonpolar solvents such as toluene, but exist as solvent separated ions in more polar solvents. Replacement of the axial CO ligand by PPh{sub 3} leads to a shortening of the N...Co separation in the solid state from 3.437(3) to 3.294(6) A. This change is accompanied by an increase in the angle between the equatorial carbonyl ligands. Thus, the crystallographic resultsmore » suggest a strengthening of the N-H...Co hydrogen bond upon increasing the basicity of the metal center, the first observation of this type in the solid state. This assertion is supported by variable-temperature {sup 1}H and {sup 13}C NMR data in toluene-d{sub 8} solution which, discussed in the light of ab initio calculations, indicate that the barrier to a fluxional process involving cleavage of the N-H...Co hydrogen bond is greater in 2 than in 1. The crystal structures of 1 and 2 have been determined by X-ray diffraction at 135(5) and 123(5) K, respectively. 19 refs., 2 figs., 5 tabs.« less

Direction to practical production of hydrogen by formic acid dehydrogenation with Cp*Ir complexes bearing imidazoline ligands

DOE PAGES

Onishi, Naoya; Ertem, Mehmed Z.; Xu, Shaoan; ...

2016-11-10

In a Cp*Ir complex with a bidentate pyridyl-imidazoline ligand achieved the evolution of 1.02 m 3 of H 2/CO 2 gases by formic acid dehydrogenation without any additives or adjustments in the solution system. Furthermore, the pyridyl-imidazoline moieties provided the optimum pH to be 1.7, resulting in high activity and stability even at very acidic conditions.

Direction to practical production of hydrogen by formic acid dehydrogenation with Cp*Ir complexes bearing imidazoline ligands

DOE Office of Scientific and Technical Information (OSTI.GOV)

Onishi, Naoya; Ertem, Mehmed Z.; Xu, Shaoan

In a Cp*Ir complex with a bidentate pyridyl-imidazoline ligand achieved the evolution of 1.02 m 3 of H 2/CO 2 gases by formic acid dehydrogenation without any additives or adjustments in the solution system. Furthermore, the pyridyl-imidazoline moieties provided the optimum pH to be 1.7, resulting in high activity and stability even at very acidic conditions.