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1.  Compounds with a ‘stuffed’ anti-bixbyite-type structure, analysed in terms of the Zintl–Klemm and coordination-defect concepts 
Compounds with a ‘stuffed anti-bixbyite’ structure, such as Li3AlN2, were analysed in terms of both the extended Zintl–Klemm concept and the coordination-defect concept. For the first time, inorganic crystal structures are seen as a set of ‘multiple resonance structures’ (Klemm pseudo-structures) which co-exist as the result of unexpected electron transfers between any species pair comprising either like or unlike atoms, cations or anions. If this is the driving force controlling crystal structures, the conventional oxidation states assigned to cations and anions lose some of their usefulness.
The bixbyite structure (Mn2O3) () is often described as a distorted face-centered cubic (f.c.c.) array of Mn atoms, with O atoms occupying 3/4 of the tetrahedral holes. The empty M 4 tetrahedra are centred at 16c. In anti-bixbyite structures (Mg3N2), cation vacancies are centred in empty N4 tetrahedra. If 16 hypothetical atoms were located at this site they would form the structure of γ-Si. This means that anti-bixbyite structures are ideally prepared to accommodate Si(Ge) atoms at these holes. Several compounds (Li3AlN2 and Li3ScN2) fully satisfy this expectation. They are really anti-bixbyites ‘stuffed’ with Al(Sc). The presence of these atoms in 16c is illuminated in the light of the extended Zintl–Klemm concept (EZKC) [Vegas & García-Baonza (2007 ▶). Acta Cryst. B63, 339–345], from which a compound would be the result of ‘multiple resonance’ pseudo-structures, emerging from electron transfers between any species pair (like or unlike atoms, cations or anions). The coordination-defect (CD) concept [Bevan & Martin (2008) ▶. J. Solid State Chem. 181, 2250–2259] is also consistent with the EZKC description of the pseudo-structures. A more profound insight into crystal structures is gained if one is not restricted to the contemplation of classical anions and cations in their conventional oxidation states.
PMCID: PMC2628973  PMID: 19155554
Zintl–Klemm concept; coordination-defect concept; multiple resonance structure; electron transfer
2.  Understanding selectivity of hard and soft metal cations within biological systems using the subvalence concept. I. Application to blood coagulation: direct cation-protein electronic effects vs. indirect interactions through water networks 
Following a previous study by de Courcy et al. ((2009) Interdiscip. Sci. Comput. Life Sci. 1, 55-60), we demonstrate in this contribution, using quantum chemistry, that metal cations exhibit a specific topological signature in the electron localization of their density interacting with ligands according to its “soft” or “hard” character. Introducing the concept of metal cation subvalence, we show that a metal cation can split its outer-shell density (the so-called subvalent domains or basins) according to it capability to form a partly covalent bond involving charge transfer. Such behaviour is investigated by means of several quantum chemical interpretative methods encompasing the topological analysis of the Electron Localization Function (ELF) and Bader's Quantum Theory of Atoms in Molecules (QTAIM) and two energy decomposition analyses (EDA), namely the Restricted Variational Space (RVS) and Constrained Space Orbital Variations (CSOV) approaches. Further rationalization is performed by computing ELF and QTAIM local properties such as electrostatic distributed moments and local chemical descriptors such as condensed Fukui Functions and dual descriptors. These reactivity indexes are computed within the ELF topological analysis in addition to QTAIM offering access to non atomic reactivity local index, for example on lone pairs. We apply this “subvalence” concept to study the cation selectivity in enzymes involved in blood coagulation (GLA domains of three coagulation factors). We show that the calcium ions are clearly able to form partially covalent charge transfer networks between the subdomain of the metal ion and the carboxylate oxygen lone pairs whereas magnesium does not have such ability. Our analysis also explains the different role of two groups (high affinity and low affinity cation binding sites) present in GLA domains. If the presence of Ca(II) is mandatory in the central “high affinity” region to conserve a proper folding and a charge transfer network, external sites are better stabilised by Mg(II), rather than Ca(II), in agreement with experiment. The central role of discrete water molecules is also discussed in order to understand the stabilities of the observed X-rays structures of the Gla domain. Indeed, the presence of explicit water molecules generating indirect cation-protein interactions through water networks is shown to be able to reverse the observed electronic selectivity occuring when cations directly interact with the Gla domain without the need of water.
PMCID: PMC2856951  PMID: 20419068
Coagulation; subvalence; QTAIM; Electron Localization Function (ELF); softness; hardness; charge transfer; electrostatic moments; Fukui functions; water networks; metals; biology
3.  Glyceryl Monooleate/Poloxamer 407 Cubic Nanoparticles as Oral Drug Delivery Systems: I. In Vitro Evaluation and Enhanced Oral Bioavailability of the Poorly Water-Soluble Drug Simvastatin 
AAPS PharmSciTech  2009;10(3):960-966.
Glyceryl monooleate (GMO)/poloxamer 407 cubic nanoparticles were investigated as potential oral drug delivery systems to enhance the bioavailability of the water-insoluble model drug simvastatin. The simvastatin-loaded cubic nanoparticles were prepared through fragmentation of the GMO/poloxamer 407 bulk cubic-phase gel using high-pressure homogenization. The internal structure of the cubic nanoparticles was identified by cryo-transmission electron microscopy. The mean diameter of the cubic nanoparticles varied within the range of 100–150 nm, and both GMO/poloxamer 407 ratio and theoretical drug loading had no significant effect on particle size and distribution. Almost complete entrapment with efficiency over 98% was achieved due to the high affinity of simvastatin to the hydrophobic regions of the cubic phase. Release of simvastatin from the cubic nanoparticles was limited both in 0.1 M hydrochloride solution containing 0.2% sodium lauryl sulfate and fasted-state simulated intestinal fluid with a total release of <3.0% at 10 h. Pharmacokinetic profiles in beagle dogs showed sustained plasma levels of simvastatin for cubic nanoparticles over 12 h. The relative oral bioavailability of simvastatin cubic nanoparticles calculated on the basis of area under the curve was 241% compared to simvastatin crystal powder. The enhancement of simvastatin bioavailability was possibly attributable to facilitated absorption by lipids in the formulation rather than improved release.
PMCID: PMC2802151  PMID: 19636709
cubic nanoparticles; glyceryl monooleate; oral bioavailability; poloxamer 407; simvastatin
4.  Electrostatic doping as a source for robust ferromagnetism at the interface between antiferromagnetic cobalt oxides 
Scientific Reports  2015;5:7997.
Polar oxide interfaces are an important focus of research due to their novel functionality which is not available in the bulk constituents. So far, research has focused mainly on heterointerfaces derived from the perovskite structure. It is important to extend our understanding of electronic reconstruction phenomena to a broader class of materials and structure types. Here we report from high-resolution transmission electron microscopy and quantitative magnetometry a robust – above room temperature (Curie temperature TC ≫ 300 K) – environmentally stable- ferromagnetically coupled interface layer between the antiferromagnetic rocksalt CoO core and a 2–4 nm thick antiferromagnetic spinel Co3O4 surface layer in octahedron-shaped nanocrystals. Density functional theory calculations with an on-site Coulomb repulsion parameter identify the origin of the experimentally observed ferromagnetic phase as a charge transfer process (partial reduction) of Co3+ to Co2+ at the CoO/Co3O4 interface, with Co2+ being in the low spin state, unlike the high spin state of its counterpart in CoO. This finding may serve as a guideline for designing new functional nanomagnets based on oxidation resistant antiferromagnetic transition metal oxides.
PMCID: PMC4303864  PMID: 25613569
5.  Structural Analysis of Aliphatic vs. Aromatic Substrate Specificity in a Copper Amine Oxidase from Hansenula polymorpha†,‡ 
Biochemistry  2013;52(13):2291-2301.
Copper amine oxidases (CAOs) are responsible for the oxidative deamination of primary amines to their corresponding aldehydes. The CAO catalytic mechanism can be divided into two half-reactions: a reductive half-reaction, in which a primary amine substrate is oxidized to its corresponding aldehyde with the concomitant reduction of the organic cofactor 2,4,5-trihydroxyphenylalanine quinone (TPQ), and an oxidative half-reaction, in which reduced TPQ is re-oxidized with the reduction of molecular oxygen to hydrogen peroxide. The reductive half-reaction proceeds via Schiff base chemistry, in which the primary amine substrate first attacks the C5 carbonyl of TPQ, forming a series of covalent Schiff base intermediates. The X-ray crystal structures of copper amine oxidase-1 from the yeast Hansenula polymorpha (HPAO-1) in complex with ethylamine and benzylamine have been solved to resolutions of 2.18 and 2.25 Å, respectively. These structures reveal the two amine substrates bound at the back of the active site coincident with TPQ in its two-electron reduced aminoquinol form. Rearrangements of particular amino acid side chains within the substrate channel and specific protein-substrate interactions provide insight into substrate specificity in HPAO-1. These changes begin to account for this CAO’s kinetic preference for small, aliphatic amines over the aromatic amines or whole peptides preferred by some of its homologs.
PMCID: PMC3633420  PMID: 23452079
amine oxidase; TPQ; substrate specificity; substrate binding; amine; channel; copper
6.  Deformation-induced structural transition in body-centred cubic molybdenum 
Nature Communications  2014;5:3433.
Molybdenum is a refractory metal that is stable in a body-centred cubic structure at all temperatures before melting. Plastic deformation via structural transitions has never been reported for pure molybdenum, while transformation coupled with plasticity is well known for many alloys and ceramics. Here we demonstrate a structural transformation accompanied by shear deformation from an original <001>-oriented body-centred cubic structure to a <110>-oriented face-centred cubic lattice, captured at crack tips during the straining of molybdenum inside a transmission electron microscope at room temperature. The face-centred cubic domains then revert into <111>-oriented body-centred cubic domains, equivalent to a lattice rotation of 54.7°, and ~15.4% tensile strain is reached. The face-centred cubic structure appears to be a well-defined metastable state, as evidenced by scanning transmission electron microscopy and nanodiffraction, the Nishiyama–Wassermann and Kurdjumov–Sachs relationships between the face-centred cubic and body-centred cubic structures and molecular dynamics simulations. Our findings reveal a deformation mechanism for elemental metals under high-stress deformation conditions.
Structural phase transitions are known to accommodate plastic deformation in some metals and ceramics. Here, the authors observe the in situ transformation of body-centred cubic molybdenum to face-centred cubic, and finally to body-centred cubic, allowing for 15.4% tensile strain accommodation.
PMCID: PMC3959286  PMID: 24603655
7.  Synthesis of Silver Nanoparticles Using Hydroxyl Functionalized Ionic Liquids and Their Antimicrobial Activity 
We report a new one phase method for the synthesis of uniform monodisperse crystalline Ag nanoparticles in aqueous systems that has been developed by using newly synthesized mono and dihydroxylated ionic liquids and cationic surfactants based on 1,3-disubstituted imidazolium cations and halogens anions. The hydroxyl functionalized ionic liquids (HFILs) and hydroxyl functionalized cationic surfactants (HFCSs) also simultaneously acts both as the reductant and protective agent. By changing the carbon chain length, alcohol structure and anion of the 1,3-imidazolium based HFILs and HFCSs the particle size, uniform and dispersibility of nanoparticles in aqueous solvents could be controlled. Transmission electron microscopy (TEM), electron diffraction, UV-Vis and NMR, were used for characterization of HFILs, HFCSs and silver nanoparticles. TEM studies on the solution showed representative spherical silver nanoparticles with average sizes 2–8 nm, particularly 2.2 nm and 4.5 nm in size range and reasonable narrow particle size distributions (SD-standard distribution) 0.2 nm and 0.5 nm respectively. The all metal nanoparticles are single crystals with face centered cubic (fcc) structure. The silver nanoparticles surface of plasmon resonance band (λmax) around 420 nm broadened and little moved to the long wavelength region that indicating the formation of silver nanoparticles dispersion with broad absorption around infrared (IR) region. Silver complexes of these HFILs as well as different silver nanoparticles dispersions have been tested in vitro against several gram positive and gram negative bacteria and fungus. The silver nanoparticles providing environmentally friendly and high antimicrobial activity agents.
PMCID: PMC2635708  PMID: 19325785
Silver nanoparticles; hydroxyl functionalized ionic liquids; hydroxyl functionalized cationic surfactants; antimicrobial activity
8.  Site occupancy of interstitial deuterium atoms in face-centred cubic iron 
Nature Communications  2014;5:5063.
Hydrogen composition and occupation state provide basic information for understanding various properties of the metal–hydrogen system, ranging from microscopic properties such as hydrogen diffusion to macroscopic properties such as phase stability. Here the deuterization process of face-centred cubic Fe to form solid-solution face-centred cubic FeDx is investigated using in situ neutron diffraction at high temperature and pressure. In a completely deuterized specimen at 988 K and 6.3 GPa, deuterium atoms occupy octahedral and tetrahedral interstitial sites with an occupancy of 0.532(9) and 0.056(5), respectively, giving a deuterium composition x of 0.64(1). During deuterization, the metal lattice expands approximately linearly with deuterium composition at a rate of 2.21 Å3 per deuterium atom. The minor occupation of the tetrahedral site is thermally driven by the intersite movement of deuterium atoms along the ‹111› direction in the face-centred cubic metal lattice.
Knowledge of hydrogen content and coordination in deuterized metals is of importance. Here, the authors study the deuterization of face-centred cubic iron in-situ via neutron diffraction, observing the occupation by hydrogen of both octahedral and tetrahedral interstitial sites.
PMCID: PMC4200519  PMID: 25256789
9.  High Resolution Structure of the ba3 Cytochrome c Oxidase from Thermus thermophilus in a Lipidic Environment 
PLoS ONE  2011;6(7):e22348.
The fundamental chemistry underpinning aerobic life on Earth involves reduction of dioxygen to water with concomitant proton translocation. This process is catalyzed by members of the heme-copper oxidase (HCO) superfamily. Despite the availability of crystal structures for all types of HCO, the mode of action for this enzyme is not understood at the atomic level, namely how vectorial H+ and e- transport are coupled. Toward addressing this problem, we report wild type and A120F mutant structures of the ba3-type cytochrome c oxidase from Thermus thermophilus at 1.8 Å resolution. The enzyme has been crystallized from the lipidic cubic phase, which mimics the biological membrane environment. The structures reveal 20 ordered lipid molecules that occupy binding sites on the protein surface or mediate crystal packing interfaces. The interior of the protein encloses 53 water molecules, including 3 trapped in the designated K-path of proton transfer and 8 in a cluster seen also in A-type enzymes that likely functions in egress of product water and proton translocation. The hydrophobic O2-uptake channel, connecting the active site to the lipid bilayer, contains a single water molecule nearest the CuB atom but otherwise exhibits no residual electron density. The active site contains strong electron density for a pair of bonded atoms bridging the heme Fea3 and CuB atoms that is best modeled as peroxide. The structure of ba3-oxidase reveals new information about the positioning of the enzyme within the membrane and the nature of its interactions with lipid molecules. The atomic resolution details provide insight into the mechanisms of electron transfer, oxygen diffusion into the active site, reduction of oxygen to water, and pumping of protons across the membrane. The development of a robust system for production of ba3-oxidase crystals diffracting to high resolution, together with an established expression system for generating mutants, opens the door for systematic structure-function studies.
PMCID: PMC3141039  PMID: 21814577
10.  Topological Oxide Insulator in Cubic Perovskite Structure 
Scientific Reports  2013;3:1651.
The emergence of topologically protected conducting states with the chiral spin texture is the most prominent feature at the surface of topological insulators. On the application side, large band gap and high resistivity to distinguish surface from bulk degrees of freedom should be guaranteed for the full usage of the surface states. Here, we suggest that the oxide cubic perovskite YBiO3, more than just an oxide, defines itself as a new three-dimensional topological insulator exhibiting both a large bulk band gap and a high resistivity. Based on first-principles calculations varying the spin-orbit coupling strength, the non-trivial band topology of YBiO3 is investigated, where the spin-orbit coupling of the Bi 6p orbital plays a crucial role. Taking the exquisite synthesis techniques in oxide electronics into account, YBiO3 can also be used to provide various interface configurations hosting exotic topological phenomena combined with other quantum phases.
PMCID: PMC3622917  PMID: 23575973
11.  Single Sublattice Endotaxial Phase Separation Driven by Charge Frustration in a Complex Oxide 
Journal of the American Chemical Society  2013;135(27):10114-10123.
Complex transition-metal oxides are important functional materials in areas such as energy and information storage. The cubic ABO3 perovskite is an archetypal example of this class, formed by the occupation of small octahedral B-sites within an AO3 network defined by larger A cations. We show that introduction of chemically mismatched octahedral cations into a cubic perovskite oxide parent phase modifies structure and composition beyond the unit cell length scale on the B sublattice alone. This affords an endotaxial nanocomposite of two cubic perovskite phases with distinct properties. These locally B-site cation-ordered and -disordered phases share a single AO3 network and have enhanced stability against the formation of a competing hexagonal structure over the single-phase parent. Synergic integration of the distinct properties of these phases by the coherent interfaces of the composite produces solid oxide fuel cell cathode performance superior to that expected from the component phases in isolation.
PMCID: PMC3793895  PMID: 23750709
12.  Ab initio molecular dynamics study of high-pressure melting of beryllium oxide 
Scientific Reports  2014;4:4707.
We investigate, through first-principles molecular dynamics simulations, the high-pressure melting of BeO in the range 0 ≤ p ≤ 100 GPa. The wurtzite (WZ), zinc blend (ZB), and rocksalt (RS) phases of BeO are considered. It is shown that below 40 GPa, the melting temperature for the WZ phase is higher than that for the ZB and RS phases. When the pressure is beyond 66 GPa, the melting temperature for the RS phase is the highest one, in consistent with the previously reported phase diagram calculated within the quasiharmonic approximation. We find that in the medium pressure range between 40 to 66 GPa, the ZB melting data are very close to those of RS, which results from the fact that the ZB structure first transforms to RS phase before melting. The ZB-RS-liquid phase transitions have been observed directly during the molecular dynamics runs and confirmed using the pair correlation functions analysis. In addition, we propose the melting curve of BeO in the form Tm = 2696.05 (1 + P/24.67)0.42, the zero-pressure value of 2696.05 K falling into the experimental data range of 2693 ~ 2853 K.
PMCID: PMC3998012  PMID: 24759594
13.  The Role of Protein Crystallography in Defining the Mechanisms of Biogenesis and Catalysis in Copper Amine Oxidase 
Copper amine oxidases (CAOs) are a ubiquitous group of enzymes that catalyze the conversion of primary amines to aldehydes coupled to the reduction of O2 to H2O2. These enzymes utilize a wide range of substrates from methylamine to polypeptides. Changes in CAO activity are correlated with a variety of human diseases, including diabetes mellitus, Alzheimer’s disease, and inflammatory disorders. CAOs contain a cofactor, 2,4,5-trihydroxyphenylalanine quinone (TPQ), that is required for catalytic activity and synthesized through the post-translational modification of a tyrosine residue within the CAO polypeptide. TPQ generation is a self-processing event only requiring the addition of oxygen and Cu(II) to the apoCAO. Thus, the CAO active site supports two very different reactions: TPQ synthesis, and the two electron oxidation of primary amines. Crystal structures are available from bacterial through to human sources, and have given insight into substrate preference, stereospecificity, and structural changes during biogenesis and catalysis. In particular both these processes have been studied in crystallo through the addition of native substrates. These latter studies enable intermediates during physiological turnover to be directly visualized, and demonstrate the power of this relatively recent development in protein crystallography.
PMCID: PMC3382800  PMID: 22754303
amine oxidase; copper; biogenesis; catalysis; cofactor; protein crystallography
14.  A look inside epitaxial cobalt-on-fluorite nanoparticles with three-dimensional reciprocal space mapping using GIXD, RHEED and GISAXS 
Journal of Applied Crystallography  2013;46(Pt 4):874-881.
Three-dimensional reciprocal space mapping by X-ray and electron diffraction [namely grazing-incidence X-ray diffraction (GIXD), reflection high-energy electron diffraction (RHEED) and grazing-incidence small-angle X-ray scattering (GISAXS)] was used to explore the internal structure and shape of differently oriented epitaxial Co/CaF2 facetted nanoparticles.
In this work epitaxial growth of cobalt on CaF2(111), (110) and (001) surfaces has been extensively studied. It has been shown by atomic force microscopy that at selected growth conditions stand-alone faceted Co nanoparticles are formed on a fluorite surface. Grazing-incidence X-ray diffraction (GIXD) and reflection high-energy electron diffraction (RHEED) studies have revealed that the particles crystallize in the face-centered cubic lattice structure otherwise non-achievable in bulk cobalt under normal conditions. The particles were found to inherit lattice orientation from the underlying CaF2 layer. Three-dimensional reciprocal space mapping carried out using X-ray and electron diffraction has revealed that there exist long bright 〈111〉 streaks passing through the cobalt Bragg reflections. These streaks are attributed to stacking faults formed in the crystal lattice of larger islands upon coalescence of independently nucleated smaller islands. Distinguished from the stacking fault streaks, crystal truncation rods perpendicular to the {111} and {001} particle facets have been observed. Finally, grazing-incidence small-angle X-ray scattering (GISAXS) has been applied to decouple the shape-related scattering from that induced by the crystal lattice defects. Particle faceting has been verified by modeling the GISAXS patterns. The work demonstrates the importance of three-dimensional reciprocal space mapping in the study of epitaxial nanoparticles.
PMCID: PMC3769055  PMID: 24046491
cobalt-on-fluorite nanoparticles; grazing-incidence X-ray diffraction (GIXD); reflection high-energy electron diffraction (RHEED); grazing-incidence small-angle X-ray scattering (GISAXS); epitaxial growth; three-dimensional reciprocal space mapping
15.  Myocardial microvascular function during acute coronary artery stenosis: effect of hypertension and hypercholesterolaemia 
Cardiovascular Research  2009;83(2):371-380.
Coronary collateral arteries (CCA) reduce cardiovascular events. We tested the hypothesis that new microvessels that proliferate in early atherosclerosis may be associated with myocardial protection during acute subtotal coronary artery obstruction (CAO).
Methods and results
Acute left anterior descending CAO was induced by a balloon catheter in pigs after 12 weeks of high-cholesterol (HC) diet, renovascular hypertension (HTN), or normal control. Cardiac structure, myocardial perfusion, and functional response to iv adenosine and CAO were studied in vivo using electron beam computed tomography (CT). The intra-myocardial microvessels were subsequently evaluated ex vivo using micro-CT, and myocardial expression of growth factors using immunoblotting. Basal myocardial perfusion and microvascular permeability were similar among the groups, whereas their responses to adenosine were attenuated in HC and HTN. A significant decline in myocardial perfusion in normal pigs during acute CAO was attenuated in HC and abolished in HTN. CAO also elicited an increase in normal anterior wall microvascular permeability (+202 ± 59%, P < 0.05), which was attenuated in HC and HTN (+55 ± 9 and +31 ± 8%, respectively, P < 0.05 vs. normal). Microvascular (<200 µm) spatial density was significantly elevated in HC and HTN, accompanied by increased myocardial growth factor expression.
This study demonstrates that early exposure to the cardiovascular risk factors HC and HTN protects the heart from decreases in myocardial perfusion during acute subtotal CAO. This protective effect is associated with and potentially mediated by pre-emptive development of intra-myocardial microvessels that might serve as recruitable CCA.
PMCID: PMC2701723  PMID: 19423617
Risk factors; Coronary collateral circulation; Preconditioning
16.  Transition Metal Ions in Zeolites: Coordination and activation of O2 
Inorganic chemistry  2010;49(8):3573-3583.
Zeolites containing transition metal ions (TMI) often show promising activity as heterogeneous catalysts in pollution abatement and selective oxidation reactions. In this paper, two aspects of research on the TMI Cu, Co and Fe in zeolites are discussed: (i) coordination to the lattice and (ii) activated oxygen species. At low loading, TMI preferably occupy exchange sites in six-membered oxygen rings (6MR) where the TMI preferentially coordinate with the oxygen atoms of Al tetrahedra. High TMI loadings result in a variety of TMI species formed at the zeolite surface. Removal of the extra-lattice oxygens during high temperature pretreatments can result in auto-reduction. Oxidation of reduced TMI sites often results in the formation of highly reactive oxygen species. In Cu-ZSM-5, calcination with O2 results in the formation of a species, which was found to be a crucial intermediate in both the direct decomposition of NO and N2O and the selective oxidation of methane into methanol. An activated oxygen species, called α-oxygen, is formed in Fe-ZSM5 and reported to be the active site in the partial oxidation of methane and benzene into methanol and phenol, respectively. However, this reactive α-oxygen can only be formed with N2O, not with O2. O2 activated Co intermediates in Faujasite (FAU) zeolites can selectively oxidize α-pinene and epoxidize styrene. In Co-FAU, CoIII superoxo and peroxo complexes are suggested to be the active cores, whereas in Cu and Fe-ZSM-5 various monomeric and dimeric sites have been proposed, but no consensus has been obtained. Very recently, the active site in Cu-ZSM-5 was identified as a bent [Cu-O-Cu]2+ core (Proc. Natl. Acad. Sci. USA 2009, 106, 18908-18913). Overall, O2 activation depends on the interplay of structural factors such as type of zeolite, size of the channels and cages and chemical factors such as Si/Al ratio and the nature, charge and distribution of the charge balancing cations. The presence of several different TMI sites hinders the direct study of the spectroscopic features of the active site. Spectroscopic techniques capable of selectively probing these sites, even if they only constitute a minor fraction of the total amount of TMI sites, are thus required. Fundamental knowledge of the geometric and electronic structure of the reactive active site can help in the design of novel selective oxidation catalysts.
PMCID: PMC2881549  PMID: 20380459
17.  QM/MM computational studies of substrate water binding to the oxygen-evolving centre of photosystem II 
This paper reports computational studies of substrate water binding to the oxygen-evolving centre (OEC) of photosystem II (PSII), completely ligated by amino acid residues, water, hydroxide and chloride. The calculations are based on quantum mechanics/molecular mechanics hybrid models of the OEC of PSII, recently developed in conjunction with the X-ray crystal structure of PSII from the cyanobacterium Thermosynechococcus elongatus. The model OEC involves a cuboidal Mn3CaO4Mn metal cluster with three closely associated manganese ions linked to a single μ4-oxo-ligated Mn ion, often called the ‘dangling manganese’. Two water molecules bound to calcium and the dangling manganese are postulated to be substrate molecules, responsible for dioxygen formation. It is found that the energy barriers for the Mn(4)-bound water agree nicely with those of model complexes. However, the barriers for Ca-bound waters are substantially larger. Water binding is not simply correlated to the formal oxidation states of the metal centres but rather to their corresponding electrostatic potential atomic charges as modulated by charge-transfer interactions. The calculations of structural rearrangements during water exchange provide support for the experimental finding that the exchange rates with bulk 18O-labelled water should be smaller for water molecules coordinated to calcium than for water molecules attached to the dangling manganese. The models also predict that the S1→S2 transition should produce opposite effects on the two water-exchange rates.
PMCID: PMC2614095  PMID: 17971333
oxomanganese complexes; photosystem II; oxygen evolution; photosynthesis; quantum mechanics/molecular mechanics; density functional theory
18.  Gas-Phase Reactivity of Protonated 2-, 3- and 4-Dehydropyridine Radicals Toward Organic Reagents 
The journal of physical chemistry. A  2009;113(49):13663-13674.
In order to explore the effects of the electronic nature of charged phenyl radicals on their reactivity, reactions of the three distonic isomers of ndehydropyridinium cation (n = 2, 3 or 4) have been investigated in the gas phase by using Fourier-transform ion cyclotron resonance mass spectrometry. All three isomers react with cyclohexane, methanol, ethanol and 1-pentanol exclusively via hydrogen atom abstraction, and with allyl iodide mainly via iodine atom abstraction, with a reaction efficiency ordering: 2 > 3 > 4. The observed reactivity ordering correlates well with the calculated vertical electron affinities of the charged radicals (i.e., the higher the vertical electron affinity, the faster the reaction). Charged radicals 2 and 3 also react with tetrahydrofuran exclusively via hydrogen atom abstraction, but the reaction of 4 with tetrahydrofuran yields products arising from nonradical reactivity. The unusual reactivity of 4 is likely to result from the contribution of an ionized carbene-type resonance structure that facilitates nucleophilic addition to the most electrophilic carbon atom (C-4) in this charged radical. The influence of such a resonance structure on the reactivity of 2 is not obvious, and this may be due to stabilizing hydrogen-bonding interactions in the transition states for this molecule. Charged radicals 2 and 3 abstract a hydrogen atom from the substituent in both phenol and toluene, but 4 abstracts a hydrogen atom from the phenyl ring – a reaction that is unprecedented for phenyl radicals. Charged radical 4 reacts with tert-butyl isocyanide mainly by hydrogen cyanide (HCN) abstraction while CN abstraction is the principal reaction for 2 and 3. The different reactivity observed for 4 (compared to 2 and 3) is likely to result from different charge and spin distributions of the reaction intermediates for these charged radicals.
PMCID: PMC2804851  PMID: 19902945
19.  S K-edge XAS as a Probe of Ligand-Metal Bond Covalency: Metal vs Ligand Oxidation in Cu and Ni Dithiolene Complexes 
A combination of Cu L-edge and S K-edge X-ray absorption data and density functional theory (DFT) calculations have been correlated with 33S EPR superhyperfine results to obtain the dipole integral (Is) for the S 1s→3p transition for the dithiolene ligand MNT (maleonitriledithiolate) in (TBA)2[Cu(MNT)2]. The results have been combined with the Is of sulfide derived from XPS studies to experimentally obtain a relation between the S 1s→4p transition energy (which reflects the charge on the S atom (QmolS)) and the dipole integral over a large range of QmolS. The results show that for high charges on S, Is can vary from the previously reported Is calculated using data over a limited range of QmolS. A combination of S K-edge and Cu K and L-edge X-ray absorption data and DFT calculations have been used to investigate the one-electron oxidation of [Cu(MNT)2]2- and [Ni(MNT)2]2-. The conversion of [Cu(MNT)2]2- to [Cu(MNT)2]- results in a large change in the charge on the Cu atom in the molecule (QmolCu) and is consistent with a metal-based oxidation. This is accompanied by extensive charge donation from the ligands to compensate the high charge on the Cu in [Cu(MNT)2]- based on the increased S K-edge and decreased Cu L-edge intensity, respectively. In contrast, the oxidation of [Ni(MNT)2]2- to [Ni(MNT)2]- results in a small change in QmolNi indicating a ligand-based oxidation consistent with oxidation of a molecular orbital, ψSOMO∗ (singly occupied molecular orbital), with predominant ligand character.
PMCID: PMC2880206  PMID: 17269767
XAS; S K-edge; Cu; Ni; Dithiolene; Dipole Integral; Covalency
20.  Abnormal Elastic and Vibrational Behaviors of Magnetite at High Pressures 
Scientific Reports  2014;4:6282.
Magnetite exhibits unique electronic, magnetic, and structural properties in extreme conditions that are of great research interest. Previous studies have suggested a number of transitional models, although the nature of magnetite at high pressure remains elusive. We have studied a highly stoichiometric magnetite using inelastic X-ray scattering, X-ray diffraction and emission, and Raman spectroscopies in diamond anvil cells up to ~20 GPa, while complementary electrical conductivity measurements were conducted in a cubic anvil cell up to 8.5 GPa. We have observed an elastic softening in the diagonal elastic constants (C11 and C44) and a hardening in the off-diagonal constant (C12) at ~8 GPa where significant elastic anisotropies in longitudinal and transverse acoustic waves occur, especially along the [110] direction. An additional vibrational Raman band between the A1g and T2g modes was also detected at the transition pressure. These abnormal elastic and vibrational behaviors of magnetite are attributed to the occurrence of the octahedrally-coordinated Fe2+-Fe3+-Fe2+ ions charge-ordering along the [110] direction in the inverse spinel structure. We propose a new phase diagram of magnetite in which the temperature for the metal-insulator and distorted structural transitions decreases with increasing pressure while the charge-ordering transition occurs at ~8 GPa and room temperature.
PMCID: PMC4153994  PMID: 25186916
21.  X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water 
A recently proposed electronic structure-based force field called the explicit polarization (X-Pol) potential is used to study many-body electronic polarization effects in a protein, in particular by carrying out a molecular dynamics (MD) simulation of bovine pancreatic trypsin inhibitor (BPTI) in water with periodic boundary conditions. The primary unit cell is cubic with dimensions ~54 × 54 × 54 Å3, and the total number of atoms in this cell is 14281. An approximate electronic wave function, consisting of 29026 basis functions for the entire system, is variationally optimized to give the minimum Born–Oppenheimer energy at every MD step; this allows the efficient evaluation of the required analytic forces for the dynamics. Intramolecular and intermolecular polarization and intramolecular charge transfer effects are examined and are found to be significant; for example, 17 out of 58 backbone carbonyls differ from neutrality on average by more than 0.1 electron, and the average charge on the six alanines varies from −0.05 to +0.09. The instantaneous excess charges vary even more widely; the backbone carbonyls have standard deviations in their fluctuating net charges from 0.03 to 0.05, and more than half of the residues have excess charges whose standard deviation exceeds 0.05. We conclude that the new-generation X-Pol force field permits the inclusion of time-dependent quantum mechanical polarization and charge transfer effects in much larger systems than was previously possible.
PMCID: PMC2873214  PMID: 20490369
22.  Lipid-based supramolecular systems for topical application: A preformulatory study 
AAPS PharmSci  2003;5(4):62-76.
This article describes the production and characterization of monoglyceride-based supramolecular systems by a simple processing technique, avoiding time-consuming procedures, high energy input, and the use of organic solvents. A preformulatory study was performed to study the influence of the experimental parameters on the production of monoglyceride-based disperse systems. In particular the effects of (1) stirring speed, (2) type and concentration of monoglyceride mixture, and (3) type and concentration of surfactant were investigated on the recovery, fraction of larger particles, mean diameter, and shape of smaller particles (so called nanosomes). Dispersions were first characterized by optical microscopy and freeze-fracture electron microscopy. The mean diameter of standard nanosomes, analyzed by photon correlation spectroscopy (PCS) after elimination of larger particles by filtration, was 193.5 nm. Cryotransmission electron microscopy studies, conducted in order to investigate the structure of dispersions, showed the coexistence of vesicles and particles characterized by a cubic organization. X-ray diffraction data revealed the coexistence of 2 different cubic phases, the first being a bicontinuous cubic phase of spatial symmetry Im3m (Q229) and the second belonging to the Pn3m spatial symmetry. A study on the stability of monoglyceride-based dispersions based on macroscopical analysis of organoleptic properties and dimensional analysis by time was performed after elimination of larger particles by filtration. Organoleptic and morphological features do not change by time, appearing free from phase-separation phenomena for almost 1 year from production. PCS studies showed that nanosomes undergo an initial increase in mean diameter within the first month following production; afterwards they generally maintain their dimensions for the next 4 months.
PMCID: PMC2750992  PMID: 15198518
monoglycerides; nanosome dispersions; photon correlation spectroscopy
23.  Hydrophobic moiety of cationic lipids strongly modulates their transfection activity 
Molecular pharmaceutics  2009;6(3):951-958.
Synthetic cationic lipids are widely used component of non-viral gene carriers and the factors regulating their transfection efficiency are subject of considerable interest. In view of the important role that electrostatic interactions with the polyanionic nucleic acids play in formation of lipoplexes, a common empirical approach to improving transfection has been the synthesis and testing of amphiphiles with new versions of positively charged polar groups, while much less attention has been given to the role of the hydrophobic lipid moieties. On basis of data for ~20 cationic phosphatidylcholine (PC) derivatives, here we demonstrate that hydrocarbon chain variations of these lipids modulate by over two orders of magnitude their transfection efficiency. The observed molecular structure-activity relationship manifests in well expressed dependences of activity on two important molecular characteristics - chain unsaturation and total number of carbon atoms in the lipid chains, which is representative of the lipid hydrophobic volume and hydrophilic-lipophilic ratio. Transfection increases with decrease of chain length and increase of chain unsaturation. Maximum transfection was found for cationic PCs with monounsaturated 14:1 chains. It is of particular importance that the high-transfection lipids strongly promote cubic phase formation in zwitterionic membrane phosphatidylethanolamine (PE). These remarkable correlations point to an alternative, chain-dependent process in transfection, not related to the electrostatic cationic-anionic lipid interactions.
PMCID: PMC3014849  PMID: 19341312
cationic phospholipid; phosphatidylethanolamine; hydrophobic chain; lipoplex; cubic phase; hexagonal phase; transfection
24.  Role of Radical Formation at Tyrosine 193 in the Allene Oxide Synthase Domain of a Lipoxygenase–AOS Fusion Protein from Coral† 
Biochemistry  2003;42(22):6871-6880.
Coral allene oxide synthase (cAOS), a fusion protein with 8R-lipoxygenase in Plexaura homomalla, is a hemoprotein with sequence similarity to catalases. cAOS reacts rapidly with the oxidant peracetic acid to form heme compound I and intermediate II. Concomitantly, an electron paramagnetic resonance (EPR) signal with tyrosyl radical-like features, centered at a g-value of 2.004–2.005, is formed. The radical is identified as tyrosyl by changes in EPR spectra when deuterated tyrosine is incorporated in cAOS. The radical location in cAOS is determined by mutagenesis of Y193 and Y209. Upon oxidation, native cAOS and mutant Y209F exhibit the same radical spectrum, but no significant tyrosine radical forms in mutant Y193H, implicating Y193 as the radical site in native cAOS. Estimates of the side chain torsion angles for the radical at Y193, based on the β-proton isotropic EPR hyperfine splitting, Aiso, are θ1 = 21 to 30° and θ2 = −99 to −90°. The results show that cAOS can cleave nonsubstrate hydroperoxides by a heterolytic path, although a homolytic course is likely taken in converting the normal substrate, 8R-hydroperoxyeicosatetraenoic acid (8R-HpETE), to product. Coral AOS achieves specificity for the allene oxide formed by selection of the homolytic pathway normally, while it inactivates by the heterolytic path with nonoptimal substrates. Accordingly, with the nonoptimal substrate, 13R-hydroperoxyoctadecadienoic acid (13R-HpODE), mutant Y193H is inactivated after turning over significantly fewer substrate molecules than required to inactivate native cAOS or the Y209F mutant because it cannot absorb oxidizing equivalents by forming a radical at Y193.
PMCID: PMC1382190  PMID: 12779342
25.  Qgrid: clustering tool for detecting charged and hydrophobic regions in proteins 
Nucleic Acids Research  2004;32(Web Server issue):W104-W107.
We have developed a simple but powerful method and web server to quickly locate charged and hydrophobic clusters in proteins ( For the charged clusters, each atom in the protein is first assigned a charge according to a standard force field. Then a box is created with dimensions corresponding to the range of atomic coordinates. This box is then divided into cubic grids of selected size, which now have one or more charged atoms in them. This leaves each grid with a certain amount of charge. Cubic grids with more than a cutoff charge are then clustered using a hierarchical clustering method based on Euclidean distance. A tree diagram made from the resulting clusters indicates the distribution of charged and hydrophobic regions of the protein. Hydrophobic clusters are developed by grouping the positions of Cα atoms of such residues. We propose that such a tree representation will be helpful in detecting protein–protein interfaces, structure similarity and motif detection.
PMCID: PMC441501  PMID: 15215360

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