Change In Coordination Number Research Articles

Phase Transitions Wholly within the Liquid State

After a quite brief discussion of the quantal liquids 4He, 3He and H, 'classical' elemental liquids which are treated in turn are C, P, Se and S. Phase boundaries in the (p, T) plane exist for each of these liquids, characterized by a change in local coordination number across these boundaries. Corresponding changes in other physical properties are briefly noted. Finally, following this review of elemental liquids, some liquids with two types of atom are briefly considered, the most important but also the most controversial being water.

Partial Coordination Numbers in Pb-Bi Molten Alloys

The study of the partial coordination numbers for the Pb-Bi liquid alloy showed an increase in the partial coordination number for the Pb-Pb species at 0.75 atomic fraction Bi. This anomaly suggests that the Pb atoms manifest some level of homocoordination within the neighbourhood of that concentration. It also provides an explanation for the observed change in the total coordination number of the liquid alloy at high Bi concentration.

Density-functional investigation on the mechanism of H-atom abstraction by lipoxygenase.

Using experimentally calibrated density functional calculations on models of the active site of soybean lipoxygenase 1 (SLO-1), insight has been obtained into the coordination flexibility of the iron active site and its molecular mechanism of catalysis. The ferrous form of SLO-1 shows a variation in coordination number in solution that is related to a weakly coordinating Asn694 ligand. From the calculations it is determined that the weak Fe-O(694) bond associated with this coordination flexibility is due to a sideways tilted geometry of Asn694 that is imposed on the site by the protein. Release of this constraint (by altering the hydrogen bonding network) leads to a pure six-coordinate site. In contrast, the ferric form of the enzyme stays five-coordinate. In this case, deprotonation of a coordinated water gives a strong hydroxo donor in the cis position to Asn694, weakening the Fe-O(694) bond. Hence, Asn694 is a stronger ligand to the reduced relative to the oxidized site. Using these experimentally calibrated models, the reaction energy for H-atom transfer in SLO-1 has been calculated to be about -18 kcal/mol. The observed change in coordination number going from five-coordinate in ferric to six-coordinate in ferrous SLO-1 increases the reduction potential of the iron active site. Hence, the protein adjusts the active site for optimal reactivity. Analysis of the electronic structure along the reaction coordinate shows that the H-atom transfer in SLO-1 actually corresponds to a proton-coupled electron transfer (PCET). The transferred electron does not localize on the proton, but tunnels directly from the substrate to the ferric active site in a concerted proton tunneling-electron tunneling (PTET) process. The covalently linked Fe-O-H-C bridge in the transition state lowers the energy barrier and provides an efficient superexchange pathway for this tunneling. The thermal barrier for the PTET process is estimated from the calculations to be about +15 kcal/mol including zero-point energy corrections. This corresponds to a thermal reaction rate of k(therm) approximately 1 s(-1). In comparison, the rate of proton tunneling can be as high as 2 x 10(9) s(-1) under these conditions.

In situ EXAFS study on GeS 2 glass under high-pressure

A GeS 2 glass was compressed up to 8 GPa at room temperature, heated up to 270 °C under 8 GPa and then decompressed to ambient pressure at room temperature, using a large volume high-pressure apparatus. The local structural-changes around Ge were examined by means of an in situ EXAFS method. The Ge–S bond length became monotonously short with increasing applied-pressure up to 8 GPa at room temperature. When the specimen was heated to 270 °C under 8 GPa, however, the bond length became slightly long. The elongated bond length was almost kept even after the temperature was descended to room temperature. In decompression process, the bond length became gradually long with releasing applied-pressure down to 2 GPa, following a change in compression process. Below 2 GPa, however, the Ge–S bond length was largely elongated, being longer than the initial one. No significant change of coordination number was found in the compression and decompression processes up to 8 GPa. This change can be explained by a combined effect of elastic and inelastic structural-changes.

Supporting conformational change at metal centres. Part 2: four and five coordinate geometry

The X-ray crystal structures of pyridino-( N, N′-bis(salicylidene)-1,2-ethylenediamine)zinc, bis-( N, N′-bis(salicylidene)-1,3-propanediamine zinc) and bis-((μ-acetato- O, O′)-( N, N′-bis(salicylidene)-1,4-butanediamine) zinc) zinc are reported. These elusive motifs complete a structure based matrix of compounds for the late transition metals zinc with the popular ligands N,N′-bis(salicylidene)-1,2-ethylenediamine, N,N′-bis(salicylidene)-1,3-propanediamine and N, N′-bis(salicylidene)-1,4-butanediamine. Coupled with the structural data from previously reported zinc complexes, it is possible to provide an in depth analysis of the behaviour of these three ligand systems within a five coordinate environment. The information is further combined with structural data on the homologous copper and nickel complexs to provide an overview of the conformational flexibility of these three ligands within a four, five or six coordinate environment. It is demonstrated that the more neglected N, N′-bis(salicylidene)-1,4-butanediamine motif may have great potential for supporting chemistry at a metal centre where significant changes in coordination number and geometry are desired.

LOCAL STRUCTURE OF PHOTO-INDUCED PHASES PROBED BY X-RAY ABSORPTION SPECTROSCOPY: PHOTO-INDUCED ANISOTROPY IN CHALCOGENIDE GLASSES

We describe X-ray absorption spectroscopy (XAS) technique to probe the local structure of photo-induced phase. Photo-induced melting of chalcogenide glass (amorphous selenium, a-Se) was investigated. A grazing-incidence fluorescence excitation and a high efficiency X-ray detector were used to detect a small change of coordination number due to photo-induced transformation. It was shown that photo-induced three-fold coordinated sites are formed upon light irradiation forming cross-linking between selenium chains (photo-induced melting). A simple model is proposed which describes the reorientation of selenium chain perpendicular to the polarization direction of excitation light leading to photo-induced dichroism (anisotropy). Potential of XAS as a local probe of nanoscale structural modifications induced by photo-excitation is clearly demonstrated.

X-ray absorption spectroscopic investigation of the resting ferrous and cosubstrate-bound active sites of phenylalanine hydroxylase.

Previous studies of ferrous wild-type phenylalanine hydroxylase, [Fe(2+)]PAH(T)[], have shown the active site to be a six-coordinate distorted octahedral site. After the substrate and cofactor bind to the enzyme ([Fe(2+)]PAH(R)[L-Phe,5-deaza-6-MPH(4)]), the active site converts to a five-coordinate square pyramidal structure in which the identity of the missing ligand had not been previously determined. X-ray absorption spectroscopy (XAS) at the Fe K-edge further supports this coordination number change with the binding of both cosubstrates to the enzyme, and determines this to be due to the loss of a water ligand.

Density of alkali germanate glasses related to structure

The structural origin of the `germanate anomaly' effect remains a matter of controversy. We employ in this study a quantitative description of the germanate network structure to simulate the experimental density of potassium germanate glasses with K 2O contents up to 40 mol%. The results show that the short range order structure, including the change of germanium co-ordination number from four to six, cannot reproduce the maximum in density. The `germanate anomaly' effect seems to involve both short and medium range order structural changes as metal oxide is added to GeO 2.

Electrochemical Infrared Characterization of Carbon-Supported Platinum Nanoparticles: A Benchmark Structural Comparison with Single-Crystal Electrodes and High-Nuclearity Carbonyl Clusters

Electrode potential-dependent infrared spectra for carbon monoxide dosed onto carbon-supported platinum nanoparticle films, significant as commercial fuel-cell catalysts as well as of fundamental importance, are reported with the aim of elucidating their structure as a function of particle size. The need to acquire absolute unipolar, rather than bipolar, spectra by means of potential-difference infrared tactics for such nanoparticle films is demonstrated, given the broad asymmetric C−O stretching band shapes. For larger particle diameters (d ≥ 4 nm), the potential-dependent peak stretching frequencies ( ) for saturated CO are closely similar to atop CO on Pt(111) electrodes, indicating a preponderance of 9-coordinate Pt sites. However, for nanoparticle diameters in the range d ≈ 2−4 nm, the values at a given potential, E, redshift sharply with decreasing d, approaching frequencies compatible with those measured at the same surface potential for atop CO in chargeable high-nuclearity Pt carbonyl solutes. The latter, structurally well-characterized, nanoparticles are known to contain predominantly edge- rather than (111) terrace-bound CO. The implication that the nanoparticle size-dependent structural transition is associated with changes in the Pt surface coordination number, consistent with pseudo-spherical packing-density considerations, is supported by comparisons of the −E data for lower CO coverages with corresponding potential-dependent spectra for CO bound to step sites on high-index Pt electrodes. The broad-based value of vibrational measurements at controlled surface potentials for characterizing conducting nanomaterials is pointed out.

Structural changes of quartz-type crystalline and vitreous GeO2 under pressure.

Using a large volume high pressure apparatus, quartz-type crystalline GeO2 and Li2O-4GeO2 glass have been compressed up to 14 GPa at room temperature and their local structural changes have been investigated by an in-situ XAFS method. In quartz-type crystalline GeO2, the change of the coordination number from 4 to 6 begins above 8 GPa and finishes below 12 GPa. On decompression, reversal transition begins below 8 GPa and there is a large hysteresis. Almost no sixfold coordination of Ge is preserved after releasing pressure. Change of coordination number in vitreous Li2O-4GeO2 begins above 6 GPa and is completed below 10 GPa. Reversal transition begins below 10 GPa and the hysteresis is smaller than that of quartz-type GeO2. Change of coordination number in vitreous Li2O-4GeO2 is also reversal.

First principles modelling of amorphous polymer electrolytes: Li +–PEO, Li +–PEI, and Li +–PES complexes

Several structures of the 1:1 (cation:molecule) complexes of a lithium ion with linear oligomers, CH 3X(CH 2CH 2X) n CH 3, ( n=0–5; X=O, NH or S) have been shown to be stable with ab initio calculations at the Hartree–Fock level of theory employing the 6-31G ∗ basis set. Total energies and binding energies were further evaluated using single-point density functional theory calculations (B3LYP/6-311++G ∗∗//HF/6-31G ∗). The total binding energy is found to increase with increasing glyme length and follows: NH>O>S. The binding energy for the different glymes reaches a maximum of ∼582 kJ mol −1 for the Li +–PEI pentaglyme ( n=5, X=NH) complex. From the present results we conclude the donicity of the heteroatom to be the dominant factor for the relative coordination strength, further supported by the suitability of the coordination geometry provided. Furthermore, transition states and associated energy barriers have been calculated for the conformational changes leading to changes in coordination number for lithium from three to two. The large energy barrier decreases as: O>NH>S. Implications for lithium ion transport and lithium salt solvation are discussed.

Regularities in the Change in Coordination Number of Lanthanide in Aqueous Solutions of LnL Complexes with an Increase in the Atomic Number of the Ln3+Ion

A method is proposed where the values of entropy change upon formation of LnL (H2O)nand AnL (H2O)nlanthanide and actinide complexes in aqueous solutions are used to determine the coordination numbers of Ln3+and An3+and the number of coordinated water molecules in these complexes.

Change of Coordination Number during Melting and in the Liquid Phase

A procedure is suggested for the of calculation of the coordination number in a lattice system consisting of (N+ N v) spherically symmetric cells, where N vcells are vacant. Atoms of the system interact via the Mie–Lennard-Jones pair potential and may be in localized or delocalized states. Concrete calculations performed for argon reveal good agreement with the experimental data for the solid, liquid, and gas phases, and for phase transitions between them. It is found that, in the region of the solid phase and melting, the delocalization of atoms occurs via the vacancy mechanism, and in the region of boiling and in the gas phase, the delocalization occurs mainly by continuous mass transfer over the entire volume.

Solubility of silicon in liquid metal at high pressure: implications for the composition of the Earth’s core

Silicon solubility in liquid Fe-rich metal was measured experimentally as a function of pressure, temperature and oxygen fugacity to determine if silicon could be a major light element in the Earth’s core. At the P, T, fO2 conditions of the experiments, Si solubility in liquid metal increases with increasing pressure, increasing temperature and decreasing oxygen fugacity. Evaluating single-stage core formation scenarios, the experimental results show that if the core segregated at low pressure (∼2.5 GPa) and an oxygen fugacity consistent with the current FeO content (8 wt%) of the mantle, the liquid metal would contain negligible Si (<0.01 wt%). If, as proposed recently [1]; [2] ; [3] however, the metallic liquid equilibrated with the mantle at the base of a deep magma ocean (∼700 km depth, 25 GPa) the experimental results suggest a core containing several wt% Si. For example, at the melting temperature of a peridotite mantle (∼2800 K), which represents the temperature at the base of a magma ocean, 2 wt% Si (conceivably as much as 6 wt%) could dissolve in liquid Fe metal at 25 GPa. In order to generate a core containing 7 wt% Si, as required by the CI chondrite Earth model, a magma ocean extending to 850 km (28–30 GPa) would be required. We conclude therefore that equilibration at the base of a deep magma ocean is consistent with Si being a major part of the light element inventory of the core. Extrapolation to the core–mantle boundary pressure shows that the solubility of Si in the metal, after increasing in the upper mantle, decreases with increasing depth in the lower mantle due to the change of Si coordination number in solid silicates from 4 to 6. This result is in agreement with predictions based on theoretical arguments [4] and on EOS measurements of FeSi alloys [5]. Therefore, a core segregated at the base of a deep magma ocean and containing several wt% Si must now be back-reacting with the mantle, expelling Si and absorbing Fe from the silicate. Progressive reaction of this kind may, in part, be responsible for a chemical boundary layer represented by the D″ layer at the core–mantle boundary.

A new relation between bond valence and bond distance.

A new empirical relationship s = s0(R0 - lambda)3/(R - lambda)3 between bond distances and bond valences is proposed, where s is the bond valence for the bond distance R, s0 is the reference bond valence for the reference system with the reference bond distance R0 and lambda is the sum of the cation radii of bonding atoms defined by Pauling. Since lambda is the size of the inner electron region, R - lambda represents the valence electron region between bonding atoms. The new relationship was derived based on the following three hypotheses. (i) The number of electrons (p) in the volumes of (R - lambda)3 in a coordination polyhedron are equal, even if the bond distances are not equal to each other. (ii) The average electron density p/(R - lambda)3 is a measure of covalent bond strength. (iii) The sum of the average electron densities around the central atom is conserved, even if the coordination number changes. The new relationship is applicable not only to polyhedra with one type of ligand atom, but also to polyhedra with two or more types of ligand atoms and explains why the Brown-Shannon formula [Brown & Shannon (1973). Acta Cryst. A29, 266-282] and the Brown-Altermatt formula [Brown & Altermatt (1985). Acta Cryst. B41, 244-247] work well. The new relationship was applied to a penta-coordinated silicon compound, strong hydrogen-bond systems and some organic compounds with carbon-carbon bonds.

In-situ Observation of Structural Evolution of Zr60Al15Ni25 Bulk Metallic Glass in the Supercooled Liquid Region

In-situ observation of a structural change in a particular alloy of Zr 60 Al 15 Ni 25 supercooled liquid has been carried out by a devised x-ray apparatus adopting the geometry of the Debye-Scherrer camera with an imaging plate instead of an x-ray film usually used. A drastic change of coordination numbers in the nearest neighbor region has been noted in a certain annealing time that corresponds to the exothermic reaction in the isothermal differential scanning calorimetry (DSC). In contrast, the coordination numbers and atomic distances show little change even for a long annealing time at 693 K just below the glass transition temperature (T g ). Furthermore, the structural parameters of the Zr 60 Al 15 Ni 25 supercooled liquid were found independent upon annealing temperature.

Catalase-peroxidase (Mycobacterium tuberculosis KatG) catalysis and isoniazid activation.

Resonance Raman spectra of native, overexpressed M. tuberculosis catalase-peroxidase (KatG), the enzyme responsible for activation of the antituberculosis antibiotic isoniazid (isonicotinic acid hydrazide), have confirmed that the heme iron in the resting (ferric) enzyme is high-spin five-coordinate. Difference Raman spectra did not reveal a change in coordination number upon binding of isoniazid to KatG. Stopped-flow spectrophotometric studies of the reaction of KatG with stoichiometric equivalents or small excesses of hydrogen peroxide revealed only the optical spectrum of the ferric enzyme with no hypervalent iron intermediates detected. Large excesses of hydrogen peroxide generated oxyferrous KatG, which was unstable and rapidly decayed to the ferric enzyme. Formation of a pseudo-stable intermediate sharing optical characteristics with the porphyrin pi-cation radical-ferryl iron species (Compound I) of horseradish peroxidase was observed upon reaction of KatG with excess 3-chloroperoxybenzoic acid, peroxyacetic acid, or tert-butylhydroperoxide (apparent second-order rate constants of 3.1 x 10(4), 1.2 x 10(4), and 25 M(-1) s(-1), respectively). Identification of the intermediate as KatG Compound I was confirmed using low-temperature electron paramagnetic resonance spectroscopy. Isoniazid, as well as ascorbate and potassium ferrocyanide, reduced KatG Compound I to the ferric enzyme without detectable formation of Compound II in stopped-flow measurements. This result differed from the reaction of horseradish peroxidase Compound I with isoniazid, during which Compound II was stably generated. These results demonstrate important mechanistic differences between a bacterial catalase-peroxidase and the homologous plant peroxidases and yeast cytochrome c peroxidase, in its reactions with peroxides as well as substrates.

Structural examination of the nickel site in chromatium vinosum hydrogenase: redox state oscillations and structural changes accompanying reductive activation and CO binding.

An X-ray absorption spectroscopic study of structural changes occurring at the Ni site of Chromatium vinosum hydrogenase during reductive activation, CO binding, and photolysis is presented. Structural details of the Ni sites for the ready silent intermediate state, SI(r), and the carbon monoxide complex, SI-CO, are presented for the first time in any hydrogenase. Analysis of nickel K-edge energy shifts in redox-related samples reveals that reductive activation is accompanied by an oscillation in the electron density of the Ni site involving formally Ni(III) and Ni(II), where all the EPR-active states (forms A, B, and C) are formally Ni(III), and the EPR-silent states are formally Ni(II). Analysis of XANES shows that the Ni site undergoes changes in the coordination number and geometry that are consistent with five-coordinate Ni sites in forms A, B, and SI(u); distorted four-coordinate sites in SI(r) and R; and a six-coordinate Ni site in form C. EXAFS analysis reveals that the loss of a short Ni-O bond accounts for the change in coordination number from five to four that accompanies formation of SI(r). A shortening of the Ni-Fe distance from 2.85(5) A in form B to 2.60(5) A also occurs at the SI level and is thus associated with the loss of the bridging O-donor ligand in the active site. Multiple-scattering analysis of the EXAFS data for the SI-CO complex reveals the presence of Ni-CO ligation, where the CO is bound in a linear fashion appropriate for a terminal ligand. The putative role of form C in binding H(2) or H(-) was examined by comparing the XAS data from form C with that of its photoproduct, form L. The data rule out the suggestion that the increase in charge density on the NiFe active site that accompanies the photoprocess results in a two-electron reduction of the Ni site [Ni(III) --> Ni(I)] [Happe, R. P., Roseboom, W., and Albracht, S. P. J. (1999) Eur. J. Biochem. 259, 602-608]; only subtle structural differences between the Ni sites were observed.

Major changes in copper coordination accompany reduction of peptidylglycine monooxygenase: implications for electron transfer and the catalytic mechanism.

X-ray absorption spectroscopy has been used to probe the local coordination of the copper centers in the oxidized and reduced states of the peptidylglycine monooxygenase catalytic core (PHMcc) in both the resting and substrate-bound forms of the enzyme. The results indicate that reduction causes significant changes in coordination number and geometry of both Cu centers (CuH and CuM). The CuH center changes from 4- or 5-coordinate tetragonal to a 2-coordinate configuration, with one of the three histidine ligands becoming undetectable by EXAFS (suggesting that it has moved away from the CuH by at least 0.3 A). The CuM center changes from 4- or 5-coordinate tetragonal to a trigonal or tetrahedral configuration, with an estimated 0.3-0.5 A movement of the M314 S ligand. Reduction also leads to loss of coordinated water from both of the coppers. Substrate binding has little or no effect on the local environment of the Cu centers in either oxidation state. These findings bring into question whether direct electron transfer between CuH and CuM via a tunneling mechanism can be fast enough to support the observed catalytic rate, and suggest that some other mechanism for electron transfer, such as superoxide channeling, should be considered.

The interaction of gold clusters with methanol molecules: Ab initio molecular dynamics of Aun+CH3OH and AunCH3OH

Structural, dynamical, and electronic properties of adducts obtained by adsorbing one methanol molecule onto charged and neutral gold clusters, Aun+–CH3OH and Aun–CH3OH, are investigated using Car–Parrinello ab initio molecular dynamics as a function of the cluster size n. The absorption process occurs by the formation of a Au⋆–O coordination bond to one particular gold atom Au⋆ without altering the structure of the underlying cluster. This chemical bond is much stronger for the charged metal clusters Aun+ than for the neutral analogs Aun. In the charged case, the C–O stretching vibration of the interacting methanol molecule is found to increase discontinuously as the underlying cluster structure changes from two-dimensional to three-dimensional. The weaker C–O bond in the neutral species however has “insufficient strength” to be sensitive to changes in coordination number and cluster structure. This leads to a constant C–O stretching frequency as the size of the cluster increases, including the regime where the Aun cluster changes from planar to three-dimensional.