Biomedical subjects

L Kloo

Publications and source records attributed to L Kloo.

9 recordsLinked to original sources

PubMed2006

Silver nitrate in silver zeolite A: three-dimensional incommensurate guest ordering in a zeolite framework.

We report the results of a detailed examination of the occlusion of silver nitrate in silver zeolite A (AgA). The superlattice reported to occur in (AgNO3)9-AgA was found to melt at between 80 and 100 degrees C on heating and reappear when the sample was cooled down to 80 degrees C. Annealing in this temperature range and rigorous exclusion of water produced an enhancement of the superlattice peaks, which results from ordering of the contents of the zeolite cages. Peaks assigned to the superlattice were indexed with the tetragonal lattice parameters a = 17.440(5) and c = 12.398(4) A and proposed space group P4/nmm. The sharp peaks representing the lattice of the framework (a = 12.3711(5) A, Pm3m) remained largely unaffected by the guest in this compound, which was found to exhibit strong negative thermal expansion. The host and guest lattices are incommensurate with the tetragonal guest lattice being slightly larger than the cubic host in the c-direction and slightly smaller in the a- and b-directions.

Journal Article↗

PubMed2003

New metal-rich sulfides Ni(6)SnS(2) and Ni(9)Sn(2)S(2) with a 2D metal framework: synthesis, crystal structure, and bonding.

Two new, metal-rich nickel-tin sulfides Ni(6)SnS(2) and Ni(9)Sn(2)S(2) were found by establishing phase relations in the ternary Ni-Sn-S system at 540 degrees C. Their single crystals were prepared by means of chemical vapor transport reactions. Single crystal X-ray diffraction was used for the determination of their crystal structures. Both compounds crystallize in a tetragonal system (I4/mmm, No. 139, Z = 2, a = 3.646(1) A, c = 18.151(8) A for Ni(6)SnS(2), and a = 3.678(1) A, c = 25.527(8) A for Ni(9)Sn(2)S(2)). Their crystal structures represent a new structure type and can be considered as assembled from bimetallic nickel-tin and nickel-sulfide slabs alternating along the crystallographic c axis. DFT band structure calculations showed the bonding within the bimetallic slabs to have a delocalized, multicenter nature, typical for metallic systems, and predominantly classical, pairwise bonding between nickel and sulfur.

Journal Article↗

PubMed2003

Quasi-1D cations 1 infinity [Ni8Bi8S]n + of variable charge: infinite columns 1 infinity [Ni8Bi8S]2+ in the novel compound Ni8Bi8SI2.

The new compound Ni(8)Bi(8)SI(2) has been synthesized and its crystal structure determined by X-ray crystallography. The structure contains one-dimensional (1D) cations (1)( infinity )[Ni(8)Bi(8)S](2+) separated by iodine anions. The geometry of the columns is similar to that of the recently reported (1)( infinity )[Ni(8)Bi(8)S](+), and the main difference between them is only their formal charge. Electronic structure calculations and physical properties measurements were performed to analyze the influence of the number of valence electrons on the bonding and properties of compounds containing these 1D cations. It was shown that the removal of one electron (i.e., (1)( infinity )[Ni(8)Bi(8)S](+) --> (1)( infinity )[Ni(8)Bi(8)S](2+)) mainly affects the Ni-S bonding within the cation and essentially has no influence on the intermetallic Ni-Bi bonding. It was found that Ni(8)Bi(8)SI(2) containing double-charged columns has conductivity properties more similar to a pure 1D metal than the congener Ni(8)Bi(8)SI containing mono-charged columns.

Journal Article↗

PubMed2001

Influence of sodium ions on the dynamics and structure of single-stranded DNA oligomers: a molecular dynamics study.

The effects of sodium counterion presence and chain length on the structure and dynamics of single DNA strands of polythymidylate were studied by means of molecular dynamics simulations. The importance of the base-base stacking phenomenon increases with the chain length and partially reduces the flexibility of the strand. Sodium ions directly interact with the phosphate groups and keto oxygens of the thymine bases, complexes showing lifetimes below 400 ps. Simultaneous phosphate and keto complexes were observed for one of the sodium ions with lifetimes around 1 ns. The implications of such complexes in the folding process experienced by the strand are considered. Structurally, cation inner- and outer-sphere complexes were observed in the coordination of phosphate groups. For the inner-sphere complexes, the structural information retrieved from the simulations is in very good agreement with experimental data. The diffusion properties of the sodium ions also reflect both types of coordination modes.

Cations, Monovalent↗

PubMed2001

Unique [(1)infinityNi(8)Bi(8)S] metallic wires in a novel quasi-1D compound. Synthesis, crystal and electronic structure, and properties of Ni(8)Bi(8)SI.

A new quasi-one-dimensional compound Ni(8)Bi(8)SI has been synthesized and its crystal structure determined from single-crystal X-ray diffraction data. The structure of Ni(8)Bi(8)SI consists of [(1)infinityNi(8)Bi(8)S] columns separated by iodine atoms. Conductivity and magnetic susceptibility measurements (down to 4.2 K) show that Ni(8)Bi(8)SI is a one-dimensional metal and exhibits Pauli paramagnetic properties. These observations are in good agreement with the results from electronic structure calculations. An analysis of the chemical bonding employing difference electron charge density maps reveals strong multicenter Ni-Bi bonds and pair Ni-S interactions within the [(1)infinityNi(8)Bi(8)S] columns. Only electrostatic interactions are inferred between the columns and iodine atoms.

Journal Article↗

PubMed2001

The stability of gold iodides in the gas phase and the solid state.

The stability of gold iodides in the oxidation state +I and +III is investigated at the ab initio and density functional level using relativistic and nonrelativistic energy-adjusted pseudopotentials for gold and iodine. The calculations reveal that relativistic effects stabilize the higher oxidation state of gold as expected, that is Au2I6 is thermodynamically stable at the relativistic level, whilst at the nonrelativistic level the complex of two iodine molecules weakly bound to both gold atoms in Au2I2 is energetically preferred. The rather low stability of AuI3 with respect to dissociation into AuI and I2 will make it difficult to isolate this species in the solid state as (possibly) Au2I6 or detect it by matrix-isolation techniques. The monomer AuI3 is Jahn-Teller distorted from the ideal trigonal planar (D3h) form, but adopts a Y-shaped structure (in contrast to AuF3 and AuCl3), and in the nonrelativistic case can be described as I2 weakly bound to AuI. Relativistic effects turn AuI3 from a static Jahn-Teller system to a dynamic one. For the yet undetected gas-phase species AuI accurate coupled-cluster calculations for the potential energy curve are used to predict vibrational-rotational constants. Solid-state density functional calculations are performed for AuI and Au2I6 in order to predict cohesive energies.

Journal Article↗

PubMed2001

Electrochemical synthesis, X-ray single crystal, IR spectroscopic, and quantum chemical investigation of molybdenum and tungsten hexamethoxides.

The anodic oxidation of molybdenum metal in MeOH at both low anodic and cathodic current density (0.025 A/cm2) and electrolyte temperatures kept below 20 degrees C provides an efficient approach to Mo(OMe)6 (I). W(OMe)6 (II) can be obtained from the electrolytes, prepared via anodic dissolution of tungsten, by fractional crystallization. The symmetrically independent units in the structures of I and II, being isomorphous, follow the C1 (slightly distorted D2d) symmetry. Theoretical calculations performed for a free molecule of I indicate that this low symmetry may be the result of the packing of the molecules in the crystal structure and also an inherent property imposed by the bonding in this compound. Crystal data for I: Mo(OMe)6 at 22 degrees C, a = 7.0976(13), b = 6.6103(12), and c = 12.286(2) A, beta = 90.068(3) degrees, V = 576.41(18) A3, monoclinic P2/n, Z = 2. Crystal data for II: W(OMe)6 at 22 degrees C, a = 7.1164(19), b = 6.6414(18), and c = 12.304(3) A, beta = 90.047(5) degrees, V = 581.5(3) A3, monoclinic P2/n, Z = 2.

Journal Article↗

PubMed2001

Ab initio calculations on bismuth cluster polycations.

Ab initio calculations on bismuth polycationic species of the types Bi(n(n-2))+, Bi(n(n-4))+, and Bi(n(n-6))+ (n = 3 - 12) were performed at the Hartree-Fock and density functional theory levels in order to investigate their general properties and the applicability of Wade's rules on bismuth polycations. Some exceptions to Wade's rules were encountered, and, moreover, several predicted and calculated minima show only meta-stable behavior. The bonding in bismuth polycations is characterized by a high degree of electron delocalization and "three-dimensional aromaticity".

Journal Article↗

PubMed2000

The solution structure of ribosomal protein L36 from Thermus thermophilus reveals a zinc-ribbon-like fold.

We have determined the solution NMR structure of the ribosomal protein L36 from Thermus thermophilus. L36 is the smallest protein in the large subunit of the prokaryotic ribosome. The sequence contains three completely conserved cysteine residues and one conserved histidine residue in a C-X(2)-C-X(12)-C-X(4)-H motif. Extended X-ray absorption fine structure spectroscopy was used to confirm that a purified L36 sample contains an equimolar amount of zinc. The structure of L36 was determined using simulated annealing based on NOE distance restraints, dihedral angle restraints and hydrogen bond distance restraints derived from NMR spectra of (15)N-labeled and non-labeled L36 samples at pH 7 and 12 degrees C, and by imposing tetrahedral zinc ion coordination geometry. The L36 fold is characterized by a triple-stranded antiparallel beta-sheet with the zinc-binding site at one end. The structure of the zinc site is well-determined and shows that the three cysteine sulphur atoms are supported by hydrogen bonds to backbone amide protons. The conserved histidine residue is located in a short 3(10)-helix and coordinates zinc by the N(delta1) atom. The electrostatic surface potential and location of conserved Arg, Lys and His side-chains suggest a large continuous L36-rRNA interaction interface. The folding topology as well as position and conformation of many conserved side-chains in L36 are very similar to those of zinc-ribbon domains found in the archaeal transcription factor TFIIB N terminus and the eukaryal transcription elongation factor hTFIIS C terminus. Given the relative antiquity of the ribosome it is possible that L36 reflects the parent of transcription-related zinc ribbons.

Amino Acid Motifs↗