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PubMed1997

Five-Coordinate Hydrogen: Neutron Diffraction Analysis of the Hydrido Cluster Complex

Pentacoordinate hydrogen atoms were identified by single-crystal neutron diffraction analysis of [N(CH3)4]3[H2Rh13(CO)24]. The hydrogen atoms are located in square pyramidal cavities of the Rh13 cluster, in positions almost coplanar with the Rh4 faces on the surface of the cluster. They are slightly displaced inward, toward the central rhodium atom of the cluster, with average H-Rh(central) and H-Rh(surface) distances of 1.84(2) and 1.97(2) angstroms, respectively. This result shows that hydrogen, which normally forms only one bond, can be attached to five other atoms simultaneously in a large metal cluster.

Journal Article↗

PubMed2003

[Di-n-butytin tridentate acylhydrazone Schiff base complexes: synthesis and studies by infrared spectroscopy].

Four tridentate acylhydrazone schiff base ligands H2L [H2L1:C6H5C(O)NHN = CHC6H4OH-2, H2L2:C6H5C(O)NHN = CHC6H3(OH)(2)-2,4, H2L3:NC5H4C(O)NHN = CHC6H4OH-2, H2L4:NC5H4C(O)NHN = CHC6H3(OH)(2)-2,4] were synthesized and use to form four novel di-n-Butytin complexes of the type (n-Bu)2SnL with di-n-Butytin oxide [(n-Bu)2SnO]. All these ligands and complexes were characterized by elemental analysis and infrared spectroscopy. Their principal infrared spectral absorption peaks were assigned and discussed for the region of 4,000-400 cm-1. A comparison of the infrared spectra of the ligands with those of the corresponding complexes reveals that the disappearance of the bands assigned to carbonyl unambiguously confirms that the ligands coordinate with tin in the enol form. The coordination manner for tridentate acylhydrazone schiff base ligands with tin atom in the complexes was determined. The results indicated that the Sn atom in these complexes is five-coordinated.

Hydrazones↗

PubMed2004

Bis[1,1-dimethylbiguanide(1-)-kappa2N2,N5]copper(II) monohydrate.

The crystal structure of the title compound, [Cu(C(4)H(10)N(5))(2)].H(2)O, contains two independent copper N,N-dimethylbiguanide complex units, each with square-planar coordination of the Cu atom by four N atoms. The two complexes have different symmetry, with one Cu atom lying on an inversion centre and the other on a twofold rotation axis. The Cu-N bond lengths are 1.923 (2) and 1.950 (2) A in the centrosymmetric complex, and 1.928 (2) and 1.938 (2) A in the non-centrosymmetric complex. The crystal structure is stabilized by N-H...O, O-H...N and N-H...N hydrogen bonds; each water molecule forms four hydrogen bonds involving three different Cu complexes.

Journal Article↗

PubMed2003

The ring structure and organization of light harvesting 2 complexes in a reconstituted lipid bilayer, resolved by atomic force microscopy.

The main function of the transmembrane light-harvesting complexes in photosynthetic organisms is the absorption of a light quantum and its subsequent rapid transfer to a reaction center where a charge separation occurs. A combination of freeze-thaw and dialysis methods were used to reconstitute the detergent-solubilized Light Harvesting 2 complex (LH2) of the purple bacterium Rhodopseudomonas acidophila strain 10050 into preformed egg phosphatidylcholine liposomes, without the need for extra chemical agents. The LH2-containing liposomes opened up to a flat bilayer, which were imaged with tapping and contact mode atomic force microscopy under ambient and physiological conditions, respectively. The LH2 complexes were packed in quasicrystalline domains. The endoplasmic and periplasmic sides of the LH2 complexes could be distinguished by the difference in height of the protrusions from the lipid bilayer. The results indicate that the complexes entered in intact liposomes. In addition, it was observed that the most hydrophilic side, the periplasmic, enters first in the membrane. In contact mode the molecular structure of the periplasmic side of the transmembrane pigment-protein complex was observed. Using Föster's theory for describing the distance dependent energy transfer, we estimate the dipole strength for energy transfer between two neighboring LH2s, based on the architecture of the imaged unit cell.

Crystallography↗

PubMed1993

Atomic force microscopy of bacteriophage T4 and its tube-baseplate complex.

Bacteriophage T4 was imaged by atomic force microscopy with the finest resolution to date with a clear image of tail fibers of an estimated diameter of 2-3 nm. T4 phages were spread on a clean surface of silicon wafer and dried under air before observation with an atomic force microscope. The head, tail and tail fibers were routinely imaged with somewhat distorted dimensions. The ease of imaging isolated phage particles with a good resolution raised our expectation for the further use of AFM in biomedical applications.

Bacteriophage T4↗

PubMed2006

Energy-dependent disassembly of self-assembled SNARE complex: observation at nanometer resolution using atomic force microscopy.

Full-length v-SNARE protein reconstituted in lipid vesicles, when exposed to t-SNARE-reconstituted lipid membrane, results in the self-assembly of a t-/v-SNARE complex in a ring pattern, forming pores and the establishment of continuity between the opposing bilayers. In contrast, when v-SNARE protein alone (without liposomes) is exposed to t-SNARE-reconstituted lipid membrane, they also self-assemble to form t-/v-SNARE complexes, although such complexes fail to possess the characteristic ring pattern, nor do they help in the establishment of continuity between the opposing bilayers. Hence, t-SNAREs and v-SNARE need to be membrane-associated to interact in a circular array to form conducting pores in the presence of calcium. This study demonstrates that, irrespective of their arrangement, both forms of the SNARE complex can be disassembled in the presence of NSF-ATP.

Adenosine Triphosphate↗

PubMed1990

All atom molecular mechanics simulations on covalent complexes of anthramycin and neothramycin with deoxydecanucleotides.

We present molecular mechanics simulations on covalent complexes between d[(GC)5]2, d(G10).d(C10), d(GCGCGAGCGC).d(GCGCTCGCGC), d(GCGCGTGCGC).d(GCGCACGCGC), d(G5AG4).d(C4TC5), and d(G5TG4).d(C4AC5) on one hand and potent antitumor antibiotics anthramycin and neothramycin A on the other, using the all atom force field in the framework of the program AMBER(UCSF). The energy-refined models of both the sets of complexes show minimal distortions for the nucleotides, consistent with the results of 2D NMR studies on these complexes. The drugs have 3'-orientation in the minor groove, consistent with the previously reported investigations employing the united atom force field and with the experimental observations. Both anthramycin and neothramycin are calculated to bind preferentially to the puGpu sequences over pyGpy. This is in qualitative agreement with experimental studies for anthramycin, while for neothramycin A, this result is in apparent disagreement with experimental observations which have reported preferential binding of neothramycin A to poly(dG-dC).poly(dG-dC) over poly(dG).poly(dC). While the present study brings out the usefulness of the simple molecular mechanics approach (using an all atom force field) in rationalizing substantial experimental observations, it also emphasizes the need for further investigations on solvent and dynamics effects in understanding the sequence specificity of drug-DNA binding.

Anthramycin↗

PubMed2002

Five atomic resolution structures of endothiapepsin inhibitor complexes: implications for the aspartic proteinase mechanism.

Endothiapepsin is derived from the fungus Endothia parasitica and is a member of the aspartic proteinase class of enzymes. This class of enzyme is comprised of two structurally similar lobes, each lobe contributing an aspartic acid residue to form a catalytic dyad that acts to cleave the substrate peptide bond. The three-dimensional structures of endothiapepsin bound to five transition state analogue inhibitors (H189, H256, CP-80,794, PD-129,541 and PD-130,328) have been solved at atomic resolution allowing full anisotropic modelling of each complex. The active sites of the five structures have been studied with a view to studying the catalytic mechanism of the aspartic proteinases by locating the active site protons by carboxyl bond length differences and electron density analysis. In the CP-80,794 structure there is excellent electron density for the hydrogen on the inhibitory statine hydroxyl group which forms a hydrogen bond with the inner oxygen of Asp32. The location of this proton has implications for the catalytic mechanism of the aspartic proteinases as it is consistent with the proposed mechanism in which Asp32 is the negatively charged aspartate. A number of short hydrogen bonds (approximately 2.6 A) with ESD values of around 0.01 A that may have a role in catalysis have been identified within the active site of each structure; the lengths of these bonds have been confirmed using NMR techniques. The possibility and implications of low barrier hydrogen bonds in the active site are considered.

Aspartic Acid Endopeptidases↗

PubMed2004

Bis(mu-cystamine-kappa4N,S:S',N')bis[(2-aminoethanethiolato-kappa2N,S)-iridium(III)] tetrabromide dihydrate.

In the complex cation of the title compound, [Ir2(C2H6NS)2(C4H12N2S2)2]Br4.2H2O, which was obtained by rearrangement of [Re[Ir(aet)3]2]3+ (aet is 2-aminoethanethiolate) in an aqueous solution, two approximately octahedral fac(S)-[Ir(NH2CH2CH2S)3] units are linked by two coordinated disulfide bonds. The complex cation has a twofold axis, and the two non-bridging thiolate S atoms in the complex are located on opposite sides of the two disulfide bonds. Considering the absolute configurations of the two octahedral units (Delta and Lambda) and the four asymmetric disulfide S atoms (R and S), the complex consists of the Delta(RR)Delta(RR) and Lambda(SS)Lambda(SS) isomers, which combine to form the racemic compound.

Journal Article↗

PubMed1998

(Nitro)Iron(III) Porphyrins. EPR Detection of a Transient Low-Spin Iron(III) Complex and Structural Characterization of an O Atom Transfer Product.

The reaction of BF(3).OEt(2) with the bis(nitro) complex of iron(III) picket-fence porphyrin, [K(18C6)(OH(2))][Fe(TpivPP)(NO(2))(2)], leads to the formation of a transient porphyrin intermediate, assigned on the basis of its rhombic low-spin EPR spectrum as the five-coordinate N-bound mono(nitro) iron(III) derivative, [Fe(TpivPP)(NO(2))]. This species is reactive and readily undergoes oxygen atom transfer to form [Fe(III)(TpivPP)(NO(3))] and [Fe(II)(TpivPP)(NO)]. The reactions have been followed by EPR and IR spectroscopy. [Fe(TpivPP)(NO(2))] has a rhombic EPR spectrum (g = 2.60, 2.35, and 1.75) in chlorobenzene and CH(2)Cl(2) and is spectroscopically distinct from the bis(nitro) starting material (g = 2.70, 2.50, and 1.57). Oxidation of the nitrosyl species to [Fe(TpivPP)(NO(3))] proceeds via an intermediate assigned as [Fe(TpivPP)(NO(2))] on the basis of its EPR spectrum. The crystal structure of one of the reaction products, [Fe(TpivPP)(NO(3))], has been determined. The nitrate ion of [Fe(TpivPP)(NO(3))] is bound to the iron(III) ion in a "symmetric" bidentate fashion within the ligand-binding pocket of the porphyrin pickets. Individual Fe-O distances are 2.123(3) and 2.226(3) Å. The dihedral angle between the plane of the nitrate ion and the closest N(p)-Fe-N(p) plane is 10.0 degrees. The Fe-N(p) bonds (and trans N(p)-Fe-N(p) angles) perpendicular and parallel to the plane of the axial ligand average to 2.060(5) Å (154.84(9) degrees ) and 2.083(3) Å (146.14(9) degrees ), respectively. Crystal data for [Fe(TpivPP)(NO(3))]: a = 23.530(2) Å, b = 10.0822(5) Å, c = 48.748(3) Å, beta = 92.145(5) degrees, monoclinic, space group I2/a, V = 11556.4(14) Å(3), Z = 8, FeN(9)O(7)C(64)H(64), 8798 observed data, R(1) = 0.0606, wR(2) = 0.1313, all observations at 127(2) K.

Journal Article↗

PubMed1999

Determination of platinum complexes in clinical samples by a rapid flameless atomic absorption spectrometry assay.

The frequent use of platinum (Pt) complexes in cancer chemotherapy and the application of new therapeutic options and dosing strategies have increased the need for rapid analytic procedures to determine Pt concentrations in the biologic fluids of patients. Therefore a flameless atomic absorption spectrometry method for the quantification of Pt in plasma and ultrafiltrate was developed and validated. A simple sample preparation of only one dilution step was established. Only 400 microL of whole blood was required for duplicate analysis of Pt in both matrices. The matrix-specific temperature programs took less than 75 seconds. The lower limit of quantification was 40 ng Pt/mL and 20 ng Pt/mL for plasma and ultrafiltrate, respectively. Suitable linearity could be reached using separate calibration curves for the high and low Pt concentration ranges. Recovery of Pt was complete, and there were no major stability problems. The accuracy and precision of the new method met the international criteria for the validation of bioanalytic methods. In addition, the use of different anticoagulants for clinical sampling, ultrafiltration systems, and ultrafiltration conditions were investigated. The assay has already been extensively applied to pharmacokinetic studies. In conclusion, the new Pt assay proved to be rapid, simple, sensitive, and suitable for clinical use.

Anticoagulants↗

PubMed2004

Spectroscopic investigation of nonbonding interactions of group-14 atoms with rare gases: the SnAr van der Waals complex.

The laser fluorescence excitation spectra of the SnAr van der Waals complex, in the vicinity of the individual fine-structure lines of the Sn 5s25p6s3P0<-- 5s25p2(3)P atomic resonance transition in the spectral region 317-270 nm are reported. Excited-state (v',0) progressions of bands built upon the individual J'<-- J" fine-structure atomic lines were observed. Because the collisional spin-orbit relaxation was slow, transitions were observed out of the lower SnAr states built upon all the J'' atomic asymptotes. The spectra were interpreted through model potential energy curves based on the isoelectronic SiAr system. Lower bounds to the dissociation energies of all lower SnAr states were determined. The binding energies of the group-13, and -14-atom-argon complexes and the effect of the spin-orbit interaction on moderating nonbonding interactions are discussed.

Journal Article↗

PubMed2002

Determination of trace levels of dissolved vanadium in seawater by use of synthetic complexing agents and inductively coupled plasma-atomic emission spectroscopy (ICP-AES).

In the determination of traces of dissolved vanadium in complex matrices such as seawater, separation and enrichment from the matrix is of special importance. A wide variety of methods has been proposed for preconcentration, depending to the nature of samples and the methods to be used for measurement. Among these methods separation techniques based on sorption on to chelating resins seem convenient, rapid, and capable of achieving a high concentration factor. The methods proposed in this paper are based on the transformation of all dissolved vanadium species in seawater into organic complexes by use of synthetic complexing agents such as dithizone, luminol, or 8-hydroxyquinoline; the resulting vanadium-organic complexes were sorbed on to a C(18) column at a flow rate of 5 mL min(-1). The vanadium sorbed on the C(18) columns was then stripped by use of nitric acid (2 mol L(-1)) and analysed by inductively coupled plasma-atomic emission spectroscopy, ICP-AES. This method was optimised and use of other chelating resins, such as chelamine, chelex-100, and immobilised 8-hydroxyquinoline and was compared by passing seawater samples directly over the resins. The experimental conditions (pH, acid used for elution, and contact time between the liquid sample and the resin) were optimised. The results were compared for all the resins used and were indicative of excellent and coherent reproducibility.

Chelating Agents↗

PubMed2002

Calculation of electronic g-tensors for transition metal complexes using hybrid density functionals and atomic meanfield spin-orbit operators.

We report the first implementation of the calculation of electronic g-tensors by density functional methods with hybrid functionals. Spin-orbit coupling is treated by the atomic meanfield approximation. g-Tensors for a set of small main group radicals and for a series of ten 3d and two 4d transition metal complexes have been compared using the local density approximation (VWN functional), the generalized gradient approximation (BP86 functional), as well as B3-type (B3PW91) and BH-type (BHPW91) hybrid functionals. For main group radicals, the effect of exact-exchange mixing is small. In contrast, significant differences between the various functionals arise for transition metal complexes. As has been shown previously, local and in particular gradient-corrected functionals tend to underestimate the "paramagnetic" contributions to the g-tensors in these cases and thereby recover only about 40-50% of the range of experimental g-tensor components. This is improved to ca. 60% by the B3PW91 functional, which also gives slightly reduced standard deviations. The range increases to almost 100% using the half-and-half functional BHPW91. However, the quality of the correlation with experimental data worsens due to a significant overestimate of some intermediate g-tensor values. The worse performance of the BHPW91 functional in these cases is accompanied by spin contamination. Although none of the functionals tested thus appears to be ideal for the treatment of electronic g-tensors in transition metal complexes, the B3PW91 hybrid functional exhibited the overall most satisfactory performance. Apart from the validation of hybrid functionals, some aspects in the treatment of spin-orbit contributions to the g-tensor are discussed.

Journal Article↗

PubMed1986

Atomic and Raman spectroscopy of the dipalmitoylphosphatidic acid-calcium complex and phase transitions.

Calcium binding measurements by atomic absorption spectroscopy and temperature-dependent phase transitions studies by Raman spectroscopy were combined in order to investigate the effect of Ca2+ binding on dipalmitoylphosphatidic acid (DPPA) dispersed in CaCl2 solutions of varying concentration at pH 7. The peak heights for the Raman CH stretch bands observed at 2885 cm-1 and 2935 cm-1 were used as a measure of hydrocarbon chain randomization and aggregate ultrastructure. Two transitions were observed for both pure DPPA and DPPA-Ca2+ mixtures. Ca2+ binding caused greatly increased DPPA chain rigidity in the melted state above Tm, but had much less effect on the solid phases below Tm. The increase in rigidity in the fluid state was observed to vary linearly with the molar ratio of bound Ca2+ to total DPPA throughout the range 0 to 1. The results of the Raman and Ca2+ binding measurements are explained by a model in which two populations of DPPA co-exist in the fluid state when Ca2+ binding has not reached saturation. One population consists of the Ca2+-bound DPPA complex with stoichiometric 1:1 binding ratio (determined from an atomic absorption Ca2+ binding study), and the second population is free DPPA. We propose that Ca2+-induced clustering and separation of the two components occurs chiefly because of differences in chain fluidity of the two components.

Calcium↗

PubMed2004

Comparative kinetics and mechanism of oxygen and sulfur atom transfer reactions mediated by bis(dithiolene) complexes of molybdenum and tungsten.

Although the kinetics and mechanism of metal-mediated oxygen atom (oxo) transfer reactions have been examined in some detail, sulfur atom (sulfido) transfer reactions have not been similarly scrutinized. The reactions [M(IV)(O-p-C(6)H(4)X')(S(2)C(2)Me(2))(2)](1-) + Ph(3)AsQ --> [M(VI)Q(O-p-C(6)H(4)X')(S(2)C(2)Me(2))(2)](1-) + Ph(3)As (M = Mo, W; Q = O, S) with variable substituent X' have been investigated in acetonitrile in order to determine the relative rates of oxo versus sulfido transfer at constant structure (square pyramidal) of the atom acceptor and of atom transfer at constant structure of the atom donor and metal variability of the atom acceptor. All reactions exhibit second-order kinetics and entropies of activation (-25 to -45 eu) consistent with an associative transition state. At parity of atom acceptor, k(2)(S) (0.25-0.75 M(-1)s(-1)) > k(2)(O) (0.023-0.060 M(-1)s(-1)) with M = Mo and k(2)(S) (4.1-66.7 M(-1)s(-1)) > k(2)(O) (1.8-9.8 M(-1)s(-1)) with M = W. At constant atom donor and X', k(2)(W) > k(2)(Mo) with reactivity ratios k(2)(W)/k(2)(Mo) = 78-184 (Q = O) and 16-89 (Q = S). Rate constants refer to 298 K. At constant M and Q, rates increase in the order X' = Me less, similar OMe < H < Br < COMe < CN; increasing electron-withdrawing propensity accelerates reaction rates. The probable transition state involves significant Ph(3)AsQ...M bond-making (X' rate trend) and concomitant As-Q bond weakening (bond energy order As-O > As-S). Orders of oxo and sulfido donor ability of substrates and complexes are deduced on the basis of qualitative reactivity properties determined here and elsewhere. This work complements previous studies of the reaction systems [M(IV)(O-p-C(6)H(4)X')(S(2)C(2)Me(2))(2)](1-)/XO where the substrates are N-oxides and S-oxides and k(2)(W) > k(2)(Mo) at constant substrate also applies. The reaction order of substrates is Me(3)NO > (CH(2))(4)SO > Ph(3)AsS > Ph(3)AsO. This research provides the first quantitative information of metal-mediated sulfido transfer.

Crystallography, X-Ray↗

PubMed2006

Stoichiometric and catalytic secondary O-atom transfer by Fe(III)-NO2 complexes derived from a planar tetradentate non-heme ligand: reminiscence of heme chemistry.

An Fe(III) nitro complex [(bpb)Fe(NO2)(py)] (2) of the tetradentate ligand 1,2-bis(pyridine-2-carboxamido)benzene (H2bpb, H is the dissociable amide proton) has been synthesized via addition of NaNO2 to [(bpb)Fe(py)2](ClO4) (1) in MeCN or DMF. This structurally characterized Fe(III) nitro complex exhibits its nuNO2 at 1384 cm(-1). The reaction of 1 with 2 equiv of Et4NX (X = Cl-, Br-) affords the high-spin complexes (Et4N)[(bpb)Fe(Cl2)] (3) and (Et4N)[(bpb)Fe(Br)2] (4), respectively. The structure of 4 has been determined. The addition of an equimolar amount of Et4NCl, Et4NBr, or Et4NCN to a solution of 2 affords the mixed-ligand complexes (Et4N)[(bpb)Fe(NO2)(Cl)] (5), (Et4N)[(bpb)Fe(NO2)(Br)] (6), and (Et4N)[(bpb)Fe(NO2)(CN)] (7), respectively. These complexes are all low spin with isotropic g values of 2.15. Under anaerobic conditions, the reactions of 5-7 with Ph3P in MeCN afford the five-coordinate {Fe-NO}7 nitrosyl [(bpb)Fe(NO)] (and Ph3PO) via secondary oxygen-atom (O-atom) transfer. The O-atom transfer to Ph3P by 5-7 becomes catalytic in the presence of dioxygen with transfer rates in the range of 1.70-13.59 x 10-3 min(-1). The O-atom transfer rates and turnover numbers (5 > 6 > 7) are reflective of the strength of the axial donors (Cl- > Br- > CN-). The catalytic efficiencies of complexes 5-7 are limited due to formation of the thermodynamic end products [(bpb)Fe(X)2]- (where X = Cl- for 5, Br- for 6, and CN- for 7).

Benzene↗

PubMed2005

Coordination polymers formed by bridging 2-substituted tetrazole ligands: poly[[dichlorocopper(II)]-di-mu2-2-propyl-2H-tetrazole-kappa2N1:N4] and poly[[dichlorocopper(II)]-di-mu2-2-allyl-2H-tetrazole-kappa2N1:N4].

Two polymeric complexes, [CuCl2L2]n, where L is 2-propyltetrazole (C4H8N4) or 2-allyltetrazole (C4H6N4), are the first coordination polymers of 2-substituted tetrazoles in which only the tetrazole rings bridge neighbouring Cu atoms. In both complexes, the Cu atoms lie on inversion centres and are six-coordinated in tetragonally distorted octahedral geometries, CuCl2N4, with two N1 tetrazole ring atoms in the axial positions and two Cl atoms and two N4 tetrazole ring atoms in the equatorial sites. The Cl atoms do not participate in the polymeric layer formation.

Journal Article↗