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At least 433 records · Page 24Linked to original sources
PubMed2000

Structure of nu-Al(80.61)Cr(10.71)Fe(8.68), a giant hexagonal approximant of a quasicrystal determined by a combination of electron microscopy and X-ray diffraction

Nu-Al(80.61)Cr(10.71)Fe(8.68), P6(3)/m (No. 176), a = 40.68 (7), c = 12.546 (1) A, V = 17,983 (8) A3, atoms/cell = 1184.56, Dx = 3.518 g cm(-3), lambda(Mo K alpha) = 0.71069 A, mu = 5.032 mm(-1), F(000) = 18,433, T = 293 K, final R = 0.075 for 3854 reflections with Fo > 4sigma(Fo). The [001] high-resolution electron-microscopic image of the nu-AlCrFe phase clearly shows similar local characteristics to those given by the complex icosahedral cluster found in somewhat smaller hexagonal approximant structures, such as kappa-Al76Cr18Ni6 [a = 17.674 (3), c = 12.516 (3) A; Sato et al. (1997). Acta Cryst. C53, 1531-1533; Marsh (1998). Acta Cryst. B54, 925-926] and lambda-Al(4.32)Mn [a = 28.382 (9), c = 12.389 (2) A; Kreiner & Franzen (1997). J. Alloys Compd. 261, 83-104]. Using the known atomic distribution of this icosahedral cluster in the kappa and lambda phases as the starting point, the structure of the nu phase, a hexagonal intermetallic compound with probably the largest a parameter, was solved by X-ray single-crystal diffraction using direct methods. As in kappa and lambda phases, almost all TM (transition metal) atoms in the complex icosahedral cluster are icosahedrally coordinated. However, contrary to the lambda structure in which about 98% of the TM atoms have icosahedral-coordination, the TM atoms in the v structure also form capped pentagonal prisms in the region between these complex icosahedral clusters, yielding an average icosahedral coordination of about 70% for TM atoms. After rapid solidification, the v phase occurs together with a decagonal quasicrystal with a periodicity of about 12.5 A along its tenfold axis and thus also consists of six layers, two flat ones each sandwiched between two puckered layers in mirror reflection, stacked along the c axis.

Journal Article↗
PubMed2003

A multicentered approach to integrated QM/QM calculations. Applications to multiply hydrogen bonded systems.

A multicentered integrated QM/QM technique has been developed. By separating high-level calculations in distinct regions of molecules, the multicentered approach supplants a single large high-level calculation with several smaller calculations. Due to the steep polynomial scaling of traditional ab initio quantum chemical methods, this separation significantly enhances the computational efficiency of QM/QM methods. The straightforward implementation of this multicentered approach is illustrated with several large poly-alcohols that form hydrogen bonds with water. The largest alcohol-water complex contains 81 atoms. For properly selected model systems, this multicentered approach introduces essentially no error in the dissociation energies of these complexes relative to conventional QM/QM schemes. This multicentered technique should be easily extended to other, more general integrated methods (QM/MM, ONIOM, etc).

Journal Article↗
PubMed1997

The Complexing Properties of 1-Aminosquarate Derivatives with Lead.

Reaction of three different 1-(dialkylamino) derivatives of 3,4-dihydroxycyclobut-3-ene-1,2-dione (squaric acid) with lead(II) nitrate in aqueous solution yielded polymeric complexes which have been characterized by single-crystal X-ray analysis. Pb[(CH(3))(2)NC(4)O(3)](2)(OH(2))(2).H(2)O (1) produced from 1-(dimethylamino)-2-methoxycyclobutenedione crystallizes in the triclinic space group P&onemacr;, with a = 8.591(5) Å,b = 9.308(4) Å, c = 10.571(4) Å, alpha = 95.58(2) degrees, beta = 94.96(3) degrees, gamma = 95.78(4) degrees, and Z = 2. The complex of formula Pb[(C(2)H(5))(2)NC(4)O(3)](2)(H(2)O) (2) formed from the corresponding 1-(diethylamino) analogue of the ligand also crystallizes in space group P&onemacr;, with a = 7.521(2) Å, b = 10.928(4) Å, c = 11.749(4) Å, alpha = 90.10(2) degrees, beta = 97.84(2) degrees, gamma = 95.12(2) degrees, and Z = 2. In both of these complexes, the lead atom is eight-coordinate with the ligands being bound in bidentate and binucleating fashions. The di-n-propylamino substituent in the di-n-propyl homologue hydrolyzed during crystallization, and a lead(II) squarate, Pb(C(4)O(4))(H(2)O)(4) (3), was produced: monoclinic space group P2(1), with a = 6.466(2) Å, b = 7.898(3) Å, c= 8.307(3) Å, beta = 92.88(3) degrees, and Z = 2. The lead atom is again eight-coordinate, and the squarate moiety, bidentate and binucleating. The respective coordination polyhedra for the complexes are square antiprismatic (1), bicapped trigonal prismatic (2), and distorted mono faced-capped and edge-capped trigonal prismatic (3).

Journal Article↗
PubMed2005

Theoretical study on the bromomethane-water 1:2 complexes.

Bromomethane-water 1:2 complexes have been theoretically studied to reveal the role of hydrogen bond and halogen bond in the formation of different aggregations. Four stable structures exist on the potential energy surface of the CH3Br(H2O)2 complex. The bromine atom acts mainly as proton acceptor in the four studied structures. It is also capable of participating in the formation of the halogen bond. The properties and characteristics of the hydrogen bond and the halogen bond are investigated employing several different quantum chemical analysis methods. Cooperative effects for the pure hydrogen bonds or the mixed hydrogen bonds with halogen bonds and the possibility of describing cooperative effects in terms of the topological analysis of the electronic density or the charge-transfer stabilization energy are discussed in detail. An atoms-in-molecules study of the hydrogen bond or the halogen bond in the bromomethane-water 1:2 complexes suggests that the electronic density topology of the hydrogen bond or the halogen bond is insensitive to the cooperative effect. The charge-transfer stabilization energy is proportional to the cooperative effect, which indicates the donor-acceptor electron density transfer to be mainly responsible for the trimer nonadditive effect.

Journal Article↗
PubMed2005

Template synthesis of tungsten complexes with saturated N-heterocyclic carbene ligands.

Tungsten complex with a coordinated 2-azidoethyl isocyanide ligand reacts with PMe3 at the azido function to give a complex with a coordinated iminophosphorane which upon hydrolysis of the P=N bond yields a complex with an NH,NH-stabilized N-heterocyclic carbene ligand, 7; alkylation of the carbene ring nitrogen atoms gives a complex with an N,N'-dialkylated imidazolidin-2-ylidene ligand, 8 .

Journal Article↗
PubMed2003

Discovering the interaction propensities of amino acids and nucleotides from protein-RNA complexes.

With the availability of many genome sequences, the mining of biological data is attracting much attention, most of it limited to the sequences of macromolecules. Sequence data are easy to analyze as they can be treated as strings of characters, whereas the structure of a macromolecule is much more complex. We developed a set of algorithms to analyze the structures of protein-RNA complexes at the atomic level and used them to analyze protein-RNA interactions using structural data on 51 protein-RNA complexes. The analysis revealed, among other things, that: (1) polar and charged amino acids have a strong tendency to interact with nucleotides, (2) arginine and asparagine tend to hydrogen bond with uracil, and (3) histidine favors uracil in water-mediated bonding with RNA. We analyzed a large set of structural data of protein-RNA complexes involving water-mediated hydrogen bonds as well as direct hydrogen bonds. The interaction patterns discovered from the analysis provide useful information for predicting the structure of RNA that binds proteins, and of proteins that bind RNA.

Algorithms↗
PubMed2007

MTO Schiff-base complexes: synthesis, structures and catalytic applications in olefin epoxidation.

Several Schiff-base ligands readily form complexes with methyltrioxorhenium(VII) (MTO) by undergoing a hydrogen transfer from a ligand-bound OH group to a ligand N atom. The resulting complexes are stable at room temperature and can be handled and stored in air without problems. Due to the steric demands of the ligands they display distorted trigonal-bipyramidal structures in the solid state, as shown by X-ray crystallography, with the O(-) moiety binding to the Lewis acidic Re atom and the Re-bound methyl group being located either in cis or trans position to the Schiff base. In solution, however, the steric differences seem not to be maintained, as can be deduced from (17)O NMR spectroscopy. Furthermore, the Schiff-base ligands exchange with donor ligands. Nevertheless, the catalytic behaviour is influenced significantly by the Schiff bases coordinated to the MTO moiety, which lead either to high selectivities and good activities or to catalyst decomposition. A large excess of ligand, in contrast to the observations with aromatic N-donor ligands, is detrimental to the catalytic performance as it leads to catalyst decomposition.

Journal Article↗
PubMed1985

Fe(III).ATP complexes. Models for ferritin and other polynuclear iron complexes with phosphate.

Polynuclear iron complexes of Fe(III) and phosphate occur in seawater and soils and in cells where the iron core of ferritin, the iron storage protein, contains up to 4500 Fe atoms in a complex with an average composition of (FeO.OH)8FeO.OPO3H2. Although phosphate influences the size of the ferritin core and thus the availability of stored iron, little is known about the nature of the Fe(III)-phosphate interaction. In the present study, Fe-phosphate interactions were analyzed in stable complexes of Fe(III).ATP which, in the polynuclear iron form, had phosphate at interior sites. Such Fe(III).ATP complexes are important not only as models but also because they may play a role in intracellular iron transport and in iron toxicity; the complexes were studied by extended x-ray absorption fine structure, EPR, NMR spectroscopy, and measurement of proton release. Mononuclear iron complexes exhibiting a g' = 4.3 EPR signal were formed at Fe:ATP ratios less than or equal to 1:3, and polynuclear iron complexes (Fe greater than or equal to 250, EPR silent at g' = 4.3) were formed at an Fe:ATP ratio of 4:1. No NMR signals due to ATP were observed when Fe was in excess (Fe:ATP = 4:1). Extended x-ray absorption fine structure analysis of the polynuclear Fe(III).ATP complex was able to distinguish an Fe-P distance at 3.27 A in addition to the octahedral O at 1.95 A and 4-5 Fe atoms at 3.36 A. The Fe-O and Fe-Fe distances are the same as in ferritin, and the Fe-P distance is analogous to that in another metal-ATP complex. An observable Fe-P environment in such a large polynuclear iron cluster as the Fe(III).ATP (4:1) complex indicates that the phosphate is distributed throughout rather than merely on the surface, in contrast to earlier models of chelate-stabilized iron clusters. Complexes of Fe(III) and ATP similar to those described here may form in vivo either as normal components of intracellular iron metabolism or during iron excess where the consequent alteration of free nucleotide triphosphate pools could contribute to the observed toxicity of iron.

Adenosine Triphosphate↗
PubMed2005

[A theoretical study of the influence of interaction between transition metal atoms and carbon monoxide on infrared and Raman intensities of the C--O stretching vibration].

The structures and the spectral properties of the transition metal M-CO complexes have been investigated by performing the calculation of the hybrid density functional theory approach. The calculated results show that for each M-CO complex the infrared intensity of the C--O stretching mode is significantly larger than that of the M-C stretching mode and the bending modes. The Raman scattering factor of the C--O stretching mode is the largest among three modes. Comparison of the calculated results indicates that the C--O modes of M-CO complexes, the metal atom of which belongs to the fourth periodic metals and the Cu group, have larger Raman scattering factors than those in the other M-CO comnplexes.

Algorithms↗
PubMed2004

Isomerization and oxygen atom transfer reactivity in oxo-Mo complexes of relevance to molybdoenzymes.

Both dioxo Mo(VI) and mono-oxo Mo(V) complexes of a sterically restrictive N2O heteroscorpionate ligand are found to exist as cis and trans isomers. The thermodynamically stable isomer differs for the two oxidation states, but in each case, we have isolated the kinetically labile isomer and followed its isomerization to the thermodynamically stable form. The Mo(VI) complex is more stable in the cis geometry and isomerizes more than 6 times faster than the Mo(V) complex, which prefers the trans geometry. In OAT reactions with PPh3, the trans isomer of the dioxo-Mo(VI) reacts approximately 20 times faster than the cis isomer. Thus, there are both oxidation state and donor atom dependent differences in isomeric stability and reactivity that could have significant functional implications for molybdoenzymes such as DMSO reductase.

Crystallography, X-Ray↗
PubMed2004

Ultrahigh resolution drug design. II. Atomic resolution structures of human aldose reductase holoenzyme complexed with Fidarestat and Minalrestat: implications for the binding of cyclic imide inhibitors.

The X-ray structures of human aldose reductase holoenzyme in complex with the inhibitors Fidarestat (SNK-860) and Minalrestat (WAY-509) were determined at atomic resolutions of 0.92 A and 1.1 A, respectively. The hydantoin and succinimide moieties of the inhibitors interacted with the conserved anion-binding site located between the nicotinamide ring of the coenzyme and active site residues Tyr48, His110, and Trp111. Minalrestat's hydrophobic isoquinoline ring was bound in an adjacent pocket lined by residues Trp20, Phe122, and Trp219, with the bromo-fluorobenzyl group inside the "specificity" pocket. The interactions between Minalrestat's bromo-fluorobenzyl group and the enzyme include the stacking against the side-chain of Trp111 as well as hydrogen bonding distances with residues Leu300 and Thr113. The carbamoyl group in Fidarestat formed a hydrogen bond with the main-chain nitrogen atom of Leu300. The atomic resolution refinement allowed the positioning of hydrogen atoms and accurate determination of bond lengths of the inhibitors, coenzyme NADP+ and active-site residue His110. The 1'-position nitrogen atom in the hydantoin and succinimide moieties of Fidarestat and Minalrestat, respectively, form a hydrogen bond with the Nepsilon2 atom of His 110. For Fidarestat, the electron density indicated two possible positions for the H-atom in this bond. Furthermore, both native and anomalous difference maps indicated the replacement of a water molecule linked to His110 by a Cl-ion. These observations suggest a mechanism in which Fidarestat is bound protonated and becomes negatively charged by donating the proton to His110, which may have important implications on drug design.

Aldehyde Reductase↗
PubMed1985

Direct evidence of nitrogen coupling in the copper(II) complex of bovine serum albumin by S-band electron spin resonance technique.

ESR spectra of the tight binding Cu(II) complex of bovine serum albumin (BSA) has been studied using S-band. At physiological pH, only one form of copper binding to BSA was detected from the ESR spectra. From previous X-band ESR spectra, nitrogen superhyperfine splittings were observable in the g perpendicular region; however, the resolution of the g parallel region was not sufficient to confirm the exact donor atoms of the complex. Using low-frequency ESR (2-4 GHz) at 77 K, we have resolved the nitrogen superhyperfine structure in the g parallel region. A computer simulation method has been developed for distinguishing between three and four nitrogen donor atoms. The Hyde-Froncisz theory of g and A strain broadening has been modified to use a field-swept calculation for the line shape. The observed intensity pattern and the computer simulation of such spectra positively confirm the structure of Cu(II) ion coordinated to four in-plane nitrogen atoms in frozen aqueous solutions of Cu(II)-BSA complexes at physiological pH. This is the first time that this binding site has been confirmed on the protein instead of a protein fragment or model compound. This work is another example of the usefulness of the S-band ESR technique for characterizing the metal-protein interactions when random variation in g factors cause line broadening in conventional X-band ESR spectra.

Animals↗
PubMed2003

Structural and functional models for the dinuclear copper active site in catechol oxidases. Synthesis, X-ray crystal structures, magnetic and spectroscopic properties of mu-methoxo-bridged dinuclear copper(II) complexes with N-substituted sulfonamide ligands.

Two new mu-methoxo-bridged dinuclear copper(II) complexes with a N-substituted sulfonamide, [Cu(mu-OMe)(L)(NH(3))](2) (1) and [Cu(mu-OMe)(L)(DMSO)](2) (2) [HL, N-2-(4-methylbenzothiazole)benzenesulfonamide], have been prepared and characterized by single-crystal X-ray difraction analyses. Compound 1 crystallizes in the monoclinic space group C(2)/c with a=22.0678(18), b=7.9134(7), c=21.1186(18)A, beta=113.788(4) degrees and Z=8. Compound 2 crystallizes in the monoclinic space group C(2)/c with a=18.0900(10), b=9.5720(10), c=24.2620(10) A, beta=98.7120(10) degrees and Z=8. In both complexes the copper atoms have square-planar environments bridged by two oxygen atoms from methoxide groups. Magnetic susceptibility measurements indicate a very strong antiferromagnetic coupling between the copper(II) ions in both complexes (2J<-1000 cm(-1)). Electronic Paramagnetic Resonance (EPR) spectra of the two complexes both in solid and in solution are silent. 13C NMR spectra of the complexes in solid state have been studied. The complexes have been evaluated as model systems for the catechol oxidase enzyme using 3,5-di-tert-butylcatechol as the test substrate. Complex 2 is slightly more active than complex 1.

Binding Sites↗
PubMed1997

Topography of ribosomes and initiation complexes from rat liver as revealed by atomic force microscopy.

Atomic force microscopy (AFM) was used to image ribosomes and ribosomal subunits (60S, 40S and native 40S ribosomal subunits) isolated from rat liver. A variety of topographic images were obtained directly and found to be consistent with models established by other biophysical methods. In addition, the ternary complex of eIF-2 x GTP x Met-tRNA(i) and the 43S preinitiation complex have been discerned by AFM directly. Detailed information about the binding sites for eIF-1A, eIF-2, eIF-3, and Met-tRNA(i) on the 40S ribosomal subunit was derived from the AFM images. Finally, factors which may give rise to artifactual images, namely, convolution of the AFM tip on ribosomes, surface tension collapse effect and dehydration, are discussed. This work demonstrates that AFM is useful for imaging ribosomes and translational complexes and provides valuable information that can be used to complement other well-established techniques.

Animals↗
PubMed2002

Synthesis, characterization, and crystal structures of two divalent metal diphosphonates with a layered and a 3D network structure.

Reactions of N-methyliminobis(methylenephosphonic acid), CH(3)N(CH(2)PO(3)H(2))(2) (H(4)L), with divalent metal acetates under different conditions result in metal diphosphonates with different structures. Mn(H(3)L)(2).2H(2)O (complex 1) with a layer structure was prepared by a layering technique. It is triclinic, P1 macro with a = 9.224(3) A, b = 9.780(3) A, c = 10.554(3) A, alpha = 82.009(6) degrees, beta = 74.356(6) degrees, gamma = 89.853(6) degrees, Z = 2. The Mn(II) ion is octahedrally coordinated by six phosphonate oxygen atoms from four ligands, two of them in a bidentate and two in a unidentate fashion. Each MnO(6) octahedron is further linked to four neighboring MnO(6) octahedra through four bridging phosphonate groups, resulting in a two-dimensional metal phosphonate (002) layer. These layers are held together by strong hydrogen bonds between uncoordinated phosphonate oxygen atoms. The zinc complex Zn(3)(HL)(2) (complex 2) was synthesized by hydrothermal reactions (4 days, 438 K, autogenous pressure). It is monoclinic, P2(1)/n with a = 7.7788(9) A, b = 17.025(2) A, c = 13.041(2) A, beta = 94.597(2) degrees, Z = 4. The structure of complex 2 features a 3D network built from ZnO(4) tetrahedra linked together by bridging phosphonate groups. Each zinc cation is tetrahedrally coordinated by four phosphonate oxygen atoms from four ligands, each of which connects with six zinc atoms, resulting in voids of various sizes. Magnetic measurements for the manganese complex shows an antiferromagnetic interaction at low temperature. The effect of the extent of deprotonation of phosphonic acids on the type of complex formed is discussed.

Journal Article↗
PubMed1987

A universe for molecular modeling of self-replication.

An abstract two-dimensional universe is presented, in which self-replication can be modeled and studied by computer simulation. Two types of permanent elements (atoms) occupy squares of the universe. Atoms sharing a common square form a particle, with properties determined by its component atoms. Atoms, particles, and complexes of particles move and collide according to rules like those of classical mechanics. At a higher level of organization, the string of atoms in a particle is viewed as a program, whose execution can affect the space around the particle in ways similar to the operation of enzymes. Two systems that exhibit self-replication when embedded in the universe are demonstrated. The first is very simple showing elementary self-replication activity. The second is relatively elaborate and intended to show "on paper" how a collection of particle complexes could behave in a manner resembling mitosis in a simple cell.

Biological Evolution↗
PubMed2001

New class of oligonuclear platinum-thallium compounds with a direct metal-metal bond. 5. Structure determination of heterodimetallic cyano complexes in aqueous solution by EXAFS and vibrational spectroscopy.

The structures of three closely related heterodimetallic cyano complexes, [(NC)(5)Pt-Tl(CN)(n)()](n)()(-) (n = 1-3), formed in reactions between [Pt(II)(CN)(4)](2)(-) and Tl(III) cyano complexes, have been studied in aqueous solution. Multinuclear NMR data ((205)Tl, (195)Pt, and (13)C) were used for identification and quantitative analysis. X-ray absorption spectra were recorded at the Pt and Tl L(III) edges. The EXAFS data show, after developing a model describing the extensive multiple scattering within the linearly coordinated cyano ligands, short Pt-Tl bond distances in the [(NC)(5)Pt-Tl(CN)(n)()](n)()(-) complexes: 2.60(1), 2.62(1), and 2.64(1) A for n = 1-3, respectively. Thus, the Pt-Tl bond distance increases with increasing number of cyano ligands on the thallium atom. In all three complexes the thallium atom and five cyano ligands, with a mean Pt-C distance of 2.00-2.01 A, octahedrally coordinate the platinum atom. In the hydrated [(NC)(5)Pt-Tl(CN)(H(2)O)(4)](-) species the thallium atom coordinates one cyano ligand, probably as a linear Pt-Tl-CN entity with a Tl-C bond distance of 2.13(1) A, and possibly four loosely bound water molecules with a mean Tl-O bond distance of about 2.51 A. In the [(NC)(5)Pt-Tl(CN)(2)](2)(-) species, the thallium atom probably coordinates the cyano ligands trigonally with two Tl-C bond distances at 2.20(2) A, and in [(NC)(5)Pt-Tl(CN)(3)](3)(-) Tl coordinates tetrahedrally with three Tl-C distances at 2.22(2) A. EXAFS data were reevaluated for previously studied mononuclear thallium(III)-cyano complexes in aqueous solution, [Tl(CN)(2)(H(2)O)(4)](+), [Tl(CN)(3)(H(2)O)], and [Tl(CN)(4)](-), and also for the solid K[Tl(CN)(4)] compound. A comparison shows that the Tl-C bond distances are longer in the dinuclear complexes [(NC)(5)Pt-Tl(CN)(n)()](n)()(-) (n = 1-3) for the same coordination number. Relative oxidation states of the metal atoms were estimated from their (195)Pt and (205)Tl chemical shifts, confirming that the [(NC)(5)Pt-Tl(CN)(n)()](n)()(-) complexes can be considered as metastable intermediates in a two-electron-transfer redox reaction from platinum(II) to thallium(III). Vibrational spectra were recorded and force constants from normal-coordinate analyses are used for discussing the delocalized bonding in these species.

Chemical Phenomena↗