Mapping the domains of molecules and complexes by mass and heavy atom loading.
Explore the source record for details and available documents.
Microscopy, Electron↗
SEARCH · PubMed Health
Results for “ATOM complex”
Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
X-ray structure characterization of palladium(II) ternary complexes of pyridinedicarboxylic and phthalic acid with phenanthroline and bipyridine.
The crystal structures of the series of four ternary complexes, [Pd(phen)(2,6-PDCA)].4H(2)O (1) (phen=1,10-phenanthroline; 2,6-PDCA=2,6-pyridinedicarboxylic acid), [Pd(bpy)(2,3-PDCA)].3H(2)O (2) (bpy=2,2'-bipyridineand; 2,3-PDCA=2,3-pyridinedicarboxylic acid) and [Pd(phen)(PHT)].2.5H(2)O (3) (PHT=o-phthalic acid ) and [Pd(bpy)(PHT)].1.5H(2)O (4), are determined and the coordination modes of palladium(II) ternary complexes are characterized. All complexes take the mononuclear Pd(II) complexes, in which central Pd(II) atom of each complex has a similar distorted square-planar four coordination geometry. In all complexes, the aromatic heterocyclic compounds, phen and bpy, behave as a bidentate N, N' ligand. In the complex 1 and 2, 2,6-PDCA and 2,3-PDCA behave as a bidentate N, O ligand, and in complex 3 and 4, PHT behaves as a bidentate O, O' ligand.
Crystallography, X-Ray↗
Visualization of membrane RNAs.
Using fluorescence microscopy, we show that previously isolated membrane-binding RNAs coat artificial phospholipid membranes relatively uniformly, except for a frequent tendency to concentrate at bends, membrane junctions, and other unusual sites. Membrane RNAs can also be visualized as single molecules or isolated complexes by atomic force microscopy (AFM) of free RNAs on mica. Finally, RNAs can be seen within membranes by AFM of RNA-liposomes immobilized on hydrophobic mica surfaces. Monomer RNAs appear globular, as expected for small RNAs. When mixed under conditions in which RNAs bind bilayers, RNA 9 and RNA 10 combine to yield about 80% of RNAs as mainly linear oligomers of approximately 2-8 molecules. Once inserted in membranes, the RNAs oligomerize further, yielding larger, irregular ropelike structures that prefer the edges of altered lipid patches. These properties can be interpreted in terms of RNA-RNA loop interactions, and the RNA effects on membranes can be explained in terms of an RNA preference for irregular lipid conformations. The RNA-bilayer system poses new opportunities for combining the properties of membranes and RNA in contemporary cells, and also in the ribocytes of an RNA world.
Binding Sites↗
[ALBOMYCIN AND FERRICHROMIUM COMPLEX WITH THE 2ND IRON ATOM].
Explore the source record for details and available documents.
Anti-Bacterial Agents↗
A novel isomerization on interaction of antitumor-active azole-bridged dinuclear platinum(II) complexes with 9-ethylguanine. Platinum(II) atom migration from N2 to N3 on 1,2,3-triazole.
The reactions of the dinuclear platinum(II) complexes, [[cis-Pt(NH(3))(2)](2)(mu-OH)(mu-pz)](NO(3))(2) (1, pz = pyrazolate), [[cis-Pt(NH(3))(2)](2)(mu-OH)(mu-1,2,3-ta-N1,N2)](NO(3))(2) (2, 1,2,3-ta = 1,2,3-triazolate), and a newly prepared [[cis-Pt(NH(3))(2)](2)(mu-OH)(mu-4-phe-1,2,3-ta-N1,N2)](NO(3))(2) (3, 4-phe-1,2,3-ta = 4-phenyl-1,2,3-triazolate), whose crystal structure was determined, with 9-ethylguanine (9EtG) have been monitored in aqueous solution at 310 K by means of (1)H NMR spectroscopy. The dinuclear platinum(II) complexes 1-3 each react with 9EtG in a bifunctional way to form 1:2 complexes, [[cis-Pt(NH(3))(2)(9EtG-N7)](2)(mu-pz)](3+) (4), [[cis-Pt(NH(3))(2)(9EtG-N7)](2)(mu-1,2,3-ta-N1,N3)](3+) (5), and [[cis-Pt(NH(3))(2)(9EtG-N7)](2)(mu-4-phe-1,2,3-ta-N1,N3)](3+) (6). The reactions of 2 and 3 involve a novel isomerization, in which the Pt atom, initially bound to N2 on the 1,2,3-ta, migrates to N3 after the first substitution by N7 of 9EtG. This isomerization reaction has been unambiguously characterized by 1D and 2D NMR spectroscopy and pH titration. The reactions of 2 and 3 with 9EtG show faster kinetics, and the second-order rate constants (k) for the reactions of 1-3are 1.57 x 10(-4), 2.53 x 10(-4), and 2.56 x 10(-4) M(-1) s(-1), respectively. The pK(a) values at the N1H site of 9EtG were determined for 4-6 from the pH titration curves. Cytotoxicity assays of 1-3 were performed in L1210 murine leukemia cell lines, respectively sensitive and resistant to cisplatin. In the parent cell line, 2 and 3 exhibit higher cytotoxicity compared to cisplatin, especially, 2 is 10 times as active as cisplatin. 1 was found to be less cytotoxic than cisplatin, but still in the active range and more active than cisplatin in a cisplatin-resistant cell line.
Animals↗
FAB MS/MS for phosphatidylinositol, -glycerol, -ethanolamine and other complex phospholipids.
Fast atom bombardment (FAB) of phosphatidylinositol, phosphatidylethanolamine, cardiolipin, phosphatidic acid and phosphatidylglycerol produces a limited number of very informative negative ions. Especially significant is the formation of (M-H)-ions and ions that correspond to the carboxylate portions of these molecules. FAB desorption in combination with collisional activation allows for characterization of fragmentation and determination of structural features. Collisional activation of the carboxylate anion from complex lipids is especially informative. Structural characterization of the fatty acids can be achieved as the released saturated carboxylate anions undergo highly specific charge remote fragmentations that are entirely consistent with the chemistry of carboxylate anions desorbed from free fatty acids. This permits both identification of the modification and assignment of its location on the acid chain. FAB-desorbed alkyl acetyl glycerophosphocholines (platelet-activating factor) do not produce (M-H)-ions. However, significant high mass ions are formed, and these can be collisionally activated for structural characterization.
Mass Spectrometry↗
Utilization of colorimetric and atomic absorption spectrometric determination of aztreonam through ion pair complex formation.
Three rapid and sensitive, colorimetric and atomic absorption spectrometric methods were developed for the determination of aztreonam. The proposed methods depend upon the reaction of cobaltthiocyanate (I) or reineckate (II) ions with the drug to form stable ion-pair complexes which extractable with chloroform. The greenish blue and pink color complexes are determined either colorimetrically at lambda(max) 625 and 525 nm for I and II reagents, respectively, or by atomic absorption spectrometry, directly using the organic extracted complex, or indirectly, using the supernatant. The three procedures are applied for the determination of aztreonam in pure and in pharmaceutical dosage forms applying the standard additions technique and the results obtained agreed well with those obtained by the official method.
Aztreonam↗
Infrared spectra and density functional calculations of CH2 = MHX and CH[triple bond]MH2X complexes prepared in reactions of methyl halides with Mo and W atoms.
The simple methylidene and methylidyne complexes (CH2=MHX and CH[triple bond]MH2X; X = F, Cl, Br, and I) are prepared in reactions of laser-ablated Mo and W atoms with the methyl halides and investigated by matrix infrared spectroscopy and density functional theory calculations. These complex structures are photoreversible: visible irradiation converts the methylidene complex to the methylidyne complex, and UV irradiation reverses this effect via alpha-hydrogen migration. While the higher oxidation state complexes are readily formed regardless of halogen size, the Mo methylidyne complex is relatively less favored with increasing halogen size, and the W complex shows the opposite tendency. The group 6 metal methylidenes are predicted to have the most agostically distorted structures among the early transition-metal methylidenes. The computed carbon-metal bond shortens with increasing halogen size for both the methylidene and methylidyne complexes. Harmonic and anharmonic frequencies computed by DFT converge on the experimental values and thus provide support for the identification of these new Mo and W complexes.
Journal Article↗
Noble gas-actinide compounds: evidence for the formation of distinct CUO(Ar)(4-n)(Xe)(n) and CUO(Ar)(4-n)(Kr)(n) (n = 1, 2, 3, 4) complexes.
Laser-ablated U atoms react with CO in excess argon to produce CUO, which gives rise to 852.5 and 804.3 cm-1 infrared absorptions for the triplet state CUO(Ar)n complex in solid argon at 7 K. Relativistic density functional calculations show that the CUO(Ar) complex is stable and that up to four or five argon atoms can complex to CUO. When 1-3% Xe is added to the argon/CO reagent mixture, strong absorptions appear at 848.0 and 801.3 cm-1 and dominate new four-band progressions, which increase on annealing to 35-50 K as Xe replaces Ar in the intimate coordination sphere. Analogous spectra are obtained with 1-2% Kr added. This work provides evidence for eight distinct CUO(Ng)n(Ar)4-n (Ng = Kr, Xe, n = 1, 2, 3, 4) complexes and the first characterization of neutral complexes involving four noble-gas atoms on one metal center.
Journal Article↗
Atomic structures of human dihydrofolate reductase complexed with NADPH and two lipophilic antifolates at 1.09 a and 1.05 a resolution.
The crystal structures of two human dihydrofolate reductase (hDHFR) ternary complexes, each with bound NADPH cofactor and a lipophilic antifolate inhibitor, have been determined at atomic resolution. The potent inhibitors 6-([5-quinolylamino]methyl)-2,4-diamino-5-methylpyrido[2,3-d]pyrimidine (SRI-9439) and (Z)-6-(2-[2,5-dimethoxyphenyl]ethen-1-yl)-2,4-diamino-5-methylpyrido[2,3-d]pyrimidine (SRI-9662) were developed at Southern Research Institute against Toxoplasma gondii DHFR-thymidylate synthase. The 5-deazapteridine ring of each inhibitor adopts an unusual puckered conformation that enables the formation of identical contacts in the active site. Conversely, the quinoline and dimethoxybenzene moieties exhibit distinct binding characteristics that account for the differences in inhibitory activity. In both structures, a salt-bridge is formed between Arg70 in the active site and Glu44 from a symmetry-related molecule in the crystal lattice that mimics the binding of methotrexate to DHFR.
Amino Acid Sequence↗
Movement of the Rieske iron-sulfur protein in the p-side bulk aqueous phase: effect of lumenal viscosity on redox reactions of the cytochrome b6f complex.
Based on the atomic structures of the mitochondrial cytochrome bc(1) complex, it has been proposed that the soluble domain of the [2Fe-2S] Rieske iron-sulfur protein (ISP) must rotate by ca. 60 degrees and translate through an appreciable distance between two binding sites, proximal to cytochrome c(1) and to the lumen-side quinol binding site. Such motional freedom implies that the electron-transfer rate should be affected by the lumenal viscosity. The flash-induced oxidation of cytochrome f, the chloroplast analogue of cytochrome c(1), was found to be inhibited reversibly by increased lumenal viscosity, as was the subsequent reduction of both cytochrome b(6) and cytochrome f. The rates of these three redox reactions correlated inversely with lumenal viscosity over a viscosity range of 1-10 cP. Reduction of cytochrome b(6) and cytochrome f was not concerted. The rate of cytochrome f reduction was observed to be approximately half that of cytochrome b(6) regardless of the actual viscosity, implying that the path length traversed by the ISP in reduction of cytochrome f is twice that of cytochrome b(6). This suggests that upon initiation of electron transfer by a light flash, cytochrome b(6) reduction requires movement of reduced ISP from an initial position predominantly proximal to cytochrome f, apparently favored by the reduced ISP, to the quinol binding site at which the oxidant-induced reduction of cytochrome b(6) is initiated. Subsequent reduction of cytochrome f requires the additional movement of the ISP back to a site proximal to cytochromef. There is no discernible viscosity dependence for cytochrome b(6) reduction under oxidizing conditions, presumably because the oxidized ISP preferentially binds proximal to the quinone binding niche. The dependence of the cytochrome redox reaction on ambient viscosity implies that the tethered diffusional motion of the ISP is part of the rate limitation for charge transfer through the b(6)f complex.
Chloroplasts↗
Foliacenes: ab initio modeling of metallocomplexes exhibiting a unique form of 16-electron, metal-induced aromaticity.
Ab initio calculations predict that the cyclic trefoilenes 2 can be stabilized by formation of a complex 4 with early transition metals. The metal atom within the complex is nested within the carbon ring and is considerably closer to the ring centroid than in traditional metallocene complexes. Stabilization is explained by a unique form of 16-electron delocalization involving the metal atom, for which we suggest the name "foliate aromaticity". The aromaticity of various polyfoliate systems such as 9 suggests this 16-electron motif is more robust than Clar-like aromatic 6pi-sextets. The open hemisphere of the metal in such foliacene complexes is predicted to coordinate a variety of ligands.
Journal Article↗
Noble gas-transition-metal complexes: coordination of VO2 and VO4 by Ar and Xe atoms in solid noble gas matrixes.
The matrix isolation infrared spectroscopic and quantum chemical calculation results indicate that vanadium oxides, VO2 and VO4, coordinate noble gas atoms in forming noble gas complexes. The results showed that VO2 coordinates two Ar or Xe atoms and that VO4 coordinates one Ar or Xe atom in solid noble gas matrixes. Hence, the VO2 and VO4 molecules trapped in solid noble gas matrixes should be regarded as the VO2(Ng)2 and VO4(Ng) (Ng = Ar or Xe) complexes. The total V-Ng binding energies were predicted to be 12.8, 18.2, 5.0, and 7.3 kcal/mol, respectively, for the VO2(Ar)2, VO2(Xe)2, VO4(Ar), and VO4(Xe) complexes at the CCSD(T)//B3LYP level of theory.
Journal Article↗
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes.
MolProbity is a general-purpose web service offering quality validation for three-dimensional (3D) structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules and can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. The results are reported in multiple forms: as overall numeric scores, as lists, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown on-line in the KiNG viewer. This service is available free to all users at http://kinemage.biochem.duke.edu.
Hydrogen Bonding↗
Nuclear pore complex structure and plasticity revealed by electron and atomic force microscopy.
To study the ultrastructure of nuclear pore complexes (NPCs), a wide spectrum of different electron microscopy (EM) or atomic force microscopy (AFM) techniques can be employed. The combination of these methods can reveal new insights into the structural and functional organization of this important supramolecular machine through which nucleocytoplasmic transport occurs. Negative staining, quick freezing/freeze-drying/rotary metal shadowing, embedding and thin sectioning, cryoelectron microscopy and tomography, scanning electron microscopy, or combination with immunolabeling techniques are tools for collecting data and information about the three-dimensional structure and architecture of the NPCs. AFM enables investigation of the functional dynamics of native NPCs under physiological conditions.
Animals↗
DNA bending and unbending by MutS govern mismatch recognition and specificity.
DNA mismatch repair is central to the maintenance of genomic stability. It is initiated by the recognition of base-base mismatches and insertion/deletion loops by the family of MutS proteins. Subsequently, ATP induces a unique conformational change in the MutS-mismatch complex but not in the MutS-homoduplex complex that sets off the cascade of events that leads to repair. To gain insight into the mechanism by which MutS discriminates between mismatch and homoduplex DNA, we have examined the conformations of specific and nonspecific MutS-DNA complexes by using atomic force microscopy. Interestingly, MutS-DNA complexes exhibit a single population of conformations, in which the DNA is bent at homoduplex sites, but two populations of conformations, bent and unbent, at mismatch sites. These results suggest that the specific recognition complex is one in which the DNA is unbent. Combining our results with existing biochemical and crystallographic data leads us to propose that MutS: (i) binds to DNA nonspecifically and bends it in search of a mismatch; (ii) on specific recognition of a mismatch, undergoes a conformational change to an initial recognition complex in which the DNA is kinked, with interactions similar to those in the published crystal structures; and (iii) finally undergoes a further conformational change to the ultimate recognition complex in which the DNA is unbent. Our results provide a structural explanation for the long-standing question of how MutS achieves mismatch repair specificity.
Adenosine Triphosphatases↗
Electronic Structure of Metallacyclophosphazene and Metallacyclothiazene Complexes.
The electronic structure of metallacyclotriphosphazene complexes with several substituents at the phosphorus atoms and metallacyclothiazene complexes is explored for a variety of transition metal elements using density functional theory methods. Accordingly the metallacyclophosphazenes possess a large HOMO-LUMO energy separation while the metallacyclothiazenes bear stronger open-shell character. In addition our calculations predict the existence of experimentally so far unknown dimetallacyclophosphazenes. All structures show to be highly dynamical. The double bond character of the transition metal nitrogen bond is much less pronounced than in nitrido or imido complexes. For the ring compounds vibrational spectra are reported and compared with experimental data.
Journal Article↗
A comprehensive theoretical view of the bonding in actinide molecular complexes.
While usual atomic population methods give a consistent view of trivalent lanthanide or a uranium-ligand bond, the description of the bonding of americium(III), which is a key element for nuclear fuel processes, is a challenge. Neither experimental data nor theoretical calculations have been able so far to evidence covalency effects in the americium-ligand bond. We show herein that the use of more sophisticated methods based on a topological approach (AIM and ELF) gives a consistent view of such an interaction for the first time, showing a weak covalent back-bonding interaction with the CO ligand.
Journal Article↗