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Molecular Complexes (molecular + complex)
Selected AbstractsSynthesis, Crystal Structure, and Optical Properties of a New Molecular Complex of C60 with a Covalently Linked (FeIIITPP)2O DimerEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 21 2003Aleksey L. Litvinov Abstract A new molecular complex of C60 with covalently linked ,-oxo dimer (FeIIITPP)2O are (TPP = tetraphenylporphyrin) was obtained. The complex has a neutral ground state and is formed mainly by van der Waals forces. The X-ray analysis of the crystal structure of the complex showed it to have isolated packing of fullerenes in which each fullerene molecule is embraced in a pocket built by porphyrins. Optical properties and EPR behavior of the complex are described. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] "Hot" Surface Activation of Molecular Complexes: Insight from Modeling Studies,ANGEWANDTE CHEMIE, Issue 11 2010Ettore Fois Prof. Tanz auf dem Vulkan: Das Modellieren der ersten Aktivierungsstufen eines Cu-Komplexes (siehe Bild; Cu gelb, O rot, N blau, F grün, C grau, H weiß, Si schwarz) auf einer beheizten Oberfläche (750,K) enthüllte zwei Bewegungsarten: eine langsame Diffusion durch ,Anstoßen und Taumeln" und eine schnelle Rollbewegung, die mit deutlichen temperaturinduzierten Bindungsoszillationen einhergeht. Diese Befunde geben einen Einblick in die Prozesse bei der Aktivierung durch ,heiße" Oberflächen. [source] Periodicity in proton conduction along a H-bonded chain.INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2008Application to biomolecules Abstract Molecular complexes are constructed to simulate proton transfer channels of the influenza A virus and of the active site of carbonic anhydrase. These complexes consist of proton donor and acceptor groups connected by a chain of water molecules. Quantum chemical calculations on the methylimidazole(H+)H2OCH3COO, model of the M2 virus channel indicate free translational motion of the water molecule between donor and acceptor, as well as concerted transfer of both H-bond protons. The proton transfer barrier does not depend on the position of the bridged water molecule and varies linearly with the difference of electrostatic potentials between the donor and acceptor. When the water chain is elongated, and with various donor and acceptor models, periodicity appears in the H-bond lengths and the progression of proton transfer in each link. This "wave" is shown to propagate along the chain, as it is driven by the displacement of a single proton. One can thereby estimate the velocity of the proton wave and proton conduction time. Computations are performed to examine the influence of immersing the system within a polarizable medium. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Repulsive guidance molecule/neogenin: a novel ligand-receptor system playing multiple roles in neural developmentDEVELOPMENT GROWTH & DIFFERENTIATION, Issue 6 2004Eiji Matsunaga The repulsive guidance molecule (RGM) is a membrane-bound protein originally isolated as an axon guidance molecule in the visual system. Recently, the transmembrane protein, neogenin, has been identified as the RGM receptor. In vitro analysis with retinal explants showed that RGM repels temporal retinal axons and collapses their growth cones through neogenin-mediated signaling. However, RGM and neogenin are also broadly expressed at the early embryonic stage, suggesting that they do not only control the guidance of visual axons. Gene expression perturbation experiments in chick embryos showed that neogenin induces cell death, and its ligand, RGM, blocks the pro-apoptotic activity of neogenin. Thus, RGM/neogenin is a novel dependence ligand/receptor couple as well as an axon guidance molecular complex. [source] Synthesis and Structural Characterisation of Palladium and Group-12 Metal Complexes with a Hybrid Phosphanylphosphonate Ferrocene LigandEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 5 2006Abstract Diethyl [1,-(diphenylphosphanyl)ferrocenyl]phosphonate (1) was synthesised by stepwise metallation/functionalisation of 1,1,-dibromoferrocene and studied as a ligand for palladium(II) and group-12 metals. Treatment of [PdCl2(cod)] (cod = ,2:,2 -cycloocta-1,5-diene) with 1 in 1:1 or 1:2 molar ratios gave, respectively, the dinuclear, chloride-bridged complex [{Pd(,-Cl)Cl(1 -,P2)}2] (2) and the mononuclear complex trans -[PdCl2(1 -,P2)2] (3), where 1 coordinates exclusively through the phosphane function. The reactions between 1 and group-12 metal bromides MBr2 in a 1:1 molar ratio gave the adducts [MBr2(1)] [M = Zn (4), Cd (5), and Hg (6)], whose crystal structures change considerably with the metal ion. Thus, whereas 4 is a molecular complex with 1 coordinating as an O1,P2 -chelate, its cadmium(II) analogue is a polymer built up from symmetric {CdBr(,-Br)}2 units interconnected by pairs of O1,P2 -bridging phosphanylphosphonate ligands. Finally, the mercury(II) complex 6 is a halide-bridged dimer, [{Hg(,-Br)Br(1 -,P2)}2]. However, this compound is structurally fluxional in solution (NMR spectra) and, in the crystal, it attains a structure similar to 5 owing to weak interactions between mercury and phosphonate-O1 atoms from adjacent molecules. An isomer to 6, [{HgBr2(1 -,2O1,P2)}2] (7), was isolated from attempted alkylation of 6 and structurally characterised as a dimer, where ligands 1 bridge two {HgBr2} units. All compounds were studied by spectroscopic methods (IR, NMR, mass) and the solid-state structures of 1, 2·,H2O, 3·4,CHCl3, 4, 5, 6·5,C6H6, and 7 have been determined by single-crystal X-ray diffraction. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] Synthesis, Crystal Structure, and Optical Properties of a New Molecular Complex of C60 with a Covalently Linked (FeIIITPP)2O DimerEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 21 2003Aleksey L. Litvinov Abstract A new molecular complex of C60 with covalently linked ,-oxo dimer (FeIIITPP)2O are (TPP = tetraphenylporphyrin) was obtained. The complex has a neutral ground state and is formed mainly by van der Waals forces. The X-ray analysis of the crystal structure of the complex showed it to have isolated packing of fullerenes in which each fullerene molecule is embraced in a pocket built by porphyrins. Optical properties and EPR behavior of the complex are described. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] CAST2: identification and characterization of a protein structurally related to the presynaptic cytomatrix protein CASTGENES TO CELLS, Issue 1 2004Maki Deguchi-Tawarada The cytomatrix at the active zone (CAZ) is thought to define the site of Ca2+ -dependent exocytosis of neurotransmitters. We have recently identified a novel CAZ protein from rat brain which we have named CAST (CAZ-associated structural protein). CAST forms a large molecular complex with other CAZ proteins such as Bassoon, RIM1 and Munc13-1, at least through direct binding to RIM1. Here, we have identified a rat protein that is structurally related to CAST and named it CAST2. Subcellular fractionation analysis of rat brain shows that CAST2 is also tightly associated with the postsynaptic density fraction. Like CAST, CAST2 directly binds RIM1 and forms a hetero-oligomer with CAST. In primary cultured rat hippocampal neurones, CAST2 co-localizes with Bassoon at synapses. Furthermore, immunoelectron microscopy reveals that CAST2 localizes to the vicinity of the presynaptic membrane of synapses in mouse brain. Sequence analysis reveals that CAST2 is a rat orthologue of the human protein ELKS. ELKS has also recently been identified as Rab6IP2 and ERC1. Accordingly, the original CAST is tentatively re-named CAST1. These results indicate that CAST2 is a new component of the CAZ and, together with CAST1, may be involved in the formation of the CAZ structure. [source] Order-disorder enantiotropy, monotropy, and isostructurality in a tetroxoprim-sulfametrole 1:1 molecular complex: Crystallographic and thermal studiesJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 11 2003Mino R. Caira Abstract Two enantiotropic polymorphs of a tetroxoprim (TXP)-sulfametrole (SMTR) 1:1 molecular complex monohydrate and two isostructural TXP-SMTR 1:1 molecular complex solvates with methanol and ethanol were grown and studied by X-ray diffraction and thermal methods (thermogravimetric analysis and differential scanning calorimetry). Interconversion of the polymorphic hydrates is essentially an order/disorder transition involving a substituent on the TXP molecule. These hydrated phases may be described as "nearly isostructural" with the methanol and ethanol solvates. Thermal data for decomposition of the solvates were rationalized on the basis of the location and topologies of solvent crystallographic sites. Solid-state properties of two monotropic polymorphs of the unsolvated TXP-SMTR 1:1 molecular complex were also investigated and the theoretical and experimental phase diagrams of the individual components were assessed. The existence of polymorphic and pseudopolymorphic forms is determined by conformational flexibility of the TXP-SMTR bimolecular complex components, a tendency for molecular disorder in TXP, the ability of the drug complex to form intricate, highly stabilized hydrogen-bonded frameworks, and the competition between nonspecific van der Waals and specific hydrogen bond interactions. © 2003 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 92:2164,2176, 2003 [source] A VANADIUM BROMOPEROXIDASE CATALYZES THE FORMATION OF HIGH-MOLECULAR-WEIGHT COMPLEXES BETWEEN BROWN ALGAL PHENOLIC SUBSTANCES AND ALGINATES,JOURNAL OF PHYCOLOGY, Issue 1 2009Leonardo Tavares Salgado The interaction between phenolic substances (PS) and alginates (ALG) has been suggested to play a role in the structure of the cell walls of brown seaweeds. However, no clear evidence for this interaction was reported. Vanadium bromoperoxidase (VBPO) has been proposed as a possible catalyst for the binding of PS to ALG. In this work, we studied the interaction between PS and ALG from brown algae using size exclusion chromatography (SEC) and optical tweezers microscopy. The analysis by SEC revealed that ALG forms a high-molecular-weight complex with PS. To study the formation of this molecular complex, we investigated the in vitro interaction of purified ALG from Fucus vesiculosus L. with purified PS from Padina gymnospora (Kütz.) Sond., in the presence or absence of VBPO. The interaction between PS and ALG only occurred when VBPO was added, indicating that the enzyme is essential for the binding process. The interaction of these molecules led to a reduction in ALG viscosity. We propose that VBPO promotes the binding of PS molecules to the ALG uronic acids residues, and we also suggest that PS are components of the brown algal cell walls. [source] On the fragmentation pathway of the ionized enol of glycine in the gas phaseRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 8 2001T. Marino Density functional and second-order many body perturbation approaches were used to compute the potential energy surface for the fragmentation of the ionized enol of glycine [H2NCH,=,C(OH)2]+· into water and aminoketene radical cation [H2N-HC,=,CO]+·. Two possible pathways were considered. The potential energy surfaces obtained are very similar and both predict the existence of a molecular complex in which the water is coordinated to the aminoketene moiety in two different fashions with a noticeable binding energy. The fragmentation is kinetically controlled by the step in which the molecular complex is formed from the most stable cation enol of glycine. Our quantum-mechanical data confirm the hypothesis that the ylide ion [H3NCHCOOH]+· is an intermediate in the water loss. Copyright © 2001 John Wiley & Sons, Ltd. [source] Polymorphism in the spin-crossover ferric complexes [(TPA)FeIII(TCC)]PF6ACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2009Eric Collet We have identified two polymorphs of the molecular complex [(TPA)Fe(III)(TCC)]PF6 [TPA = tris(2-pyridylmethyl)amine and TCC = 3,4,5,6-tetrachlorocatecholate dianion]: one is monoclinic and the other is orthorhombic. By lowering the temperature both undergo a thermal spin-crossover between a high-spin (S = 5/2) and a low-spin (S = 1/2) state, which we detected by magnetic, optical and X-ray diffraction measurements. The thermal crossover is only slightly shifted between the polymorphs. Their crystalline structures consist of similar cation layers alternating with PF6 anion layers, packed differently in the two polymorphs. The magnetic and optical properties of the polymorphs are presented. [source] The solid-state 2:1 molecular complex of 1,5:3,7-dimethano-1,3,5,7-benzotetrazonine with hydroquinoneACTA CRYSTALLOGRAPHICA SECTION C, Issue 9 2009Augusto Rivera The title compound, 1,5:3,7-dimethano-1,3,5,7-benzotetrazonine,hydroquinone (2/1), 2C11H14N4·C6H6O2, crystallizes with the hydroquinone molecule located on a center of inversion. In contrast to other hydroquinone,adamanzane adducts, which form extended hydrogen-bonded networks, in the present case, one hydroquinone molecule is linked to two 1,5:3,7-dimethano-1,3,5,7-benzotetrazonine molecules, forming a 2:1 cluster through O,H...N hydrogen bonds. [source] Van der Waals and Polar Intermolecular Contact Distances: Quantifying Supramolecular SynthonsCHEMISTRY - AN ASIAN JOURNAL, Issue 5 2008Parthasarathy Ganguly Prof. Abstract Crystal structures are viewed as being determined by ranges and constraints on interatomic contact distances between neighboring molecules. These distances are considered to arise from environment-dependent atomic sizes, that is, larger sizes for isotropic, van der Waals type contacts and smaller sizes for more-polar, possibly ionic contacts. Although the idea of different, or anisotropic, radii for atoms is not new, we developed a method of obtaining atomic sizes that is based on a theoretical framework. Using different atomic sizes for the same atom in different environments, we were able to rationalize some structural observations and anomalies. For example, benzene with the Pbca structure may be described in terms of two types of C,,,H interactions: a longer contact largely of the van der Waals type, and a shorter, structure-determining type (C,,,,,H,+), which we term "n-polar". Our approach is illustrated with three examples: 1),the equivalence in crystal packing of fluorobenzene, benzonitrile, pyridine N -oxide, and pyridine/HF 1:1 molecular complex, all of which take the not-so-common tetragonal P41212 space group and are practically isomorphous; 2),the similarity of the Pa3 acetylene and Pbca benzene crystal structures; and 3),the equivalence between an increase in pressure and an increase in the "n-polar" contacts in Pbca benzene; in other words, the equivalence between hydrostatic pressure and chemical pressure. In the context of crystal engineering, we describe a method whereby the topological information conveyed in a supramolecular synthon is recast in a more quantitative manner. A particular synthon, and in turn the crystal structure to which it leads, is viable within small ranges of distances of its constituent atoms, and these distances are determined by chemical factors. [source] Theoretical CD spectrum calculations of the crown-ether aralkyl-ammonium salt complex,CHIRALITY, Issue 5 2002Armand Lázár Abstract Rotatory strengths of the ,-(1-naphtyl)-ethylammonium perchlorate (NEA)-phenazino-18-crown-6 ether molecular complex is determined theoretically by the coupled oscillator model and using ab initio random phase approximation (RPA) to describe local excitations on the chromophores. The computational results are compared to the experimental circular dichroism (CD) spectrum published previously. The good qualitative agreement between calculated and measured optical rotatory strengths allows one to assign the CD bands of the complex in a unique manner. Chirality 14:377,385, 2002. © 2002 Wiley-Liss, Inc. [source] Chiral Diphosphite-Modified Rhodium(0) Nanoparticles: Catalyst Reservoir for Styrene HydroformylationEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 22 2008M. Rosa Axet Abstract The organometallic synthesis of rhodium nanoparticles stabilized with diphosphite ligands is described. These nanoparticles were investigated as catalysts in the styrene hydroformylation reaction, and their activity and selectivity were compared with those of similar molecular complexes. NMR spectroscopic studies performed during the course of the catalytic reaction showed that the synthesized nanoparticles are not stable and produce molecular species. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] Lymphoid enhancer factor interacts with GATA-3 and controls its function in T helper type 2 cellsIMMUNOLOGY, Issue 3 2008Mohammad B. Hossain Summary GATA-3 is the master transcription factor for T helper 2 (Th2) cell differentiation and is critical for the expression of Th2 cytokines. Little is known, however, about the nature of the functional molecular complexes of GATA-3. We identified a high-mobility group (HMG)-box type transcription factor, lymphoid enhancer factor 1 (LEF-1), in the GATA-3 complex present in Th2 cells using a Flag-calmodulin-binding peptide (CBP)-tag based proteomics method. The interaction between GATA-3 and LEF-1 was confirmed by co-immunoprecipitation experiments using LEF-1-introduced T-cell lineage TG40 cells. The HMG-box domain of LEF-1 and two zinc finger domains of GATA-3 were found to be important for the physical association. The introduction of LEF-1 into developing Th2 cells resulted in the suppression of Th2 cytokine production. The suppression was significantly lower in the cells into which a HMG-box-deleted LEF-1 mutant was introduced. Moreover, LEF-1 inhibited the binding activity of GATA-3 to the interleukin (IL)-5 promoter. These results suggest that LEF-1 is involved in the GATA-3 complex, while also regulating the GATA-3 function, such as the induction of Th2 cytokine expression via the inhibition of the DNA-binding activity of GATA-3. [source] Quantitative assessment of the effect of basis set superposition error on the electron density of molecular complexes by means of quantum molecular similarity measuresINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 11 2009Pedro Salvador Abstract The Chemical Hamiltonian Approach (CHA) method is applied to obtain Basis Set Superposition Error (BSSE)-free molecular orbitals at the Hartree,Fock (HF) and Density Functional Theory (DFT) levels of theory. To assess qualitatively the effect of the BSSE on the first-order electron density, we had previously applied Bader's analysis of the intermolecular critical points located on the electron density, as well as density difference maps for several hydrogen bonded complexes. In this work, Quantum Molecular Similarity Measures are probed as an alternative avenue to properly quantify the electronic relaxation due to the BSSE removal by means of distance indices between the uncorrected and corrected charge densities. It is shown that BSSE contamination is more important at the DFT level of theory, and in some cases, changes on the topology of the electron density are observed upon BSSE correction. Inclusion of diffuse functions have been found to dramatically decrease the BSSE effect in both geometry and electron density. The CHA method represents a good compromise to obtain accurate results with small basis sets. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Endothelial barriers: from hypothetical pores to membrane proteins*JOURNAL OF ANATOMY, Issue 6 2002J. A. Firth Abstract The anatomical counterpart of the physiologically defined small pore system of capillary endothelia has proved difficult to establish. In non-brain continuous capillaries, the contributions of caveolar and transmembrane pathways are likely to be small and paracellular clefts are probably the dominant routes. Analogy with epithelial paracellular pathways suggests that tight junctions may be the most restrictive elements. However, structural features of tight junction-based models are incompatible with physiological data; it is more likely that the tight junction acts as a shutter limiting the available cleft area. Proposed molecular sieves elsewhere in the paracellular pathway include the glycocalyx and the cadherin-based complexes of the adherens junctions. The molecular architecture of tight junctions and adherens junctions is moderately well defined in terms of molecular species, and there are differences at both sites between the endothelial and epithelial spectra of protein expression. However, definition of the size-restricting pore remains elusive and may require structural biology approaches to the spatial arrangements and interactions of the membrane molecular complexes surrounding the endothelial paracellular clefts. [source] A new method for the gradient-based optimization of molecular complexesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2009Jan Fuhrmann Abstract We present a novel method for the local optimization of molecular complexes. This new approach is especially suited for usage in molecular docking. In molecular modeling, molecules are often described employing a compact representation to reduce the number of degrees of freedom. This compact representation is realized by fixing bond lengths and angles while permitting changes in translation, orientation, and selected dihedral angles. Gradient-based energy minimization of molecular complexes using this representation suffers from well-known singularities arising during the optimization process. We suggest an approach new in the field of structure optimization that allows to employ gradient-based optimization algorithms for such a compact representation. We propose to use exponential mapping to define the molecular orientation which facilitates calculating the orientational gradient. To avoid singularities of this parametrization, the local minimization algorithm is modified to change efficiently the orientational parameters while preserving the molecular orientation, i.e. we perform well-defined jumps on the objective function. Our approach is applicable to continuous, but not necessarily differentiable objective functions. We evaluated our new method by optimizing several ligands with an increasing number of internal degrees of freedom in the presence of large receptors. In comparison to the method of Solis and Wets in the challenging case of a non-differentiable scoring function, our proposed method leads to substantially improved results in all test cases, i.e. we obtain better scores in fewer steps for all complexes. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] On the applicability of multireference second-order perturbation theory to study weak magnetic coupling in molecular complexes,JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2008Núria Queralt Abstract The performance of multiconfigurational second-order perturbation techniques is established for the calculation of small magnetic couplings in heterobinuclear complexes. Whereas CASPT2 gives satisfactory results for relatively strong magnetic couplings, the method shows important deviations from the expected Heisenberg spectrum for couplings smaller than 15,20 cm,1. The standard choice of the zeroth-order CASPT2 Hamiltonian is compared to alternative definitions published in the literature and the stability of the results is tested against increasing level shifts. Furthermore, we compare CASPT2 with an alternative implementation of multiconfigurational perturbation theory, namely NEVPT2 and with variational calculations based on the difference dedicated CI technique. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2003George A. Kaminski Abstract We present an approximation, which allows reduction of computational resources needed to explicitly incorporate electrostatic polarization into molecular simulations utilizing empirical force fields. The proposed method is employed to compute three-body energies of molecular complexes with dipolar electrostatic probes, gas-phase dimerization energies, and pure liquid properties for five systems that are important in biophysical and organic simulations,water, methanol, methylamine, methanethiol, and acetamide. In all the cases, the three-body energies agreed with high level ab initio data within 0.07 kcal/mol, dimerization energies,within 0.43 kcal/mol (except for the special case of the CH3SH), and computed heats of vaporization and densities differed from the experimental results by less than 2%. Moreover, because the presented method allows a significant reduction in computational cost, we were able to carry out the liquid-state calculations with Monte Carlo technique. Comparison with the full-scale point dipole method showed that the computational time was reduced by 3.5 to more than 20 times, depending on the system in hand and on the desired level of the full-scale model accuracy, while the difference in energetic results between the full-scale and the presented approximate model was not great in the most cases. Comparison with the nonpolarizable OPLS-AA force field for all the substances involved and with the polarizable POL3 and q90 models for water and methanol, respectively, demonstrates that the presented technique allows reduction of computational cost with no sacrifice of accuracy. We hope that the proposed method will be of benefit to research employing molecular modeling technique in the biophysical and physical organic chemistry areas. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 267,276, 2003 [source] Activation of large lons in FT-ICR mass spectrometryMASS SPECTROMETRY REVIEWS, Issue 2 2005Julia Laskin Abstract The advent of soft ionization techniques, notably electrospray and laser desorption ionization methods, has enabled the extension of mass spectrometric methods to large molecules and molecular complexes. This both greatly extends the applications of mass spectrometry and makes the activation and dissociation of complex ions an integral part of these applications. This review emphasizes the most promising methods for activation and dissociation of complex ions and presents this discussion in the context of general knowledge of reaction kinetics and dynamics largely established for small ions. We then introduce the characteristic differences associated with the higher number of internal degrees of freedom and high density of states associated with molecular complexity. This is reflected primarily in the kinetics of unimolecular dissociation of complex ions, particularly their slow decay and the higher energy content required to induce decomposition,the kinetic shift (KS). The longer trapping time of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) significantly reduces the KS, which presents several advantages over other methods for the investigation of dissociation of complex molecules. After discussing general principles of reaction dynamics related to collisional activation of ions, we describe conventional ways to achieve single- and multiple-collision activation in FT-ICR MS. Sustained off-resonance irradiation (SORI),the simplest and most robust means of introducing the multiple collision activation process,is discussed in greatest detail. Details of implementation of this technique, required control of experimental parameters, limitations, and examples of very successful application of SORI-CID are described. The advantages of high mass resolving power and the ability to carry out several stages of mass selection and activation intrinsic to FT-ICR MS are demonstrated in several examples. Photodissociation of ions from small molecules can be effected using IR or UV/vis lasers and generally requires tuning lasers to specific wavelengths and/or utilizing high flux, multiphoton excitation to match energy levels in the ion. Photodissociation of complex ions is much easier to accomplish from the basic physics perspective. The quasi-continuum of vibrational states at room temperature makes it very easy to pump relatively large amounts of energy into complex ions and infrared multiphoton dissociation (IRMPD) is a powerful technique for characterizing large ions, particularly biologically relevant molecules. Since both SORI-CID and IRMPD are slow activation methods they have many common characteristics. They are also distinctly different because SORI-CID is intrinsically selective (only ions that have a cyclotron frequency close to the frequency of the excitation field are excited), whereas IRMPD is not (all ions that reside on the optical path of the laser are excited). There are advantages and disadvantages to each technique and in many applications they complement each other. In contrast with these slow activation methods, the less widely appreciated activation method of surface induced dissociation (SID) appears to offer unique advantages because excitation in SID occurs on a sub-picosecond time scale, instantaneously relative to the observation time of any mass spectrometer. Internal energy deposition is quite efficient and readily adjusted by altering the kinetic energy of the impacting ion. The shattering transition,instantaneous decomposition of the ion on the surface,observed at high collision energies enables access to dissociation channels that are not accessible using SORI-CID or IRMPD. Finally, we discuss some approaches for tailoring the surface to achieve particular aims in SID. © 2004 Wiley Periodicals, Inc., Mass Spec Rev 24:135,167, 2005 [source] Molecular aspects on the interaction of protoberberine, benzophenanthridine, and aristolochia group of alkaloids with nucleic acid structures and biological perspectivesMEDICINAL RESEARCH REVIEWS, Issue 5 2007Motilal Maiti Abstract Alkaloids occupy an important position in chemistry and pharmacology. Among the various alkaloids, berberine and coralyne of the protoberberine group, sanguinarine of the benzophenanthridine group, and aristololactam-,- d -glucoside of the aristolochia group have potential to form molecular complexes with nucleic acid structures and have attracted recent attention for their prospective clinical and pharmacological utility. This review highlights (i) the physicochemical properties of these alkaloids under various environmental conditions, (ii) the structure and functional aspects of various forms of deoxyribonucleic acid (DNA) (B-form, Z-form, HL -form, protonated form, and triple helical form) and ribonucleic acid (RNA) (A-form, protonated form, and triple helical form), and (iii) the interaction of these alkaloids with various polymorphic DNA and RNA structures reported by several research groups employing various analytical techniques like absorbance, fluorescence, circular dichroism, and NMR spectroscopy; electrospray ionization mass spectrometry, thermal melting, viscosity, and DNase footprinting as well as molecular modeling and thermodynamic studies to provide detailed binding mechanism at the molecular level for structure,activity relationship. Nucleic acids binding properties of these alkaloids are interpreted in relation to their biological activity. © 2006 Wiley Periodicals, Inc. Med Res Rev, 27, No. 5, 649,695, 2007 [source] The structure of short-lived excited states of molecular complexes by time-resolved X-ray diffractionACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2005Philip Coppens Experimental and computational methods for time-resolved (TR) diffraction now allow the determination of geometry changes on molecular excitation. The first results indicate significant changes in the interatomic distances and molecular shape on photo-excitation, but also a dependence of the induced changes on the molecular environment. Though the use of high-brightness synchrotron sources is essential, it limits the time resolution to the width of the synchrotron pulse which is currently 70,100,ps. The experiments discussed fall into two categories: (i) picosecond powder diffraction experiments on the molecular excitation to a singlet state, and (ii) microsecond experiments on the excited states of inorganic complexes. Both involve reversible processes for which a stroboscopic technique can be applied. [source] Characterization and over-expression of chaperonin t-complex proteins in colorectal cancerTHE JOURNAL OF PATHOLOGY, Issue 3 2006C Coghlin Abstract The chaperonins are key molecular complexes, which are essential in the folding of proteins to produce stable and functionally competent protein conformations. One member of the chaperonin group of proteins is TCP1 (chaperonin containing t-complex polypeptide 1, or CCT), but little is known about this protein in tumours. In this study, we used comparative proteomic analysis to show that t-complex protein subunits TCP1 beta and TCP1 epsilon are over-expressed in colorectal adenocarcinomas. Monoclonal antibodies to these proteins were developed and the expression and cellular localization of these two proteins in colorectal cancer were analysed by immunohistochemistry on a colorectal cancer tissue microarray. In colorectal cancer, TCP1 beta cellular localization was exclusively cytoplasmic, whereas TCP1 epsilon staining was seen in both the nucleus and the cytoplasm. Both cytoplasmic TCP1 beta and cytoplasmic TCP1 epsilon were significantly over-expressed (p < 0.001 for each protein) in primary colorectal cancer and also showed increased expression with advancing Dukes' stage (p = 0.018 for TCP1 beta and p = 0.045 for TCP1 epsilon). A trend was also identified between over-expression of cytoplasmic TCP1 beta and reduced patient survival (p = 0.05). These results show that both TCP1 beta and TCP1 epsilon are over-expressed in colorectal cancer and indicate a role for TCP1 beta and TCP1 epsilon in colorectal cancer progression. Copyright © 2006 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. [source] 3-Nitrophenol,4,4,-bipyridyl N,N,-dioxide (2/1): a DFT study and CSD analysis of DPNO molecular complexesACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2010Rodolfo Moreno-Fuquen The title 2:1 complex of 3-nitrophenol (MNP) and 4,4,-bipyridyl N,N,-dioxide (DPNO), 2C6H5NO3·C10H8N2O2 or 2MNP·DPNO, crystallizes as a centrosymmetric three-component adduct with a dihedral angle of 59.40,(8)° between the planes of the benzene rings of MNP and DPNO (the DPNO moiety lies across a crystallographic inversion centre located at the mid-point of the C,C bond linking its aromatic rings). The complex owes its formation to O,H...O hydrogen bonds [O...O = 2.605,(3),Å]. Molecules are linked by intermolecular C,H...O and C,H...N interactions forming R21(6) and R22(10) rings, and R66(34) and R44(26) macro-rings, all of which are aligned along the [01] direction, and R22(10) and R21(7) rings aligned along the [010] direction. The combination of chains of rings along the [01] and [010] directions generates the three-dimensional structure. A total of 27 systems containing the DNPO molecule and forming molecular complexes of an organic nature were analysed and compared with the structural characteristics of the dioxide reported here. The N,O distance [1.325,(2),Å] depends not only on the interactions involving the O atom at the N,O group, but also on the structural ordering and additional three-dimensional interactions in the crystal structure. A density functional theory (DFT) optimized structure at the B3LYP/6-311G(d,p) level is compared with the molecular structure in the solid state. [source] Intermolecular interactions and molecular geometry in molecular complexes of N,N -dimethylaniline: the 1:1 complex with 1,2,4,5-tetracyanobenzeneACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2000Tor Dahl The partner molecules of N,N -dimethylaniline,1,2,4,5-tetracyanobenzene (1/1), C8H11N·C10H2N4, are stacked alternately in infinite columns. The N atom of the N,N -dimethylaniline molecule has a partially tetrahedral character and the distance between neighbouring molecules in the stack is relatively short on the side where the lone-pair electrons of this atom are located. Molecular-packing analysis of this and three other complexes of N,N -dimethylaniline shows that there is a close relationship between the strength of the intermolecular interaction on this side and the tetrahedral character of the N atom. [source] | |||||||||||||||||||||||||||||||