Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: UNIPROT:Q86TM3 (cage)
 29,987 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The recent observation [Wentworth, P., Jones, L. H., Wentworth, A. D., Zhu, X. Y., Larsen, N. A., Wilson, I. A., Xu, X., Goddard, W. A., Janda, K. D., Eschenmoser, A. & Lerner, R. A. (2001) Science 293, 1806-1811] that antibodies form H(2)O(2) from (1)O(2) plus H(2)O was explained in terms of the formation of the H(2)O(3) species that in the antibody reacts with a second H(2)O(3) to form H(2)O(2). There have been few reports of the chemistry for forming H(2)O(3), but recently Engdahl and Nelander [Engdahl, A. & Nelander, B. (2002) Science 295, 482-483] reported that photolysis of the ozone-hydrogen peroxide complex in argon matrices leads to significant concentrations of H(2)O(3). We report here the chemical mechanism for this process, determined by using first-principles quantum mechanics. We show that in an argon matrix it is favorable (3.5 kcal/mol barrier) for H(2)O(2) and O(3) to form a [(HO(2))(HO(3))] hydrogen-bonded complex [head-to-tail seven-membered ring (7r)]. In this complex, the barrier for forming H(2)O(3) plus (3)O(2) is only 4.8 kcal/mol, which should be observable by means of thermal processes (not yet reported). Irradiation of the [(HO(2))(HO(3))-7r] complex should break the HO-OO bond of the HO(3) moiety, eliminating (3)O(2) and leading to [(HO(2))(HO)]. This [(HO(2))(HO)] confined in the matrix cage is expected to rearrange to also form H(2)O(3) (observed experimentally). We show that these two processes can be distinguished isotopically. These results (including the predicted vibrational frequencies) suggest strategies for synthesizing H(2)O(3) and characterizing its chemistry. We suggest that the [(HO(2))(HO(3))-7r] complex and H(2)O(3) are involved in biological, atmospheric, and environmental oxidative processes.
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PMID:Peroxone chemistry: formation of H2O3 and ring-(HO2)(HO3) from O3/H2O2. 1243 99

Using Car-Parrinello molecular dynamics a structural diffusion mechanism for the simplest hydrophobic species in water, an H atom, is proposed. The hydrophobic solvation cavity is a highly dynamical aggregate that actually drives, by its own hydrogen-bond fluctuations, the diffusion of the enclosed solute. This makes possible an anomalously fast diffusion that falls only short of that of "Grotthuss structural diffusion" of H+ in water. Here, the picture of a static, i.e., "iceberglike," clathrate cage is a misleading concept. The uncovered scenario is similar to the "dynamical hole mechanism" found in a very different context, that is, large molecules moving in hot polymeric melts.
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PMID:Fast anomalous diffusion of small hydrophobic species in water. 1244 32

We report results from molecular dynamics (MD) simulations and quasielastic neutron-scattering (QENS) measurements on the rotational dynamics of propane in Na-Y zeolite at room temperature with a loading of four molecules per alpha cage. Rotational part of the intermediate scattering function F(Q,t) obtained from the MD simulation suggests that rotational motion is faster relative to the translational motion. Various rotational models fitted to the MD data suggest that rotation is isotropic. It is found that the hydrogen atoms lie, on the average, on a sphere of radius 1.88+/-0.05 A, which is also the average distance of the hydrogen atoms from the center of mass of the propane molecule. Results from QENS measurements are in excellent agreement with those obtained from MD, suggesting that the intermolecular potential employed in the MD simulation provides a realistic description of propane motion within faujasite. The rotational diffusion constant D(R) is 1.05+/-0.09 x 10(12) sec(-1) from the QENS data, which may be compared with that obtained from the MD data (0.82+/-0.05 x 10(12) sec(-1)).
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PMID:Rotational dynamics of propane in Na-Y zeolite: a molecular dynamics and quasielastic neutron-scattering study. 1251 71

A synthetic sequence involving the initial reaction of a substituted phosphorus dihalide (RPCl(2), R = CH(3), C(6)H(5)) with the arachno-CB(8)H(13)(-) (1-) monoanion followed by an in situ dehydrohalogenation reaction initiated by Proton Sponge, resulted in phosphorus cage insertion to yield the first 10-vertex arachno- and nido-phosphamonocarbaboranes, exo-6-R-arachno-6,7-PCB(8)H(12) (2a, 2b) and PSH(+)6-R-nido-6,9-PCB(8)H(9)(-) (PSH+3a-, PSH+3b-) (R = C(6)H(5) (a), CH(3) (b)). Alternatively, 2a and 2b were synthesized in high yield as the sole product of the reaction of the arachno-4-CB(8)H(12)(2-) (1(2-)) dianion with RPCl(2). Crystallographic determinations of PSH+3a- and PSH+3b- in conjunction with DFT/GIAO computational studies of the anions have confirmed the expected nido cage framework based on an octadecahedron missing the six-coordinate vertex. DFT/GIAO computational studies have also shown that while the gross cage geometries of the exo-6-R-arachno-6,7-PCB(8)H(12) compounds 2a and 2b resemble the known isoelectronic arachno-6,9-SCB(8)H(12), the phosphorus and carbon atoms are in thermodynamically unfavorable adjacent positions on the six-membered puckered face. They also each have an endo-hydrogen at the P6-position arising from proton transfer to the basic phosphorus during the cage-insertion reaction. Possible stepwise reaction pathways that can account for the formation of both the arachno and nido products are discussed. Deprotonation of 2a and 2b resulted in the formation of their corresponding conjugate monoanions, 6-R-arachno-6,7-PCB(8)H(11)(-) (2a-, 2b-), in which the proton that had been attached to the P6 atom was removed. Reactions of 2a- with O(2), S(8), BH(3).THF, or Br(2) further demonstrated the basicity of the P6-phosphorus yielding the new arachno-substituted compounds, endo-6-O-exo-6-(C(6)H(5))-arachno-6,7-PCB(8)H(11)(-) (4a-), endo-6-S-exo-6-(C(6)H(5))-arachno-6,7-PCB(8)H(11)(-) (5a-), endo-6-BH(3)-exo-6-(C(6)H(5))-arachno-6,7-PCB(8)H(11)(-) (6a-), and endo-6-Br-exo-6-(C(6)H(5))-arachno-6,7-PCB(8)H(11) (7a), respectively, in which the O, S, BH(3), and Br substituents are bound to the phosphorus at the endo position.
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PMID:Syntheses, crystallographic/computational characterizations, and reactions of the first 10-vertex arachno- and nido-phosphamonocarbaboranes. 1251 23

A homology model of the M(1) muscarinic acetylcholine receptor, based on the X-ray structure of bovine rhodopsin, has been used to interpret the results of scanning and point mutagenesis studies on the receptor's transmembrane (TM) domain. Potential intramolecular interactions that are important for the stability of the protein fold have been identified. The residues contributing to the binding site for the antagonist, N -methyl scopolamine, and the agonist, acetylcholine, have been mapped. The positively charged headgroups of these ligands probably bind in a charge-stabilized aromatic cage formed by amino acid side chains in TM helices TM3, TM6 and TM7, while residues in TM4 may participate as part of a peripheral docking site. Closure of the cage around the headgroup of acetylcholine may be part of the mechanism for transducing binding energy into receptor activation, probably by disrupting a set of Van der Waals interactions between residues lying beneath the binding site that help to constrain the receptor to the inactive state, in the absence of agonist. This may trigger the reorganization of a hydrogen-bonding network between highly conserved residues in the core of the receptor, whose integrity is crucial for achievement of the activated state.
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PMID:Structure and activation of muscarinic acetylcholine receptors. 1254 48

The use of 1,3,5-triaminocyclohexane (tach) as a capping ligand in generating metal-cyanide cage clusters with accessible cavities is demonstrated. The precursor complexes [(tach)M(CN)(3)] (M = Cr, Fe, Co) are synthesized by methods similar to those employed in preparing the analogous 1,4,7-triazacyclononane (tacn) complexes. Along with [(tach)Fe(CN)(3)](1)(-), the latter two species are found to adopt low-spin electron configurations. Assembly reactions between [(tach)M(CN)(3)] (M = Fe, Co) and [M'(H(2)O)(6)](2+) (M' = Ni, Co) in aqueous solution afford the clusters [(tach)(4)(H(2)O)(12)Ni(4)Co(4)(CN)(12)](8+), [(tach)(4)(H(2)O)(12)Co(8)(CN)(12)](8+), and [(tach)(4)(H(2)O)(12)Ni(4)Fe(4)(CN)(12)](8+), each possessing a cubic arrangement of eight metal ions linked through edge-spanning cyanide bridges. This geometry is stabilized by hydrogen-bonding interactions between tach and water ligands through an intervening solvate water molecule or bromide counteranion. The magnetic behavior of the Ni(4)Fe(4) cluster indicates weak ferromagnetic coupling (J = 5.5 cm(-)(1)) between the Ni(II) and Fe(III) centers, leading to an S = 6 ground state. Solutions containing [(tach)Fe(CN)(3)] and a large excess of [Ni(H(2)O)(6)](2+) instead yield a trigonal pyramidal [(tach)(H(2)O)(15)Ni(3)Fe(CN)(3)](6+) cluster, in which even weaker ferromagnetic coupling (J = 1.2 cm(-)(1)) gives rise to an S = (7)/(2) ground state. Paralleling reactions previously performed with [(Me(3)tacn)Cr(CN)(3)], [(tach)Cr(CN)(3)] reacts with [Ni(H(2)O)(6)](2+) in aqueous solution to produce [(tach)(8)Cr(8)Ni(6)(CN)(24)](12+), featuring a structure based on a cube of Cr(III) ions with each face centered by a square planar [Ni(CN)(4)](2)(-) unit. The metal-cyanide cage differs somewhat from that of the analogous Me(3)tacn-ligated cluster, however, in that it is distorted via compression along a body diagonal of the cube. Additionally, the compact tach capping ligands do not hinder access to the sizable interior cavity of the molecule, permitting host-guest chemistry. Mass spectrometry experiments indicate a 1:1 association of the intact cluster with tetrahydrofuran (THF) in aqueous solution, and a crystal structure shows the THF molecule to be suspended in the middle of the cluster cavity. Addition of THF to an aqueous solution containing [(tach)Co(CN)(3)] and [Cu(H(2)O)(6)](2+) templates the formation of a closely related cluster, [(tach)(8)(H(2)O)(6)Cu(6)Co(8)(CN)(24) superset THF](12+), in which paramagnetic Cu(II) ions with square pyramidal coordination are situated on the face-centering sites. Reactions intended to produce the cubic [(tach)(4)(H(2)O)(12)Co(8)(CN)(12)](8+) cluster frequently led to an isomeric two-dimensional framework, [(tach)(H(2)O)(3)Co(2)(CN)(3)](2+), exhibiting mer rather than fac stereochemistry at the [Co(H(2)O)(3)](2+) subunits. Attempts to assemble larger edge-bridged cubic clusters by reacting [(tach)Cr(CN)(3)] with [Ni(cyclam)](2+) (cyclam = 1,4,8,11-tetraazacyclotetradecane) complexes instead generated extended one- or two-dimensional solids. The magnetic properties of one of these solids, two-dimensional [(tach)(2)(cyclam)(3)Ni(3)Cr(2)(CN)(6)]I(2), suggest metamagnetic behavior, with ferromagnetic intralayer coupling and weak antiferromagnetic interactions between layers.
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PMID:High-nuclearity metal-cyanide clusters: synthesis, magnetic properties, and inclusion behavior of open-cage species incorporating [(tach)M(CN)3] (M = Cr, Fe, Co) complexes. 1261 5

The slightly yellow polymeric complexes [Au(2)Cl(2)(P(2)pz)(3)](n), 1 x 6CHCl(3), (P(2)pz is 3,6-bis(diphenylphosphino)pyridazine) and [[Au(2)(P(2)pz)(3)](PF(6))(2)](n), 2, are prepared by the stoichiometric reaction of AuCl(tht) (tht is tetrahydrothiophene) and P(2)pz in either dichloromethane or dichloromethane/methanol, respectively. Addition of 2 equiv of AuCl(tht) to a dichloromethane solution of 1 equiv of P(2)pz generates the simple (AuCl)(2)(P(2)pz) compound, 3. Compound 3 contains nearly linear P-Au-Cl units with intermolecular Au.Au separations of 3.570 A. Au(2)I(2)(P(2)pz)(3), 4, is prepared by reacting excess NaI with 2 in a dichloromethane/methanol mixture. Characterization of 1, 2, and 4 by X-ray crystallography confirms the 2:3 gold/ligand ratio of all three complexes. The coordination polymer 1 maintains a high degree of solvation in the solid-state with three chloroform adducts hydrogen-bonded to the chloride ligand on each gold atom. These chloroform molecules are sandwiched between the two-dimensional polymeric sheets of 1. The crystal structure of 4 reveals an empty, iodide-capped metallocryptand cage with the tetrahedrally distorted gold atoms and the nitrogen atoms on the pyridazine rings directed away from the center of the cavity. No metal ion encapsulation was observed for complex 4. Complex 2 forms one-dimensional arrays of [Au(2)(P(2)pz)(2)](2+) metallomacrocycles connected to each other by a third P(2)pz ligand. The electronic absorption spectra (CH(2)Cl(2)) of 1-4 show broad, nearly featureless absorption bands that tail into the visible with pi-pi bands at 296 nm and discernible shoulders at 314 nm for 2 and 334 nm for 3. Excitation into the low energy band of 2 produces only a modest emission in solution at 540 nm (lambda(ex) 468 nm) and 493 nm (lambda(ex) 403 nm). Under identical conditions, the P(2)pz ligand also emits at 540 and 493 nm.
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PMID:Three- and four-coordinate gold(I) complexes of 3,6-bis(diphenylphosphino)pyridazine: monomers, polymers, and a metallocryptand cage. 1263 53

The stabilities of five water hexamers (cyclic, boat, book, prism and cage structure) in the gas phase were investigated with the independent molecule model. In this model, the position and orientation of each water molecule within the hexamer are characterized with a translational vector and Eulerian angles, and then each molecule can move freely as a rigid body with respect to the others. Force field energy minimization yielded structures for each hexamer. Normal mode analyses were done on the five hexamers. Hydrogen bond strength in the hexamer decreases in the order: boat, cyclic, book, cage and prism. Hydrogen bond lifetimes also decrease in this order. By estimating the internal energy and the vibrational entropy of rigid-body motions, we determined the temperature dependence of the free energy for each hexamer in the range 100-350 K. Free energy of the hexamers increases in the previously mentioned order also. The most stable hexamer is the boat, and the least stable is the prism. The stabilities of the boat and the cyclic are very similar. The more planar hexamers (cyclic and boat) are more stable than the three-dimensional hexamers (cage and prism). Although the experiments of Liu et al. [Nature 381 (1996) 501] were interpreted in terms of a cage cluster, our calculations indicate boat is more likely.
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PMID:Application of the independent molecule model to the calculation of free energy and rigid-body motions of water hexamers. 1267 36

A new crystal form of beta-cyclodextrin (beta-CD)[bond]ethanol[bond]dodecahydrate inclusion complex [(C(6)H(10)O(5))(7).0.3C(2)H(5)OH.12H(2)O] belongs to monoclinic space group C2 (form II) with unit cell constants a=19.292(1), b=24.691(1), c=15.884(1) A, beta=109.35(1) degrees. The beta-CD macrocycle is more circular than that of the complex in space group P2(1) [form I: J. Am. Chem. Soc. 113 (1991) 5676]. In form II, a disordered ethanol molecule (occupancy 0.3) is placed in the upper part of beta-CD cavity (above the O-4 plane) and is sustained by hydrogen bonding to water site W-2. In form I, an ethanol molecule located below the O-4-plane is well ordered because it hydrogen bonds to surrounding O-3[bond]H, O-6[bond]H groups of the symmetry-related beta-CD molecules. In the crystal lattice of form I, beta-CD macrocycles are stacked in a typical herringbone cage structure. By contrast, the packing structure of form II is a head-to-head channel that is stabilized at both O-2/O-3 and O-6 sides of each beta-CD by direct O(CD)...O(CD) and indirect O(CD)...O(W)...(O(W))...O(CD) hydrogen bonds. The 12 water molecules are disordered in 18 positions both inside the channel-like cavity of beta-CD dimer (W-1[bond]W-6) and in the interstices between the beta-CD macrocycles (W-7[bond]W-18). The latter forms a cluster that is hydrogen bonded together and to the neighboring beta-CD O[bond]H groups.
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PMID:A new crystal form of beta-cyclodextrin-ethanol inclusion complex: channel-type structure without long guest molecules. 1286 Apr 29

Two conformationally constrained templates have been designed to provide selective inhibitors of the coagulation cascade serine protease, Factor Xa (FXa). The most active inhibitor, 2,7-bis[(Z)-p-amidinobenzylidene)]-3,3,6,6-tetramethylcycloheptanone, exhibits a K(i) of 42 nM against FXa, with strong selectivity against thrombin (1000-fold), trypsin (300-fold) and plasmin (900-fold). With only two freely rotatable bonds, molecular modeling suggests that one amidine group is positioned into the S1 pocket, forming hydrogen bonds with the side chain of Asp189, similar to other amidine-based inhibitors, with the second benzamidine positioned into the S4 pocket in a position to form strong cation-pi bonding with the S4 aryl cage. We suggest that this interaction plays an important role in the specificity of these inhibitors against other serine proteases.
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PMID:Design and synthesis of highly constrained factor Xa inhibitors: amidine-substituted bis(benzoyl)--diazepan-2-ones and bis(benzylidene)-bis(gem-dimethyl)cycloketones. 1287 32


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