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O Interactions (o + interaction)
Selected AbstractsTheoretical studies on high-valent manganese porphyrins: Toward a deeper understanding of the energetics, electron distributions, and structural features of the reactive intermediates of enzymatic and synthetic manganese-catalyzed oxidative processesISRAEL JOURNAL OF CHEMISTRY, Issue 1 2000Abhik Ghosh We present here a relatively comprehensive theoretical study, based on nonlocal density functional theory calculations, of the energetics, electron distributions, and structural features of the low-lying electronic states of various high-valent intermediates of manganese porphyrins. Two classes of molecules have been examined: (a) compounds with the general formula [(P)MnX2]0 (P = porphyrin; X = F, Cl, PF6) and (b) high-valent manganese-oxo species. For [(P)Mn(PF6)2]0, the calculations reveal a number of nearly equienergetic quartet and sextet states as the lowest states, consistent with experimental results on a comparable species, [(TMP)Mn(ClO4)2]0 (TMP = tetramesitylporphyrin). In contrast, [(P)MnCl2]0 and [(P)MnF2]0 have a single well-defined S = 3/2 Mn(IV) ground state, again in agreement with experiment, with the three unpaired spins largely concentrated (>90%) on the manganese atom. Manganese(IV)-oxo porphyrins have an S = 3/2 ground state, with the three unpaired spins distributed approximately 2.3:0.7 between the manganese and oxygen atoms. The metal-to-oxygen spin delocalization, as measured by the oxygen spin population, for MnIV = O porphyrins is less than, but still qualitatively similar to, that in analogous iron(IV)-oxo intermediates, indicating that the MnIV = O bond is significantly weaker than the FeIV = O bond in an analogous molecule. Thus, the optimized metal,oxygen bond distances are 1.654 and 1.674 Å for (P)FeIV(O)(Py) and (P)MnIV(O)(Py), respectively (Py = pyridine). This is consistent with the experimental observation that MnIV = O stretching frequencies are over 10% lower than FeIV = O stretching frequencies for analogous compounds. For [(P)Mn(O)(PF6)]0, [(P)Mn(O)(Py)]+, and [(P)Mn(O)(F)]0, the ground states clearly correspond to a (dxy)2 Mn(V) configuration and the short Mn,O distances of 1.541, 1.546, and 1.561 Å for the three compounds, respectively, reflect the formal triple bond character of the Mn,O interaction. Interestingly, the corresponding Mn(IV)-oxo porphyrin cation radical states are calculated to be a few tenths of an electrovolt higher than the Mn(V) ground states, suggesting that the Mn(IV)-oxo porphyrin cation radicals are not likely to exist as ground-state species. [source] Electron density and energy density view on the atomic interactions in SrTiO3ACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2002Elizabeth A. Zhurova The results of topological analysis of the electron density in an SrTiO3 crystal based on the experimental (at 145,K) and theoretical data are presented and discussed. The features of the electron density lead to the conclusion that the Ti,O interaction is of the partly polar covalent (or intermediate) type. Complicated atomic shapes defined by the zero-flux surfaces in the electron density are revealed. It is found that, in general, they are far from spherical and have very slight asphericity in the close-packed layers. The topological coordination numbers of Sr and Ti are the same as the geometrical numbers, whereas the topological coordination for the O atom (6) differs from the geometrical value (12). The latter results from the specific shape of the Ti-atom basin, which prevents bond-path formation between the O atoms. The analysis of the kinetic and potential energy densities derived from the electron density using the density functional theory formulae revealed the stabilizing crystal-forming role of the O atoms in SrTiO3. Structural homeomorphism between the experimental electron density and the potential and kinetic energy densities is observed. [source] Poly[(N,N -dimethylformamide-,O)(,3 -4,4,-ethylenedibenzoato-,5O,O,:O,:O,,,O,,,)(pyrazino[2,3- f][1,10]phenanthroline-,2N8,N9)lead(II)]ACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2009Qian Qiao In the title PbII coordination polymer, [Pb(C16H10O4)(C14H8N4)(C3H7NO)]n, each PbII atom is eight-coordinated by two chelating N atoms from one pyrazino[2,3- f][1,10]phenanthroline (L) ligand, one dimethylformamide (DMF) O atom and five carboxylate O atoms from three different 4,4,-ethylenedibenzoate (eedb) ligands. The eedb dianions bridge neighbouring PbII centres through four typical Pb,O bonds and one longer Pb,O interaction to form a two-dimensional structure. The C atoms from the L and eedb ligands form C,H...O hydrogen bonds with the O atoms of eedb and DMF ligands, which further stabilize the structure. The title compound is the first PbII coordination polymer incorporating the L ligand. [source] Hydrogen bonds and C,H,O interactions in 2-(2-methylbenzyl)malonic acid at 150,KACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2000Roger E. Gerkin The title compound, C11H12O4, crystallized in the centrosymmetric space group Pbca with one molecule as the asymmetric unit. The two hydrogen bonds have OD,OA distances of 2.667,(2) and 2.628,(2),Å, and O,H,O angles of 179,(2) and 177,(2)°. Each hydrogen bond forms an R(8) cyclic dimer about a center of symmetry. The leading intermolecular C,H,O interaction has an H,O distance of 2.66,Å and a C,H,O angle of 160°. Taken together with the hydrogen bonds, it results in a three-dimensional network of interactions. The structure is compared with that of a close analog, benzylmalonic acid. [source] 3-Acetyl-4-benzoyl-2-methyl-5-phenyl-3,3a-dihydropyrazolo[2,3- c]pyrimidine-7(6H)-thioneACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2000Mehmet Akkurt The molecule of the title compound, C22H19N3O2S, is not planar. The dihedral angle between the two phenyl rings is 27.46,(7)° and in the dihydropyrazolopyrimidine ring the total puckering amplitude QT is 0.526,(3),Å. The structure is stabilized by both intra- and intermolecular C,H,O interaction, and by an intermolecular N,H,S hydrogen bond. [source] A synchrotron radiation study of the one-dimensional complex of sodium with (1S)- N -carboxylato-1-(9-deazaadenin-9-yl)-1,4-dideoxy-1,4-imino- d -ribitol, a member of the 'immucillin' familyACTA CRYSTALLOGRAPHICA SECTION C, Issue 3 2010Graeme J. Gainsford The sodium salt of [immucillin-A,CO2H], (Imm-A), namely catena -poly[[[triaquadisodium(I)](,-aqua)[,-(1S)- N -carboxylato-1-(9-deazaadenin-9-yl)-1,4-dideoxy-1,4-imino- d -ribitol][triaquadisodium(I)][,-(1S)- N -carboxylato-1-(9-deazaadenin-9-yl)-1,4-dideoxy-1,4-imino- d -ribitol]] tetrahydrate], {[Na2(C12H13N4O6)2(H2O)7]·4H2O}n, (I), forms a polymeric chain via Na+,O interactions involving the carboxylate and keto O atoms of two independent Imm-A molecules. Extensive N,O,H...O hydrogen bonding utilizing all water H atoms, including four waters of crystallization, provides crystal packing. The structural definition of this novel compound was made possible through the use of synchrotron radiation utilizing a minute fragment (volume ,2.4 × 10,5,mm,3) on a beamline optimized for protein data collection. A summary of intra-ring conformations for immucillin structures indicates considerable flexibility while retaining similar intra-ring orientations. [source] Diazabicyclo[2.2.2]octane-1,4-diium dichromateACTA CRYSTALLOGRAPHICA SECTION C, Issue 11 2004Zhi-Min Jin The title compound, (C6H14N2)[Cr2O7], consists of a diazabicyclo[2.2.2]octane-1,4-diium cation and a discrete dichromate anion, which are linked in the crystal by N,H,O hydrogen bonds. The cation is ordered and distorted, owing to the confinement and twist of the hydrogen bonds involved. Two CrO4 tetrahedra are joined through a shared O atom to form the dichromate anion. Chiral supramolecular chains of the title compound are built up via N,H,O hydrogen bonds, and C,H,O interactions play subordinate roles in forming the structure. [source] Ethyl 2-amino-4- tert -butyl-1,3-thiazole-5-carboxylate and 6-methylimidazo[2,1- b]thiazole,2-amino-1,3-thiazole (1/1)ACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2004Daniel E. Lynch The structure of ethyl 2-amino-4- tert -butyl-1,3-thiazole-5-carboxylate, C10H16N2O2S, (I), and the structure of the 1:1 adduct 6-methylimidazo[2,1- b]thiazole,2-amino-1,3-thiazole (1/1), C6H6N2S·C3H4N2S, (II), have been determined. The molecules in (I) associate via a hydrogen-bonded R(8) dimer consisting of N,H,N interactions, with the hydrogen-bonding array additionally involving N,H,O interactions to one of the carboxylate O atoms. The 2-aminothiazole molecules in (II) also associate via an N,H,N hydrogen-bonded R(8) dimer, with an additional N,H,N interaction to the Nsp2 atom of the imidazothiazole moiety, creating hydrogen-bonded quartets. [source] Hydrogen-bonded chains of rings in 3-iodobenzaldehyde 2,4-dinitrophenylhydrazone and 4-iodobenzaldehyde 2,4-dinitrophenylhydrazone, and a three-dimensional framework in 4-iodobenzaldehyde 4-nitrophenylhydrazone generated by the combination of N,H,O and C,H,O hydrogen bonds with iodo,nitro interactionsACTA CRYSTALLOGRAPHICA SECTION C, Issue 1 2004Christopher Glidewell Molecules of 3- and 4-iodobenzaldehyde 2,4-dinitrophenylhydrazone, C13H9IN4O4, are both effectively planar. In the crystal structure of each compound, molecules are linked by a combination of N,H,O and C,H,O hydrogen bonds into complex chains of rings, containing four and three different ring motifs, respectively; neither compound contains any iodo,nitro interactions. In 3-iodobenzaldehyde 4-nitrophenylhydrazone, C13H10IN3O2, where the iodinated aryl ring is disordered over two sets of sites, the hydrogen bonds generate a chain of rings, while two independent I,O interactions generate a three-dimensional framework. [source] 2-(2-Naphthyloxy)acetate derivatives.ACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2003The title compounds, 4-(2-naphthyloxymethylcarbonyl)morpholine, C16H17NO3, (I), and 4-methyl-1-(2-naphthyloxymethylcarbonyl)piperazine, C17H20N2O2, (II), are potential antiamnesics. The morpholine ring in (I) and the piperazine ring in (II) adopt chair conformations. In (I), the molecules are linked by weak intermolecular C,H,O interactions into chains that have a graph-set motif of C(10), while in (II), the molecules are linked by weak intermolecular C,H,O interactions that generate two C(7) graph-set motifs. The dihedral angle between the naphthalene moiety and the best plane through the morpholine ring is 20.62,(4)° in (I), while the naphthalene moiety is oriented nearly perpendicular to the mean plane of the piperazine ring in (II). [source] The fungal metabolite austdiolACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2003Leonardo Lo Presti The title compound, (7R,8S)-7,8-dihydroxy-3,7-dimethyl-6-oxo-7,8-dihydro-6H -isochromene-5-carbaldehyde, C12H12O5, is a trans -vicinal diol. Of the two fused rings, which lie approximately in the same plane, the pyran ring is almost perfectly planar, while the cyclohexenone ring adopts a slightly distorted half-chair conformation. The crystal packing is dictated by two strong intermolecular O,H,O interactions, one involving hydroxy and keto groups, the other involving two hydroxy groups. Molecules are linked together through twofold axes, forming zigzag ribbons extended along the a axis. [source] A cis -stilbene derivativeACTA CRYSTALLOGRAPHICA SECTION C, Issue 3 2003K. SethuSankar The title compound, 4,-methoxy-,,2,3,,4-tetranitrostilbene, C15H10N4O9, crystallizes in the centrosymmetric space group P21/c with one molecule in the asymmetric unit. The phenyl rings are inclined to one another and form a dihedral angle of 57.4,(1)°. The size of this angle is a result of intermolecular C,H,O interactions involving the phenyl H atoms. The torsion angle between the phenyl rings, ,7.5,(3)°, indicates a cis geometry between them. The methoxy group is almost coplanar with the phenyl ring, and the nitro groups are twisted with respect to the phenyl rings because of the short H,O contacts. The crystal packing is stabilized by C,H,O hydrogen bonds, and the intermolecular hydrogen bonds form a C(12) graph-set chain running along the [010] direction. [source] The effect of molecular planarity on crystal non-centrosymmetry in benzylidene,aniline derivativesACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2002De-Chun Zhang In the title compound, N -(2-methoxyphenyl)-4-nitrobenzylideneamine, C14H12N2O3, the two phenyl rings make a dihedral angle of 48.0,(2)° and the nitro group is at an angle of 6.5,(1)° with respect to its attached phenyl ring. In the crystal structure, molecules are related as centrosymmetric pairs through ,,, interactions and are further connected through strong C,H,O hydrogen bonds [C,O 3.4259,(17),Å and C,H,O 167°], forming molecular stacks along [100]. These stacks associate further through longer C,H,O interactions, forming two-dimensional networks. In the c direction, there are only weak van der Waals interactions. The relationship between the molecular planarity and its centrosymmetry is also briefly described. [source] 9-Cyano-10-methylacridinium hydrogen dinitrateACTA CRYSTALLOGRAPHICA SECTION C, Issue 5 2002Olexyj M. Huta The title compound, C15H11N2+·HN2O6,, crystallizes in the monoclinic space group C2/c with four molecules in the unit cell. The planar 9-cyano-10-methylacridinium cations lie on crystallographic twofold axes and are arranged in layers, almost perpendicular to the ac plane, in such a way that neighbouring molecules are positioned in a `head-to-tail' manner. These cations and the hydrogen dinitrate anions are linked through C,H,O interactions involving four of the six O atoms of the anion and the H atoms attached to the C atoms of the acridine moiety in ring positions 2 and 4. The H atom of the hydrogen dinitrate anion appears to be located on the centre of inversion relating two of the four O atoms engaged in the above-mentioned C,H,O interactions. In this way, columns of either anions or cations running along the c axis are held in place by the network of C,H,O interactions, forming a relatively compact crystal lattice. [source] Hydrogen bonds and C,H,O interactions in 2-(2-methylbenzyl)malonic acid at 150,KACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2000Roger E. Gerkin The title compound, C11H12O4, crystallized in the centrosymmetric space group Pbca with one molecule as the asymmetric unit. The two hydrogen bonds have OD,OA distances of 2.667,(2) and 2.628,(2),Å, and O,H,O angles of 179,(2) and 177,(2)°. Each hydrogen bond forms an R(8) cyclic dimer about a center of symmetry. The leading intermolecular C,H,O interaction has an H,O distance of 2.66,Å and a C,H,O angle of 160°. Taken together with the hydrogen bonds, it results in a three-dimensional network of interactions. The structure is compared with that of a close analog, benzylmalonic acid. [source] Intermolecular hydrogen bonding of the two independent molecules of N -3,5-dinitrobenzoyl- l -leucineACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2000John F. Gallagher The title compound, C13H15N3O7, crystallizes as two independent molecules which differ in their conformation. Intermolecular hydrogen bonding between the amide and carboxylic acid groups as N,H,O=C interactions results in the formation of one-dimensional chains with N,O distances of 2.967,(6) and 3.019,(6),Å. Neighbouring chains are linked by C=O,H,O interactions to form a two-dimensional network, with O,O distances of 2.675,(6) and 2.778,(6),Å. [source] DNA Binding by a New Metallointercalator that Contains a Proflavine Group Bearing a Hanging Chelating UnitCHEMISTRY - A EUROPEAN JOURNAL, Issue 1 2008Carla Bazzicalupi Dr. Abstract The new bifunctional molecule 3,6-diamine-9-[6,6-bis(2-aminoethyl)-1,6-diaminohexyl]acridine (D), which is characterised by both an aromatic moiety and a separate metal-complexing polyamine centre, has been synthesised. The characteristics of D and its ZnII complex ([ZnD]) (protonation and metal-complexing constants, optical properties and self-aggregation phenomena) have been analysed by means of NMR spectroscopy, potentiometric, spectrophotometric and spectrofluorimetric techniques. The equilibria and kinetics of the binding process of D and [ZnD] to calf thymus DNA have been investigated at I=0.11,M (NaCl) and 298.1,K by using spectroscopic methods and the stopped-flow technique. Static measurements show biphasic behaviour for both D,DNA and [ZnD],DNA systems; this reveals the occurrence of two different binding processes depending on the polymer-to-dye molar ratio (P/D). The binding mode that occurs at low P/D values is interpreted in terms of external binding with a notable contribution from the polyamine residue. The binding mode at high P/D values corresponds to intercalation of the proflavine residue. Stopped-flow, circular dichroism and supercoiled-DNA unwinding experiments corroborate the proposed mechanism. Molecular-modelling studies support the intercalative process and evidence the influence of NH+,,,O interactions between the protonated acridine nitrogen atom and the oxygen atoms of the polyanion; these interactions play a key role in determining the conformation of DNA adducts. [source] A Mechanically Interlocked BundleCHEMISTRY - A EUROPEAN JOURNAL, Issue 8 2004Jovica D. Badji Abstract The prototype of an artificial molecular machine consisting of a trisammonium tricationic component interlocked with a tris(crown ether) component to form a molecular bundle with averaged C3v symmetry has been designed and synthesized. The system is based on noncovalent interactions, which include 1) N+H,,,O hydrogen bonds; 2) CH,,,O interactions between the CH2NH2+CH2 protons on three dibenzylammonium-ion-containing arms, which are attached symmetrically to a benzenoid core, and three dibenzo[24]crown-8 macrorings fused onto a triphenylene core; and 3) ,,,,, stacking interactions between the aromatic cores. The template-directed synthesis of the mechanically interlocked, triply threaded bundle involves post- assembly covalent modification, that is, the efficient conversion of three azide functions at the ends of the arms of the bound and threaded trication into bulky triazole stoppers, after 1,3-dipolar cycloaddition with di- tert -butylacetylenedicarboxylate to the extremely strong 1:1 adduct that is formed in dichloromethane/acetonitrile (3:2), on account of a cluster effect associated with the paucivalent adduct. Evidence for the averaged C3v symmetry of the molecular bundle comes from absorption and luminescence data, as well as from electrochemical experiments, 1H NMR spectroscopy, and mass spectrometry. The photophysical properties of the mechanically interlocked bundle are very similar to those of the superbundle that precedes the formation of the bundle in the process of supramolecular assistance to covalent synthesis. Although weak non-nucleophilic bases (e.g., nBu3N and iPr2NEt) fail to deprotonate the bundle, the strong tBuOK does, as indicated by both luminescence and 1H NMR spectroscopy. While deprotonation undoubtedly loosens up the interlocked structure of the molecular bundle by replacing relatively strong N+H,,,O hydrogen bonds by much weaker NH,,,O ones, the ,,,,, stacking interactions ensure that any structural changes are inconsequential, particularly when the temperature of the solution of the neutral molecular bundle in dichloromethane is cooled down to considerably below room temperature. [source] RGS7 Is Palmitoylated and Exists as Biochemically Distinct FormsJOURNAL OF NEUROCHEMISTRY, Issue 5 2000Jeremy J. Rose Abstract:Regulator of G protein signaling (RGS) proteins are GTPase-activating proteins that modulate neurotransmitter and G protein signaling. RGS7 and its binding partners G, and G,5 are enriched in brain, but biochemical mechanisms governing RGS7/G,/G,5 interactions and membrane association are poorly defined. We report that RGS7 exists as one cytosolic and three biochemically distinct membrane-bound fractions (salt-extractable, detergent-extractable, and detergent-insensitive) in brain. To define factors that determine RGS7 membrane attachment, we examined the biochemical properties of recombinant RGS7 and G,5 synthesized in Spodoptera frugiperda insect cells. We have found that membrane-bound but not cytosolic RGS7 is covalently modified by the fatty acid palmitate. G,5 is not palmitoylated. Both unmodified (cytosolic) and palmitoylated (membrane-derived) forms of RGS7, when complexed with G,5, are equally effective stimulators of G,o GTPase activity, suggesting that palmitoylation does not prevent RGS7/G,o interactions. The isolated core RGS domain of RGS7 selectively binds activated G,i/o in brain extracts and is an effective stimulator of both G,o and G,i1 GTPase activities in vitro. In contrast, the RGS7/G,5 complex selectively interacts with G,o only, suggesting that features outside the RGS domain and/or G,5 association dictate RGS7-G, interactions. These findings define previously unrecognized biochemical properties of RGS7, including the first demonstration that RGS7 is palmitoylated. [source] | ||||||||||||||||||||||