Intermolecular Coordination Bonds Research Articles

Quantum Chemical Simulation of the Qy Absorption Spectrum of Zn Chlorin Aggregates for Artificial Photosynthesis.

Zn chlorin (Znchl) is easy to synthesize and has similar optical properties to those of bacteriochlorophyll c in the nature, which is expected to be used as a light-harvesting antenna system in artificial photosynthesis. In order to further explore the optical characteristics of Znchl, various sizes of a parallel layered Znchl-aggregate model and the THF-Znchl explicit solvent monomer model were constructed in this study, and their excited state properties were simulated by using time-dependent density functional theory (TDDFT) and exciton theory. For the Znchl monomer, with a combination of the explicit solvent model and the implicit solvation model based on density (SMD), the calculated excitation energy agreed very well with the experimental one. The Znchl aggregates may be simplified to a Zn36 model to reproduce the experimental absorption spectrum by the Förster coupling theory. The proposed Znchl aggregate model provides a good foundation for the future exploration of other properties of Znchl and simulations of artificial light-harvesting antennas. The results also indicate that J-aggregrates along z-direction, due to intermolecular coordination bonds, are the dominant factor in extending the band of Znchl into the near infrared region.

Reticular synthesis of porous molecular 1D nanotubes and 3D networks.

Synthetic control over pore size and pore connectivity is the crowning achievement for porous metal-organic frameworks (MOFs). The same level of control has not been achieved for molecular crystals, which are not defined by strong, directional intermolecular coordination bonds. Hence, molecular crystallization is inherently less controllable than framework crystallization, and there are fewer examples of 'reticular synthesis', in which multiple building blocks can be assembled according to a common assembly motif. Here we apply a chiral recognition strategy to a new family of tubular covalent cages to create both 1D porous nanotubes and 3D diamondoid pillared porous networks. The diamondoid networks are analogous to MOFs prepared from tetrahedral metal nodes and linear ditopic organic linkers. The crystal structures can be rationalized by computational lattice-energy searches, which provide an in silico screening method to evaluate candidate molecular building blocks. These results are a blueprint for applying the 'node and strut' principles of reticular synthesis to molecular crystals.

Reversible transformation between ionic liquids and coordination polymers by application of light and heat.

Reversible transformation between an ionic liquid and a coordination polymer by application of light and heat has been achieved. Ultraviolet light irradiation transforms the transparent liquid to a yellow solid; a reverse reaction occurs due to the application of heat. The transformation accompanies drastic switching of intra- and intermolecular coordination bonds of a ruthenium complex. This is a novel material conversion methodology that connects the fields of ionic liquids and coordination polymers.

A pentanuclear lead(II) complex based on a strapped porphyrin with three different coordination modes.

We have previously described Pb(II) and Bi(III) bimetallic complexes with overhanging carboxylic acid strapped porphyrins in which one metal ion is bound to the N-core ("out-of-plane", OOP), whereas the second one is bound to the strap ("hanging-atop", HAT). In such complexes, the hemidirected coordination sphere of a HAT Pb(II) cation provides sufficient space for an additional binding of a neutral ligand (e.g., DMSO). Interestingly, investigations of the HAT metal coordination mode in a single strap porphyrin show that a HAT Pb(II) can also interact via intermolecular coordination bonds, allowing the self-assembly of two bimetallic complexes. In the pentanuclear Pb(II) complex we are describing in this Article, three different coordination modes were found. The OOP Pb(II) remains inert toward the supramolecular assembling process, whereas the HAT Pb(II) cation, in addition to its intramolecular carboxylate and regular exogenous acetate groups, coordinates an additional exogenous acetate. These two acetates are shared with a third lead(II) cation featuring a holo-directed coordination sphere, from which a centro-symmetric complex is assembled. Density functional theory calculations show some electron-density pockets in the vicinity of the hemidirected HAT Pb(II) atoms, which are associated with the presence of a stereochemically active lone pair of electrons. On the basis of the comparison with other HAT Pb(II) and Bi(III) systems, the "volume" of this lone pair correlates well with the bond distance distributions and the number of the proximal oxygen atoms tethered to the post-transition metal cation. It thus follows the order 6-coordinate Bi(III) > 6-coordinate Pb(II) > 5-coordinate Pb(II).

Influence of intermolecular contacts on the structure of recombinant prolidase from Thermococcus sibiricus.

Prolidases are peptidases that are specific for dipeptides with proline as the second residue. The structure of recombinant prolidase from the hyperthermophilic archaeon Thermococcus sibiricus (Tsprol) was determined at 2.6 Å resolution. The homodimer of Tsprol is characterized by a complete lack of interactions between the N- and C-terminal domains of the two subunits and hence can be considered to be the most open structure when compared with previously structurally studied prolidases. This structure exists owing to intermolecular coordination bonds between cadmium ions derived from the crystallization solution and histidine residues of a His tag and aspartate and glutamate residues, which link the dimers to each other. This linking leads to the formation of a crystal with a loose packing of protein molecules and low resistance to mechanical influence and temperature increase.

Crystal structure of N-(3-hydroxypropyl)-β-alanine and Bis(N-(3-hydroxypropyl)-β-alaninato)dicopper(II) [Cu2 (Pro-ala)2

N-(3-Hydroxypropyl)-β-alanine was synthesized by the reacti on of 3-aminopropanol with acrylic acid. From this ligand and basic copper carbonate, bis(N-(3-hydroxypropyl)-β-alaninato)dicopper(II) [Cu2 (C6H11NO3)2] was obtained. The structures of the chelating agent and the copper complex were studied by X-ray diffraction. The Cu(II) coordination polyhedron is a distorted square pyramid. Each ligand forms six-membered β-alaninate and propanolamine chelate rings. The propoxy group functions as a bridge. In the crystal structure, the molecules form intermolecular coordination bonds C=O→Cu, which are perpendicular to the layers. The EPR signal typical of dimeric copper complexes is not observed due to low occupancy of the excited paramagnetic triplet state. The weak paramagnetic signal from monomeric copper complex allowed recording of the 1H NMR spectrum of [Cu2 (Pro-ala) 2] with characteristic line broadening and contact shift. It follows from the obtained data that on dissolution, the complex dissociates by 40% to give monomeric copper complexes.

The effect of selfassociation of mercurated carbonyl compounds of mercury-199 chemical shifts

Temperature and concentration dependences of mercury-199 chemical shifts in benzene solutions of bis(methylethylketone)mercury Hg(CH 2COC 2H 5) (I) and α-bis(methylacetoacetone)mercury Hg(CH 2COCH 2COOCH 3) 2 (II) are determined by the 1H-{ 199Hg}method. The NMR data obtained and the IR spectra are indicative of selfassociation of I and II in solution with the formation of weak intermolecular coordination bonds Hg ← :OC. The enthalpies of complex formation calculated on the assumption of one mercury atom bonding with only one carbonyl function are equal to −3.2 ± 0.1 kcal/mol and −2.2 ± 0.1 kcal/mol for I and II, respectively.

Solid-state chemistry of organic polyvalent iodine compounds. I. The crystal structures of two polymorphs of 1-(2′-iodobenzoyloxy)-1,2-benziodoxolin-3-one

Solid-state reactions involving organic polyvalent iodine compounds frequently result in the formation of preferentially oriented single-crystal product phases (topotaxy). Geometrical comparisons of the mutually oriented reactant and product crystal structures may define the extent of molecular motions, and suggest geometrical mechanisms of transformation. The crystal structures of two monoclinic polymorphs (α and β) of 1-(2′-iodobenzoyloxy)-1,2-benziodoxolin-3-one are reported in this first in a series of papers describing the crystallography of the transformations. The α crystal structure is formed directly in the three-dimensionally ordered topotactic transformation of the isomeric bis-(orthoiodobenzoyl) peroxide crystal structure, and further is hydrolytically transformed to the single crystal phase of 2-iodobenzoic acid. The asymmetric unit of the acicular α form ( a = 4.21, b = 30.86, c = 22.52 Å, β = 93.3°, Cc, Z = 8) consists of two independent molecules which are mutually associated through two strong IO intermolecular coordination bonds across a pseudo inversion center. In both molecules, the monovalent 2′-iodo substituent and the carbonyl oxygen atom of the adjacent carboxyl group are oriented in an unusual transoid relationship as a consequence of the mutual coordination bonds. By contrast, the configuration of these atoms is cisoid in the prismatic β crystal structure ( a = 8.03, b = 12.58, c = 13.74 Å, β = 92.6°, P2 1 c , Z = 4 ), which moreover does not contain the common IO coordination bonds. However, closely analogous coordination bonds are indicated between the monovalent and trivalent iodine atoms in the β form. A sluggish polymorphic transformation (single crystal → polycrystal) of the α structure to the β structure occurs at ∼110°C.

On the quadrupole-coupling constants of halogen atoms in methylmercury halides

A comparison of the crystal structure of MeHgCl with the quadrupole-coupling constants of halogens in MeHgHal (Hal = Cl,Br,I) in the vapour and the solid phase shows that mercury and halogen atoms are bonded by intermolecular co-ordination bonds.

The initiation of propylene sulphide polymerization by ammonia—Zinc carbonate

Propylene sulphide and aqueous ammonia in dimethyl formamide solution react slowly to give a thiol which initiates polymerization to give low molecular weight polymer. The rate of this reaction has been measured, and an approximate estimate of the composite propagation velocity constant has been made.Added zinc carbonate does not affect the rate of formation of thiol significantly but dissolves to give zinc thiolates, which initiate polymerization less rapidly and so give lower molecular weight polymer.Polymer obtained in the presence of excess zinc carbonate, although of low molecular weight, is a soft elastomer, because of intermolecular coordination bonds between zinc atoms and terminal amino groups in the polymer. These bonds can be destroyed by the addition of a stronger donor or by treatment with acid.