Hierarchical Self-Assembly of Lactams into Supramolecular CO-Spiked “Sea Urchins” and Then into a Channeled Crystal (original) (raw)
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4_delange_et_al_2017_Struct_Chem.pdf
We have discovered, using developed by us recently FALDI and FAMSEC computational techniques, fundamentally distinct mechanisms of intramolecular red-and blue-shifted H-bond formation that occurred in different conformers of the same molecule (amino-acid β-alanine) involving the same heteroatoms (O-H⋅⋅⋅N and N-H⋅⋅⋅O). Quantitative topological, geometric and energetic data of both H-bonds obtained with well-known QTAIM and IQA methodologies agree with what is known regarding H-bonding in general. However, the FALDI charge and decomposition scheme for calculating in real space 3D conformational deformation densities provided clear evidence that the process of electron density redistribution taking place on the formation of the stronger red-shifted H-bond is fundamentally distinct from the weaker blue-shifted H-bond. Contributions made by atoms of the X-H⋅⋅⋅Y-Z fragment (IUPAC notation) as well as distinct atoms on the H-bond formation were fully explored. The FAMSEC energy decomposition approach showed that the atoms involved in formation of the red-shifted H-bond interact in a fundamentally different fashion, both locally and with the remainder of the molecule, as compared with those of the blue-shifted H-bond. Excellent correlations of trends obtained with QTAIM, IQA, FAMSEC and FALDI techniques were obtained. Commentary regarding IUPAC recommended definition of an H-bond and validity of observed AILs (or bond paths) of the two H-bond kinds is also discussed.
Ibotomba J. of Structural Chem -2013
A new monoclinic Cu(II) salt complex 6 6 2 (C H N) + [Cu(2,6-dipico) 2 ] 2-⋅6H 2 O, (2,6-dipico=pyridine-2,6dicarboxylic acid) is synthesized and characterised by CHN analyses, IR, UV-Vis, magnetic susceptibility measurements, and single crystal X-ray crystallography. The structure contains two pyridine-2,6dicarboxylate species as tridentate ligands with protonated aniline acting as a counter cation and six uncoordinated water molecules. The complex crystallizes in the monoclinic space group C2/c with unit cell parameters a = 20.9393(4) Å, b = 7.94330(10) Å, c = 19.9093(4) Å, V(Å 3) = 2932.32(9), Z = 4. Crystal packing is stabilized by N-H…O, O-H…O intermolecular hydrogen bonds and weak π…π interactions. The water molecules are trapped by a cooperative association of coordination interactions forming water clusters as well as by a hydrogen bond to the Cu (II) complex.
Bioinorg. Chem. Appl. 2010, 618202
N,N'-diethylurea (DEU) was employed as a ligand to form the octahedral complexes [M(DEU) 6 ] 2+ (M=Co, Ni and Zn). Compounds [Co(DEU) 6 ](BF 4 ) 2 (1), [Co(DEU) 6 ](CIO 4 ) 2 (2), [Ni(DEU) 6 ](CIO 4 ) 2 (3), and [Zn(DMU) 6 ](CIO 4 ) 2 (4) have been prepared from the reactions of DEU and the appropriate hydrated metal(II) salts in EtOH in the presence of 2,2dimethoxypropane. Crystal structure determinations demonstrate the existence of [M(DEU) 6 ] 2+ cations and CIO 4 − (in 2-4) or BF 4 − (in 1) counterions. The [M(DEU) 6 ] 2+ cations in the solid state are stabilized by a pseudochelate effect due to the existence of six strong intracationic N-H · · · O (DEU) hydrogen bonds. The [M(DEU) 6 ] 2+ cations and counterions self-assemble to form hydrogen-bonded 2D architectures in 2-4 that conform to the kgd (kagome dual) network, and a 3D hydrogen-bonded rtl (rutile) network in 1. The nature of the resulting supramolecular structures is influenced by the nature of the counter-ion. The complexes were also characterized by vibrational spectroscopy (IR).
Eur. J. Inorg. Chem. 2005, 879
Keywords: Cobalt(ii) cubanes / Dicyanamide complexes / Di-2-pyridyl ketone / Magnetic properties / Manganese (ii) cubanes / Nickel(ii) cubanes The use of di-2-pyridyl ketone [(2-py) 2 CO]/dicyanamide "blend" in cobalt(II), manganese(II) and nickel acetate chemistry has yielded neutral cubane clusters. The preparation of [Mn 4 (O 2 CMe) 2 {N(CN) 2 } 2 {(2-py) 2 C(OH)O} 4 ]·2(2-py) 2 -CO·4H 2 O (1) and [M 4 (O 2 CMe) 2 {N(CN) 2 } 2 {(2-py) 2 C(OH) O} 4 ]·10H 2 O [M = Ni (2), Co (3)] was achieved by the reaction of [M(O 2 CMe) 2 ]·4H 2 O with (2-py) 2 CO and Na[N(CN) 2 ] in MeOH/H 2 O (1:5, v/v) at room temperature. The metal(II)-mediated hydrolysis of (2-py) 2 CO to give the coordinated monoanion of the hydrate gem-diol form involves a nucleophilic attack of H 2 O on the carbonyl group. In the case of the cobalt reaction system, there is a second product. Upon employing an excess of (2-py) 2 CO, long reaction times, reflux conditions and high dilution, slow oxidation of Co II takes place leading to the isolation of the mononuclear cobalt(III) complex [Co{(2-py) 2 C(OH)O} 2 ][N(CN) 2 ]·4H 2 O (4) in yields higher than 70 %. The structures of 1, 2 and 4 have been solved by single-crystal X-ray diffraction studies, while a [a] www.eurjic.org Eur. J. Inorg. Chem. 2005, 879-893 880 1: M = Mn II , n = 2, m = 4 2: M = Ni II , n = 0, m = 10 3: M = Co II , n = 0, m = 10 www.eurjic.org Eur. J. Inorg. Chem. 2005, 879-893 882 distance of 2.289 Å, whereas the two other bonds are shorter (average distance 2.179 Å). The cube deviates from the ideal geometry. The internal cube angles (RO-Mn-OR) at the metal vertices average 79.4°, whereas the comparable Eur.
Bis(benzyl-tri-methyl-ammonium) bis-[(4SR,12SR,18RS,26RS)-4,18,26-trihy-droxy-12-oxido-13,17-dioxahepta-cyclo-[14.10.0.0(3,14).0(4,12).0(6,11).0(18,26).0(19,24)]hexa-cosa-1,3(14),6,8,10,15,19,21,23-nona-ene-5,25-dione] sesquihydrate: dimeric structure formation via O-H-O negative charge-assi...
Acta crystallographica. Section E, Crystallographic communications, 2016
The reaction between bis-ninhydrin resorcinol and benzyl-tri-methyl-ammonium fluoride in ethanol has produced the title compound, 2C10H16N(+)·2C24H13O8 (-)·1.5H2O, which contains a unique centrosymmetric supra-molecular dimeric entity, where two deprotonated ligands are held together via two strong and short [O⋯O = 2.4395 (13) Å] [O-H-O](-) bonds of the type negative charge-assisted hydrogen bonds (-CAHB). The central aromatic rings of the ligands create parallel-displaced π-π stacking at an inter-planar distance of 3.381 (1) Å, which helps stabilize the dimer. In the crystal, two symmetry-related solvent water mol-ecules with a site occupancy of 0.75 are attached to the carbonyl groups of the dimer by weaker O-H⋯O hydrogen bonds, forming chains along [101].
Inorganic Chemistry, 1975
The absolute configuration of A-R-[Co(en)z(N-Me-(S)-alaO)]Iz has been determined by X-ray methods (p41, a = b = 8.878 A, c = 21.398 A. 2 = 4. R I = 5.2%, R ? = 5.5% (for 1472 unique data with I L 3 u (I)) ; the amino acid contains trans methyl groups with the R and S configurations about the N and C centers, respectively; the ethylenediamine chelates adopt 6 and X conformations. Strain energy minimization calculations predict the stability order A-S(R), A-R(S), A-S(S), & R (K) and correctly predict the energy difference between the A-S(R) and A-R(S) isomers (observed 1.0 kcal mol-I; calculated 0.8). The structure of the energy-minimized and crystal A-R(S) cations agree closely. Similar agreement is found between the calculated and observed structures of the AS -[Co(en)2(sar)]2+ (sar = sarcosinato) cation. Calculations predict the stability order S (R) , S(S), K (S) , R (R) for the A-h-RR-[Co(trien)(1V-Me-alaO)]2+ cation and the three isolated isomers6 are assigned. Structures and relative energies of the configurational isomers of A-pz-[Co(trien)(sar)]2+ are discussed.
Polyhedron, 2005
The hexadentate trans(O 5 O 6)-K[Co(1,3-pddadp)] AE 3H 2 O complex (where 1,3-pddadp represents the 1,3-propanediamine-N,N 0diacetate-N,N 0-di-3-propionate ion) has been characterized by single-crystal X-ray crystallography. The complex crystallizes in the P2/c space group of the monoclinic crystal system. In the crystal structure of trans(O 5 O 6)-K[Co(1,3-pddadp)] AE 3H 2 O the potassium ions and two solvent water molecules (O1W and O3W) are settled on a twofold axis of symmetry. The octahedral complex units trans(O 5 O 6)-[Co(1,3-pddadp)] À are bridged by carboxylate oxygen atoms with the potassium ions to build a two-dimensional polymer structure, separated by layers formed by hydrogen bonded water molecules and carboxylate oxygens. The coordination polyhedra around K1 and K2 are found to be distorted square antiprism and twisted bi-capped trigonal prism, respectively. Conformational analysis of the three possible geometrical isomers (trans(O 5), trans(O 5 O 6) and trans(O 6)) of the [Co(1,3-pddadp)] À complex, was performed using the Consistent Force Field (CFF) program, with the parameters developed previously for edta-type complexes and new parameters for Co(III). Molecular mechanics (MM) calculations reproduced very well the crystallographically characterized structures (trans(O 5 O 6)-[Co(1,3-pddadp)] À and trans(O 6)-[Co(1,3-pddadp)] À).