Coordination to metal centers: A tool to fix high energy conformations in organic molecules. Application to 2,4,4-trimethyl-1,5,9-triazacyclododec-1-ene and related macrocycles

Abstract

The solid state conformational preferences of ligand 2,4,4-trimethyl-1,5,9-triazacyclododec-1-ene (L1) and its 9-methyl derivative (L2) in transition metal complexes have been determined by a probabilistic method using data retrieved from the Cambridge Structural Database. These macrocyclic compounds, as ligands, tend to adopt a preferential conformation (85% of cases). The ring containing the C=N bond adopts a distorted half-chair conformation, the ring defined by both the N-sp(3) shows a distorted envelope conformation, and the remaining ring exhibits a chair conformation. This conformation corresponds to the enantiomer pair R(N5)S(N9)S(P)/S(N5)R(N9)R(P). Molecular mechanics calculations demonstrate that this is a high energy conformation for the organic molecule, far from the energy minimum. Two other enantiomer pairs are observed in experimental structures. The influence of the coordination on the conformation of the organic ligands has been studied by DFT calculations, and a clear correlation with the geometry of the coordination sphere has been found.

Synthesis, Structural and Thermal Studies of 3-(1-Benzyl-1,2,3,6-tetrahydropyridin-4-yl)-5-ethoxy-1H-indole (D2AAK1_3) as Dopamine D2 Receptor Ligand

“…The tetrahydropyridine ring system adopts a half-chair conformation with an N2 atom above (0.326(2) Å) and a C5 atom below (−0.317(3) Å) the mean plane defined by N2/C5/C4/C3/C14/C13 atoms. This is confirmed by the puckering parameters Q = 0.499(2) Å, θ = 49.6(2)° and = 27.6(4)° [ 28 , 29 , 30 , 31 ]. In the structure, the N1 atom participates in an intramolecular hydrogen bond (N1-H1N···N2 i , [symmetry code: (i) x − 1/2, −y + 1/2, −z + 1]), as shown in Table 3 .…”

Crystal Structures and Spectroscopic and Theoretical Properties of Pentacoordinate Nickel(II) Complexes Containing Tris(pyrazolyl)borate and Quinolinate Ligands

“…Clearly, the solid‐state spectra could be influenced by the crystal lattice, and this must be reflected in the coordination sphere. In this sense, measurement of the distortion of the polyhedron can be useful to correlate structural and energetic features 29. With this purpose, distortion of the coordination polyhedra was evaluated for complexes 2 , 3 , 5 , and 7 by using the SHAPE program 30.…”

Synthesis, Characterization, and Copper(II) Chelates of 1,11-Dithia-4,8-diazacyclotetradecane

“…Coordination of ligands L1 and L3 to copper­(II) does, however, produce noteworthy structural changes. In both [(L1Cu) 2 μ-Cl]­(ClO 4 ) 3 and L1Cu­(ClO4) 2 , the coordination of copper to both sulfur atoms exhibits a low strain chair conformation as compared to the torsion angles of cyclohexane with the connecting five-membered chelate in a favorable equatorial position. However, in the case of L1Cu­(ClO4) 2 , the coordination of copper to nitrogen induces a conformation similar to a distorted envelope …”