Jasmina Sabolović

Critical evaluation of empirical force-field models for simulation of plasticity of copper(II) coordination

Abstract The plasticity of the copper(II) coordination sphere was simulated with the empirical force-field (molecular mechanics) method. Altogether five models

Simulation of plasticity of a copper(II) coordination polyhedron with a force field based on coulombic interactions: Conformational analysis of copper(II) chelates with α-amino acids

Abstract In order to simulate the plasticity of the copper(II) coordination sphere with the empirical force-field method (molecular mechanics), a square planar complex was defined as an octahedron consisting of four charges situated in the coordination plane, and two charges above and below the plane. Between these point charges only repulsive coulombic interactions take place besides harmonic bond-stretching interactions with the central atom. The model was parametrized on tetrahedrally distorted bis( l -N, N-dimethylvalinato) copper(II) (1). The obtained force field reproduced angles around copper in both planar and non-planar copper(II)-aminoacidates with r.m.s.-deviation from 0.15 to 3.4°. The enantioselectivity effect [energy difference between Cu( l -ligand)( l -ligand) and Cu( l -ligand) ( d -ligand)] for compound 1 was reproduced within experimental error. The shape of the potential energy surface was analysed using the CuN2O2 “complex”; it yielded cis and trans conformations, but also many “false” minima. The model appears to be reliable for not too great deviations from planarity (15–30° for trans valence angles around copper).

Combined Experimental and Computational Study of cis-trans Isomerism in Bis(L-valinato)copper(II)

Heating of polycrystalline cis aquabis(L-valinato)copper(II) at 90 °C resulted in a dehydrated powder. Recrystallization from aqueous solution of the obtained product yielded anhydrous trans bis(L-valinato)copper(II). The X-ray crystal and molecular structures of trans bis(L-valinato)copper(II) and cis aquabis(L-valinato)copper(II) are presented. Molecular modeling calculations were attempted to resolve factors that influenced the isomerization and crystallization of either the aqua cis- or the anhydrous trans-isomer. Conformational analyses of trans- and cis-isomers were completed in vacuo and in crystal by molecular mechanics, and in aqueous solution by molecular dynamics (MD) simulations using the same force field. Although the conformers with trans-configuration are the most stable in vacuo, those with cis-configuration form more favorable intermolecular interactions. Consequently, both cis- and trans-isomers are predicted to be present in aqueous solution. According to the crystal structure simulations and predictions, cis-isomer requires water molecules to form energetically more stable crystal packings than trans-isomer. The MD modeling of the self-assembly of 16 bis(L-valinato)copper(II) complexes in aqueous solution for the first time predicted the crystallization nucleus formation to proceed from monomers to oligomers by Cu-to-O(carboxylato) and/or N-H···O(carboxylato) weak bonds; these oligomers then bind together via water molecules until they acquire the right positions for noncovalent bonding like in the experimental crystal structures. Fifty-nanosecond MD simulations accomplished for a system consisting of equal numbers of complexes and water molecules at 298 and 370 K suggested complete cis-to-trans transformation at the higher temperature. Prevalence of either cis- or trans-conformers in water upon dissolvation may explain the crystallization results.

Solid-State NMR Study of Paramagnetic Bis(alaninato-κ2N,O)copper(II) and Bis(1-amino(cyclo)alkane-1-carboxylato-κ2N,O)copper(II) Complexes: Reflection of Stereoisomerism and Molecular Mobility in 13C and 2H Fast Magic Angle Spinning Spectra

Solid-state stereochemistry and mobility of paramagnetic copper(II) complexes formed by aliphatic amino acids (l-alanine, d,l-alanine, 1-amino-2-methyl-alanine) and 1-amino(cyclo)alkane-1-carboxylic acids (alkane = propane, butane, pentane, hexane) as bidentate ligands has been studied by (13)C and (2)H solid-state fast magic angle spinning (MAS) NMR spectroscopy. We examined the prospective method to characterize solid-state paramagnetic compounds in a routine way. Both (13)C and (2)H MAS spectra can distinguish d,l and l,l diastereomers of natural and polydeuterated bis([Dn]alaninato)copper(II) (n = 0, 2, 8) complexes with axial and/or equatorial methyl positions (conformations) primarily due to different Fermi-contact (FC) contributions. The three-bond hyperfine couplings clearly show Karplus-like dependence on the torsional angles which turned out to be a useful assignment aid. Density functional theory calculations of the FC term and crystal structures were also used to aid the final assignments. The correlations obtained for bis(alaninato-κ(2)N,O)copper(II) complexes were successfully used to characterize other complexes. The usefulness of the (2)H MAS spectra of the deuterated complexes was underlined. Even the spectra of the easily exchangeable amine protons contained essential stereochemical information. In the case of a dimer structure of bis(1-aminohexane-1-carboxylato-κ(2)N,O)copper(II) both the (13)C and (2)H resolutions were good enough to confirm the presence of the cis and trans forms in the asymmetric unit. With regard to the internal solid-state motions in the crystal lattice, the obtained quadrupolar tensor parameters were similar for the d,l- and l,l-alaninato isomers and also for the cis-trans forms suggesting similar crystal packing effects, static amine deuterons involved in hydrogen bonding, and fast rotating methyl groups.

Distortion potential for molecular mechanics calculation of plasticity of copper(II) coordination: An approximation

Abstract A new, simpler definition is proposed for the distortion coordinate β, defining the empirical potential which was introduced earlier (J. Sabolovic and N. Raos, Polyhedron 1990, 9 , 1277) in order to reproduce the shapes of distorted coordination polyhedra of tetracoordinated copper(II) complexes. A simpler definition of β, proposed in this communication, facilitates its implementation in the programme for conformational analysis. No significant difference in the structure parameters obtained with the old and the new expression for β was observed. The new function also has a slight advantage in reducing the computational time and accelerating the convergence.

The Important Role of the Hydroxyl Group on the Conformational Adaptability in Bis(l-threoninato)copper(II) Compared to Bis(l-allo-threoninato)copper(II): Quantum Chemical Study

Detailed structural properties of physiological bis(amino acidato)copper(II) complexes are generally unknown in solutions. This paper examines how stereochemical differences between the essential amino acid l-threonine and its diastereomer l-allo-threonine, which is rarely present in nature, may affect relative stabilities of bis(l-threoninato)copper(II) and bis(l-allo-threoninato)copper(II) in the gas phase and aqueous solution. These amino acids can bind to Cu(II) via the nitrogen and carboxylato oxygen atoms, the nitrogen and hydroxyl oxygen atoms, and the carboxylato and hydroxyl oxygen atoms. We term these coordination modes G, No, and Oo, respectively. The density functional theory (DFT) calculations with the B3LYP functional of the conformational landscapes for all possible coordination modes of both complexes revealed their very similar stability in the gas phase and in aqueous solution. The conformational analyses resulted in 196 and 267 conformers of isolated copper(II) chelates with l-threonine and l-allo-threonine, respectively. The G-G coordination mode is the most stable, both in the gas phase and aqueous solution. Very similar energy values of the lowest-energy solvated cis and trans G-G conformers in implicitly accounted water medium are in accord with the experimental results that these isomers are present in aqueous solution at physiological pH values. The transition-state structures, activation Gibbs free energies, and reaction rates calculated using DFT/B3LYP and MP2 for the transformations from the most stable cis G-G and trans Oo-G conformers to trans G-G ones for the first time reveal several alternate coordination-mode transformation mechanisms in the copper(II) complexes with amino acids other than glycine. The trans Oo-G conformers are kinetically more stable than cis G-G ones in the gas phase. The only significant difference found between the two complexes is a more suitable position of the hydroxyl group in physiological bis(l-threoninato)copper(II) to form intramolecular hydrogen bonds, which may restrain its conformational space.

The shapes of the copper(II) coordination polyhedra : an attempt at a comparison

Abstract The shape of the coordination polyhedron in seven distorted structures of copper(II) chelates with naturally occurring amino acids and their N-alkylated derivatives was analysed by means of two methods: (1) the coordination polyhedron was described as a vector sum of all (four) bond vectors within the framework of spherical coordinates; (2) the coordination polyhedron was presented within the framework of angles around copper. Copper coordination can be described as being square planar with tetrahedral/pyramidal distortion. A comparison of the crystal and theoretical (molecular mechanics) structures revealed that the best agreement was obtained with the molecular mechanics model based on coulombic interactions in the first coordination sphere.