Coordination numbers in hydrated Cu(II) ions

Abstract

The potential energy surface of [Cu(HO)] clusters with n = 12, 16, and 18 was explored by using a modified version of the simulated annealing method. Such exploration was carried out by using the PM7 semiempirical method to obtain around 100,000 isomers, which provide candidates to be optimized with PBE0-D3, M06-2X, and BHLYP exchange-correlation functionals coupled with the 6-311++G** basis set. These methods based on the Kohn-Sham approach delivered isomers with coordination numbers of 4, 5, and 6. The analysis used to obtain coordination numbers was based on geometrical parameters and the quantum theory of atoms in molecules (QTAIM) approach. Our methodology found only one isomer with fourfold coordination and its probabilities to appear in these clusters are quite small for high temperatures. The procedure used in this article predicts important populations of fivefold and sixfold coordination clusters, in fact, the fivefold coordination dominates for PBE0-D3 and BHLYP methods, although the sixfold coordination starts to be important when the number of water molecules is increased. The nature of axial and equatorial contacts is discussed in the context of the QTAIM and the noncovalent interaction index (NCI), which gives a clear classification of such orientations. Also, these methods suggest a partial covalent interaction between the Cu and water molecules in both positions; equatorial and axial.

Zinc and Its Critical Role in Retinitis pigmentosa: Insights from DFT/SMD Calculations

“…As pointed out in ref , these two ions exhibit different effects upon binding. Therefore, it was of particular interest to examine their action by modeling the reaction of competition between the native zinc and its alien calcium and copper competitors. On the one side, in the case of Ca 2+ its preference toward forming heptacoordinated complexes in biological systems , was taken into account, as well as its varied composition of aqua complexes (the metal-bound water molecules ranging from 6 to 8). ,, Copper, on the other side, was modeled as an attacking particle in the form of a hexaaqua-complex [Cu­(H 2 O) 6 ] 2+ , followed by the formation of biomolecular complexes with coordination number 4 (CN = 4) according to data presented in the literature. − After the performance of the full geometry optimization procedure, it turned out that, in the case of the His195 center copper tends to deform the surrounding ligating groups into a square-planar geometry. Consequently, two schemes were applied: (i) allowing all atoms to undergo full relaxation, thus changing the initial structure of the center; (ii) “freezing” the O and N atoms of the ligating groups that coordinate to Cu 2+ , which results in retaining the original composition.…”

Computational tools to study non-covalent interactions and confinement effects in chemical systems

“…GPUAM is effective for the study of large systems or a large number of medium size systems. For example, to study the potential energy surface of isomers of ZnO, 34 Cu(H 2 O) 35 or NaCl(H 2 O) 2 36 clusters it is necessary a large number of computations to obtain total energy and the corresponding prediction of the connectivity of each isomer. The NWChem 37 suite code performs well over many CPUs for these systems.…”

“…This analysis shows that fourfold coordination is not favored, and the preferred coordination numbers are n = 5 and n = 6. 35 For (NaCl) n (H 2 O) 2 n clusters with n = 1, 2 and 4, the procedure used to search isomers candidates was performed by RISSA (Restricted Isomers Searching by Simulated Annealing). 36 In this case, QTAIM and NCI allowed us to determine the characteristics of the NaCl dehydrate clusters.…”

Manifolds of low energy structures for a magic number of hydrated sulfate: SO42−(H2O)24

“…While this permits accurate local exploration and proper account of anharmonic and temperature effects on populations and vibrational spectra, it is not yet amenable to extensive exploration of structural space. 15,[20][21][22] Global methods such as basin-hopping global optimization, [23][24][25] simulated annealing 26 and various genetic algorithms 27,28 have been developed to improve the energylandscape exploration. Approximate quantum methods have been used to extend the range of system sizes in comparison with the DFT framework.…”

“…Indeed, the semi-empirical PM7 method coupled to a simulated annealing algorithm has been successfully applied to identify the numerous isomers of [Cu(H 2 O)n] 2+ clusters, with n = 12, 16, and 18. 26 Moreover, the Self-Consistent-Charge Density-Functional Based Tight-Binding (SCC-DFTB) approach combined to a global optimization search turned out to be efficient in describing the potential energy surfaces of sulfatewater clusters up to 20 water molecules and protonated waterclusters (20 to 23 water molecules). 25,29 However, an extensive, even more an exhaustive, PES exploration for these medium-size clusters is likely to be achieved only using a classical representation of the energy with a force field.…”