Energies, Geometries, and Charge Distributions of Zn Molecules, Clusters, and Biocenters from Coupled Cluster, Density Functional, and Neglect of Diatomic Differential Overlap Models

Abstract

We present benchmark databases of Zn-ligand bond distances, bond angles, dipole moments, and bond dissociation energies for Zn-containing small molecules and Zn coordination compounds with H, CH3, C2H5, NH3, O, OH, H2O, F, Cl, S, and SCH3 ligands. The test set also includes clusters with Zn-Zn bonds. In addition, we calculated dipole moments and binding energies for Zn centers in coordination environments taken from zinc metalloenzyme X-ray structures, representing both structural and catalytic zinc centers. The benchmark values are based on relativistic-core coupled cluster calculations. These benchmark calculations are used to test the predictions of four density functionals, namely B3LYP and the more recently developed M05-2X, M06, and M06-2X levels of theory, and six semiempirical methods, including neglect of diatomic differential overlap (NDDO) calculations incorporating the new PM3 parameter set for Zn called ZnB, developed by Brothers and co-workers, and the recent PM6 parametrization of Stewart. We found that the best DFT method to reproduce dipole moments and dissociation energies of our Zn compound database is M05-2X, which is consistent with a previous study employing a much smaller and less diverse database and a much larger set of density functionals. Here we show that M05-2X geometries and single-point coupled cluster calculations with M05-2X geometries can also be used as benchmarks for larger compounds, where coupled cluster optimization is impractical, and in particular we use this strategy to extend the geometry, binding energy, and dipole moment databases to additional molecules, and we extend the tests involving crystal-site coordination compounds to two additional proteins. We find that the most predictive NDDO methods for our training set are PM3 and MNDO/d. Notably, we also find large errors in B3LYP for the coordination compounds based on experimental X-ray geometries.

Mechanism of the Asymmetric Autocatalytic Soai Reaction Studied by Density Functional Theory

“…This computational method has been recommended for the accurate energetic description of organic compounds containing zinc. [17] Eight new catalytic cycles with distinct energetics were investigated, besides the two previously investigated at the B3LYP/6-31G(d)//HF/3-21G(d) level of theory. [10] The present study confirms that the dominant mechanism of the Soai reaction is that based on the previously proposed homochiral cycle, sketched in Scheme 2 and translated at the molecular level in Scheme 3.…”

“…[14,15] This functional was recently demonstrated to outperform the popular B3LYP functional in the energetic description of organic systems, [16] and is recommended as the most suitable one for accurate calculations of geometries and energetics of Zn compounds. [17] Accordingly, here we report a complete DFT study of the Soai reaction, examining the pathways of all possible isomeric complexes 6 with the M05-2X/6-31G(d) method. Some optimizations were also carried out with the B3LYP/6-31G(d) method for comparison purposes.…”

“…Since the M05-2X functional overcomes most of the shortcomings of the B3LYP functional, [14][15][16][17] the rest of the computations were performed with the M05-2X/6-31G(d) method only.…”

Polarizability study of nematic liquid crystal 4-cyano-4′-pentylbiphenyl (5CB) and its nitrogen derivatives

“…Effect of electric field along the long axis (x-axis) on polarizability (a) was calculated using B3LYP and M062X [48] methods with 6-31G ⁄⁄ basis set using Gaussian 09. These methods are already proven in the area of intramolecular interactions, conformational studies [49], enzymatic reaction mechanism [50][51][52][53], investigations on molecular structure, spectroscopy [54], and studies of clusters [55].…”

Theoretical study on the chemical mechanism of enoyl-CoA hydratase and the form of inhibitor binding

“…The quantum chemical calculations presented herein were carried out using the functional B3LYP [22][23][24][25][26][27][28][29][30][31][32][33][34][35], as implemented in the Gaussian 09 program package [36]. The B3LYP has proven reliable in numerous theoretical simulations of mechanisms of enzyme-catalyzed reactions [22][23][24][25][26][27][28][29][30].…”