We implement a bottom-up multiscale approach for the modeling of defect localization in C(6n(2))H(6n) islands, i.e. graphene quantum dots with a hexagonal symmetry, by means of density functional and semiempirical approaches. Using the ab initio calculations as a reference, we recognize the theoretical framework under which semiempirical methods adequately describe the electronic structure of t...

Semiempirical quantum models are routinely used to study mechanisms of RNA catalysis and phosphoryl transfer reactions using combined quantum mechanical (QM)/molecular mechanical methods. Herein, we provide a broad assessment of the performance of existing semiempirical quantum models to describe nucleic acid structure and reactivity to quantify their limitations and guide the development of ne...

Reorganization energies of flexible molecules pose a challenge for machine learning (ML) models. Combining them with semiempirical electronic structure methods helps, but the benefit virtual screening is surprisingly small.

The semiempirical methods of the OMx family (orthogonalization models OM1, OM2, and OM3) are known to describe biochemical systems more accurately than standard semiempirical approaches such as AM1. We investigate the benefits of augmenting these methods with an empirical dispersion term (OMx-D) taken from recent density functional work, without modifying the standard OMx parameters. Significan...

The semiempirical orthogonalization-corrected OMx methods (OM1, OM2, and OM3) go beyond the standard MNDO model by including additional interactions in the electronic structure calculation. When augmented with empirical dispersion corrections, the resulting OMx-Dn approaches offer a fast and robust treatment of noncovalent interactions. Here we evaluate the performance of the OMx and OMx-Dn met...

BACKGROUND: Molecular mechanics (MM) and quantum chemical (QM) calculations are widely applied and powerful tools for the stereochemical and conformational investigations of molecules. The same methods have been extensively used to probe the conformational profile of Taxol (Figure 1) both in solution and at the beta-tubulin protein binding site. RESULTS: In the present work, the relative energi...

Z. Naturforsch. 54 a, 422-430 (1999); received March 29, 1999 Semiempirical calculations, based on the so-called angular overlap model, have been compared with ab initio methods (MP2) for the calculation of nuclear quadrupole interactions (NQPs) in cadmium complexes with biologically relevant ligands (H2O, O H , cysteinate, carboxylate, and imidazole). The assumptions on which the semiempirical...