Semiempirical quantum mechanical (SEQM) methods offer an attractive middle ground between fully ab initio quantum chemistry and force-field simulations, allowing for a quantum mechanical treatment of the system at a relatively low computational cost. However, SEQM methods have not been frequently utilized in the study of transition metal systems, mostly due to the difficulty in obtaining reliable parameters. This paper examines the accuracy of the PM6 and PM7 semiempirical methods to predict geometries, ionization potentials, and HOMO-LUMO energy gaps of several bare gold clusters (Au) and thiolate-protected gold nanoclusters (AuSNCs). Contrary to PM6, the PM7 method can predict qualitatively correct geometries and ionization potentials when compared to DFT. PM6 fails to predict the characteristic gold core and gold-sulfur ligand shell (staple motifs) of the AuSNC structures. Both the PM6 and PM7 methods overestimate the HOMO-LUMO gaps. Overall, PM7 provides a more accurate description of bare gold and gold-thiolate nanoclusters than PM6. Nevertheless, refining the gold parameters could help achieve better quantitative accuracy.
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http://dx.doi.org/10.1021/acs.jpca.9b11474 | DOI Listing |
J Comput Chem
December 2024
N.N. Semenov Federal Research Center for Chemical Physics RAS, Moscow, Russian Federation.
An impact of an electronic structure or force field method, gas-phase thermodynamic correction, and continuum solvation model on organic carbonate clusters (S) conformational and binding energies is explored. None of the tested force field (GFN-FF, GAFF, MMFF94) and standard semiempirical methods (PM3, AM1, RM1, PM6, PM6-D3, PM6-D3H4, PM7) can reproduce reference RI-SCS-MP2 conformational energies. Tight-binding GFNn-xTB methods provide more realistic conformational energies which are accurate enough to discard the least stable conformers.
View Article and Find Full Text PDFJ Phys Chem B
June 2024
Department of Physics, University of Science and Technology of China, Hefei 230026, China.
Predicting the binding poses of docking with an accurate estimation of binding energies is highly important but very challenging in computational drug design. A quantum mechanics (QM) calculation-based docking approach considering multiple conformations and orientations of the ligand is introduced here to tackle the problem. This QM docking consists of three steps: generating an ensemble of binding poses with a conventional docking simulation, computing the binding energies with self-consistent charge density functional theory tightly binding with dispersion correction (DFTB-D) to selecting the 10 top binding modes, and optimizing the selected binding mode structures using the ONIOM(DFTB:PM7) technique to determine the binding poses.
View Article and Find Full Text PDFJ Mol Model
August 2023
Stewart Computational Chemistry, 15210 Paddington Circle, Colorado Springs, CO, 80921, USA.
Context: In recent years, semiempirical methods such as PM6, PM6-D3H4, and PM7 have been increasingly used for modeling proteins, in particular enzymes. These methods were designed for more general use, and consequently were not optimized for studying proteins. Because of this, various specific errors have been found that could potentially cast doubt on the validity of these methods for modeling phenomena of biochemical interest such as enzyme catalytic mechanisms and protein-ligand interactions.
View Article and Find Full Text PDFJ Comput Chem
October 2023
Mulliken Center for Theoretical Chemistry, University of Bonn, Bonn, Germany.
The semiempirical GFNn-xTB ( ) tight-binding methods are extended with a spin-dependent energy term (spin-polarization), enabling the fast and efficient screening of different spin states for transition metal complexes. While GFNn-xTB methods inherently can not differentiate properly between high-spin (HS) and low-spin (LS) states, this shortcoming is corrected with the presented methods termed spGFNn-xTB. The performance of spGFNn-xTB methods for spin state energy splittings is evaluated on a newly compiled benchmark set of 90 complexes (27 HS and 63 LS complexes) containing 3d, 4d, and 5d transition metals (termed TM90S) employing DFT references at the TPSSh-D4/def2-QZVPP level of theory.
View Article and Find Full Text PDFPolymers (Basel)
May 2023
Department of Physics, College of Science, Northern Border University, Arar 73222, Saudi Arabia.
The utilization of indoor photovoltaics makes it feasible to harvest energy from artificial light sources. Although single-junction indoor photovoltaics have demonstrated exceptional efficacy when using LED lighting, there is still a need for more comprehensive testing of tandem structures. Herein, the first systematic TCAD simulation study on the potential for tandem all-polymer solar cells (all-PSCs) for indoor applications is provided.
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