Quantum Biochemistry

<p>Quantum Biochemistry </p

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Configuration of balloon run<br

Input and output files for Prediction of pKa Values Using the PM6 Semiempirical Method

Input and output files for Prediction of pKa Values Using the PM6 Semiempirical Method<div><br></div><div>Data collected in following spreadsheets</div><div><br></div><div>PM6-D3H+/SMD(*)</div><div><a href="https://docs.google.com/spreadsheets/d/1y-QAnCalkXkvfEx7vOs0CUKsORjrGRmRLzO1bwWicRo/edit?usp=sharing">https://docs.google.com/spreadsheets/d/1y-QAnCalkXkvfEx7vOs0CUKsORjrGRmRLzO1bwWicRo/edit?usp=sharing</a></div><div><br></div><div>PM6/SMD</div><div><a href="https://docs.google.com/spreadsheets/d/1tfKv1_5YbZC3FV2poOZoMCKZFzSGWWwfckML2pd6P_k/edit?usp=sharing">https://docs.google.com/spreadsheets/d/1tfKv1_5YbZC3FV2poOZoMCKZFzSGWWwfckML2pd6P_k/edit?usp=sharing</a></div><div><br></div><div>PM6/COSMO</div><div><a href="https://docs.google.com/spreadsheets/d/1h4BdkN8jCBgdGyRv2rlbZSwLNPkl90dGaMkKXjMEDy4/edit?usp=sharing">https://docs.google.com/spreadsheets/d/1h4BdkN8jCBgdGyRv2rlbZSwLNPkl90dGaMkKXjMEDy4/edit?usp=sharing</a></div

SI for Improving Solvation Energy Predictions Using The SMD Solvation Method and Semiempirical Electronic Structure Methods

Table S5 from the pape

Random Versus Systematic Errors in Reaction Enthalpies Computed Using Semi-empirical and Minimal Basis Set Methods

The connectivity-based hierarchy (CBH) protocol for computing accurate reaction enthalpies developed by Sengupta and Raghavachari is tested for fast <i>ab initio</i> methods (PBEh-3c, HF-3c, and HF/STO- 3G), tight-binding DFT methods (GFN-xTB, DFTB, and DFTB-D3), and NDDO-based semiempirical methods (AM1, PM3, PM6, PM6-DH+, PM6-D2, PM6-D3H+, PM6-D3H4X, PM7, and OM2) using the same set of 25 reactions as in the original study. For the CBH-2 scheme, which reflects the change in the immediate chemical environment of all the heavy atoms, the respective MUE relative to G4 for PBEh-3c, HF-3c, HF/STO-3G, GFN-xTB, DFTB-D3, DFTB, PM3, AM1, PM6, PM6-DH+, PM6-D3, PM6-D3H+, PM6-D3H4X, PM7, and OM2 are 1.9, 2.4, 3.0, 3.9, 3.7, 4.5, 4.8, 5.5, 5.4, 5.3, 5,4, 6.5, 5.3, 5.2, and 5.9 kcal/mol, with a single outlier removed for HF-3c, PM6, PM6-DH+, PM6-D3, PM6-D3H4X, and PM7. The increase in accuracy for the NDDO-based methods is relatively modest due to the random errors in predicted heats for formation

Fast and Accurate Prediction of the Regioselectivity of Electrophilic Aromatic Substitution Reactions

While computational prediction of chemical reactivity is possible it usually requires expert knowledge and there are relatively few computational tools that can be used by a bench chemist to help guide synthesis. The RegioSQM method for predicting the regioselectivity of electrophilic aromatic substitution reactions of heteroaromatic systems is presented in this paper. RegioSQM protonates all aromatic C-H carbon atoms and identifies those with the lowest free energies in chloroform using the PM3 semiempirical method as the most nucleophilic center. These positions are found to correlate qualitatively with the regiochemical outcome in a retrospective analysis of 96% of more than 525 literature examples of electrophilic aromatic halogenation reactions. The method is automated and requires only a SMILES string of the molecule of interest, which can easily be generated using chemical drawing programs such as ChemDraw. The computational cost is 1-10 minutes per molecule depending on size, using relatively modest computational resources and the method is freely available via a web server at regiosqm.org. RegioSQM should therefore be of practical use in the planning of organic synthesis