Large Stabilization Effects by Intramolecular Beryllium Bonds in Ortho-Benzene Derivatives

Intramolecular interactions are shown to be key for favoring a given structure in systems with a variety of conformers. In ortho-substituted benzene derivatives including a beryllium moiety, beryllium bonds provide very large stabilizations with respect to non-bound conformers and enthalpy differences above one hundred kJ·mol−1 are found in the most favorable cases, especially if the newly formed rings are five or six-membered heterocycles. These values are in general significantly larger than hydrogen bonds in 1,2-dihidroxybenzene. Conformers stabilized by a beryllium bond exhibit the typical features of this non-covalent interaction, such as the presence of a bond critical point according to the topology of the electron density, positive Laplacian values, significant geometrical distortions and strong interaction energies between the donor and acceptor quantified by using the Natural Bond Orbital approach. An isodesmic reaction scheme is used as a tool to measure the strength of the beryllium bond in these systems in terms of isodesmic energies (analogous to binding energies), interaction energies and deformation energies. This approach shows that a huge amount of energy is spent on deforming the donor–acceptor pairs to form the new rings.

Standard Molar Enthalpies of Formation of Halomethanes Based on Quantum Chemical Computations

Accurate calculations of standard molar enthalpies of formation (ΔΗf°)m(g) and carbon-halogen bond dissociation enthalpies, BDE, of a variety of halomethanes with relevance on several atmospheric chemical processes and particularly to ozone destruction, were performed in the gas phase at 298.15 K. The (ΔΗf°)m(g) of the radicals formed through bond dissociations have also been computed. Ab initio computational methods and isodesmic reaction schemes were used. It is found that for the large majority of these species, the gold standard method of quantum chemistry (CCSD(T)) and even MP2 are capable to predict enthalpy values nearing chemical accuracy provided that isodesmic reaction schemes are used. New estimates for standard molar enthalpies of formation and BDE are suggested including for species that to our knowledge there are no experimental (ΔΗf°)m(g) (CHCl2Br, CHBr2Cl, CHBrCl, CHICl, CHIBr) or BDE values (CHCl2Br, CHBr2Cl, CHBrCl, CHICl, CHIBr) available in the literature. The method and calculational procedures presented may profitably be used to obtain accurate (ΔΗf°)m(g) and BDE values for these species.

Standard Molar Enthalpies of Formation of Halomethanes Based on Quantum Chemical Computations

Accurate calculations of standard molar enthalpies of formation (ΔΗf°)m(g) and carbon-halogen bond dissociation enthalpies, BDE, of a variety of halomethanes with relevance on several atmospheric chemical processes and particularly to ozone destruction, were performed in the gas phase at 298.15 K. The (ΔΗf°)m(g) of the radicals formed through bond dissociations have also been computed. Ab initio computational methods and isodesmic reaction schemes were used. It is found that for the large majority of these species, the gold standard method of quantum chemistry (CCSD(T)) and even MP2 are capable to predict enthalpy values nearing chemical accuracy provided that isodesmic reaction schemes are used. New estimates for standard molar enthalpies of formation and BDE are suggested including for species that to our knowledge there are no experimental (ΔΗf°)m(g) (CHCl2Br, CHBr2Cl, CHBrCl, CHICl, CHIBr) or BDE values (CHCl2Br, CHBr2Cl, CHBrCl, CHICl, CHIBr) available in the literature. The method and calculational procedures presented may profitably be used to obtain accurate (ΔΗf°)m(g) and BDE values for these species.

Prediction of pKa values for drug-like molecules using semiempirical quantum chemical methods

Rapid yet accurate pKa prediction for drug-like molecules is a key challenge in computational chemistry. This study uses PM6-DH+/COSMO, PM6/COSMO, PM7/COSMO, PM3/COSMO, AM1/COSMO, PM3/SMD, AM1/SMD, and DFTB3/SMD to predict the pKa values of 53 amine groups in 48 drug-like compounds. The approach uses an isodesmic reaction where the pKa value is computed relative to a chemically related reference compound for which the pKa value has been measured experimentally or estimated using a standard empirical approach. The AM1- and PM3-based methods perform best with RMSE values of 1.4 - 1.6 pH units that have uncertainties of ±0.2-0.3 pH units, which make them statistically equivalent. However, for all but PM3/SMD and AM1/SMD the RMSEs are dominated by a single outlier, cefadoxil, caused by proton transfer in the zwitterionic protonation state. If this outlier is removed, the RMSE values for PM3/COSMO and AM1/COSMO drop to 1.0 ± 0.2 and 1.1 ± 0.3, while PM3/SMD and AM1/SMD remain at 1.5 ± 0.3 and 1.6 ± 0.3/0.4 pH units, making the COSMO-based predictions statistically better than the SMD-based predictions. So for pKa calculations where a zwitterionic state is not involved or proton transfer in a zwitterionic state is not observed then PM3/COSMO or AM1/COSMO is the best pKa prediction method, otherwise PM3/SMD or AM1/SMD should be used. Thus, fast and relatively accurate pKa prediction for 100-1000s of drug-line amines is feasible with the current setup and relatively modest computational resources.

Prediction of pKa values for drug-like molecules using semiempirical quantum chemical methods

Rapid yet accurate pKa prediction for drug-like molecules is a key challenge in computational chemistry. This study uses PM6-DH+/COSMO, PM6/COSMO, PM7/COSMO, PM3/COSMO, AM1/COSMO, PM3/SMD, AM1/SMD, and DFTB3/SMD to predict the pKa values of 53 amine groups in 48 drug-like compounds. The approach uses an isodesmic reaction where the pKa value is computed relative to a chemically related reference compound for which the pKa value has been measured experimentally or estimated using a standard empirical approach. The AM1- and PM3-based methods perform best with RMSE values of 1.4 - 1.6 pH units that have uncertainties of ±0.2-0.3 pH units, which make them statistically equivalent. However, for all but PM3/SMD and AM1/SMD the RMSEs are dominated by a single outlier, cefadoxil, caused by proton transfer in the zwitterionic protonation state. If this outlier is removed, the RMSE values for PM3/COSMO and AM1/COSMO drop to 1.0 ± 0.2 and 1.1 ± 0.3, while PM3/SMD and AM1/SMD remain at 1.5 ± 0.3 and 1.6 ± 0.3/0.4 pH units, making the COSMO-based predictions statistically better than the SMD-based predictions. So for pKa calculations where a zwitterionic state is not involved or proton transfer in a zwitterionic state is not observed then PM3/COSMO or AM1/COSMO is the best pKa prediction method, otherwise PM3/SMD or AM1/SMD should be used. Thus, fast and relatively accurate pKa prediction for 100-1000s of drug-line amines is feasible with the current setup and relatively modest computational resources.

Prediction of pKa values for drug-like molecules using semiempirical quantum chemical methods

Rapid yet accurate pKa prediction for drug-like molecules is a key challenge in computational chemistry. This study uses PM6-DH+/COSMO, PM6/COSMO, PM7/COSMO, PM3/COSMO, AM1/COSMO, PM3/SMD, AM1/SMD, and DFTB3/SMD to predict the pKa values of 53 amine groups in 48 drug-like compounds. The approach uses an isodesmic reaction where the pKa value is computed relative to a chemically related reference compound for which the pKa value has been measured experimentally or estimated using a standard empirical approach. The AM1- and PM3-based methods perform best with RMSE values of 1.4 - 1.6 pH units that have uncertainties of 0.3-0.4 pH units, which make them statistically equivalent. However, for all but PM3/SMD and AM1/SMD the RMSEs are dominated by a single outlier, cefadoxil, caused by proton transfer in the zwitterionic protonation state. If this outlier is removed, the RMSE values for PM3/COSMO and AM1/COSMO drop to 1.0 ± 0.2 and 1.1 ± 0.3, while PM3/SMD and AM1/SMD remain at 1.5 ± 0.4 and 1.6 ± 0.4 pH units, making the COSMO-based predictions statistically better than the SMD-based predictions. So for pKa calculations where a zwitterionic state is not involved or proton transfer in a zwitterionic state is not observed then PM3/COSMO or AM1/COSMO is the best pKa prediction method, otherwise PM3/SMD or AM1/SMD should be used. Thus, fast and relatively accurate pKa prediction for 100-1000s of drug-line amines is feasible with the current setup and relatively modest computational resources.