Interaction Energies Of Systems Research Articles

Carbohydrate – Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations

The geometries of the contacts between monosaccharides and aromatic rings of amino acids found in X-ray crystallography structures, in the Protein Data Bank (PDB), were analyzed, while the energies of the interactions were calculated using quantum chemical method. We found 1913 sugar/aromatic ring contacts, 1054 of them (55%) with CH/π interactions and 859 of them (45%) without CH/π interactions. We showed that only the carbohydrate/aromatic contacts with CH/π interactions are preferentially parallel and enable sliding in the plane parallel to aromatic ring. The calculated interaction energies in systems with CH/π interactions are in the range from −1.7 kcal/mol to −6.8 kcal/mol, while in the systems without CH/π interactions are in the range −0.2 to −3.2 kcal/mol. Hence, the binding that does not include CH/π interactions, can also be important for aromatic amino acid and carbohydrate binding processes, since some of these interactions can be as strong as the CH/π interactions. At the same time, these interactions can be weak enough to enable releasing of small carbohydrate fragments after the enzymatic reaction. The analysis of the protein-substrate patterns showed that every second or third carbohydrate unit in long substrates stacks with protein aromatic amino acids.

Best methods for calculating interaction energies in 2-butene and butane systems

Benchmarking study on eighteen methods, including MP2, B2PLYP-D3, B2PLYP-D3BJ, ωB97xD, M05-D3, M06-D3, M052X-D3, M06HF-D3, PBE0-D3, PBE0-D3BJ, B3LYP-D3, B3LYP-D3DJ, TPSS-D3, TPSS-D3BJ, BP86-D3, BP86-D3BJ, BLYP-D3, BLYP-D3BJ and ten basis sets: cc-pVDZ, cc-pVTZ, aug-cc-pVDZ, cc-pVQZ, def2-SVP, def2-TZVP, def2-TZVPP, def2-QZVP, 6-311++G∗∗ and 6-31G∗∗, for each method, have been performed, calculating interaction energies in (1) unsaturated/unsaturated systems (2-butene dimers), (2) unsaturated/saturated system (between butane and 2-butene) and (3) saturated/saturated (butane dimers). The calculated interaction energies are compared with accurate CCSD(T)/CBS energies. The data show that most levels of theory have the highest errors for systems with butane dimers, and calculated interaction energies in these systems are overestimated. The best levels, overall for all systems, are BLYP-D3BJ/def2-QZVP and BLYP-D3BJ/cc-pVQZ with similar root mean square deviation (RMSD) values of 0.056kcalmol−1 and 0.060kcalmol−1 compared to CCSD(T) values. The best level for (1) 2-butene dimers is B3LYP-D3BJ/aug-cc-pVDZ; for (2) interactions between 2-butene and butane is BLYP-D3BJ/def2-SVP; while for (3) butane dimers is BLYP-D3BJ/def2-QZVP. The differences in calculated energies among several methods are not high, however, it is important that most of the DFT methods overestimate interactions in butane dimers.

Pairing in Few-Fermion Systems with Attractive Interactions

We study quasi-one-dimensional few-particle systems consisting of one to six ultracold fermionic atoms in two different spin states with attractive interactions. We probe the system by deforming the trapping potential and by observing the tunneling of particles out of the trap. For even particle numbers, we observe a tunneling behavior that deviates from uncorrelated single-particle tunneling indicating the existence of pair correlations in the system. From the tunneling time scales, we infer the differences in interaction energies of systems with different number of particles, which show a strong odd-even effect, similar to the one observed for neutron separation experiments in nuclei.

On the counterpoise correction for the basis set superposition error in large systems

The appropriateness of the use of the counterpoise correction for the basis set superposition error in SCF calculations of the interaction energies for pairs of aliphatic amino acids is analyzed in this paper. Our results show that for this type of molecule where the magnitude of the basis set superposition error can become quite big, the use of the counterpoise method provides interaction energies in good agreement with near Hartree-Fock values. The inaccuracies associated with the counterpoise method are much less important compared with the basis set superposition error itself. It is shown that the use of a well-balanced minimal basis set together with the counterpoise method is a good compromise (quality versus computational cost) for calculating interaction energies in systems involving molecules of biological interest.