Further analysis and comparative study of intermolecular interactions using dimers from the S22 database

Abstract

Accurate MP2 and CCSD͑T͒ complete basis set ͑CBS͒ interaction energy curves ͑14 points for each curve͒ have been obtained for 20 of the dimers reported in the S22 set and analytical Morse curves have been fitted that can be used in developing updated density functional theory ͑DFT͒ and force field models. The magnitude and the effect of the basis set superposition error ͑BSSE͒ were carefully investigated. We found that going up to aug-cc-pVDZ and aug-cc-pVTZ basis sets is enough to obtain accurate CBS MP2 energies when BSSE corrected values are used but aug-cc-pVTZ and aug-cc-pVQZ basis sets are needed when the BSSE uncorrected total energies are used in CBS extrapolations. MP2 interaction energies with smaller basis sets such as 6-31G ‫ء‬ are found to have very little dispersion energy and that the true source of dispersion attributed attractive interactions is almost entirely due to BSSE. MP2 and CCSD͑T͒ CBS interaction energies are found to be very close to one another if aromatic systems are not involved. Comparative analyses have been performed with semiempirical and ab initio methods utilizing the moderate in size but affordable 6-31G ‫ء‬ basis set both of which can be readily applied to macromolecular systems. The new M06-2X and M06-L DFT functionals were found to be more accurate than all methods tested herein. Interaction energy curves using the SG1 grid showed discontinuities for several of the dimer systems but this problem disappeared when finer DFT numerical grids were used.

Theoretical constraints on the effects of pH, salinity, and temperature on clumped isotope signatures of dissolved inorganic carbon species and precipitating carbonate minerals

“…In this section we summarize the reasons for our choice of the 2p) Models constructed using the 2 largest basis sets 6-311++G(2d,2p) and aug-cc-pVTZ were similar, with D 63 values deviating from each other by less than 0.001& on average (range 0.000 to 0.006&), most likely indicating approach to the complete basis set limit for hybrid density functionals (e.g., Molnar et al, 2009;Bryantsev et al, 2009;Suârez et al, 2011). The 6-311++G(2d,2p) basis set has fewer basis functions and allows faster computations than aug-cc-pVTZ.…”

“…We used aug-cc-pVTZ for direct comparison with 6-311++G(2d,2p) instead of the smaller aug-cc-pVDZ (valence double zeta, used by Rustad et al (2008)). The largest two basis sets, 6-311++G(2d,2p) and aug-cc-pVTZ, appear to be near reasonable basis set convergence thresholds for the chosen density functionals (e.g., Molnar et al, 2009;Bryantsev et al, 2009;Suârez et al, 2011).…”

Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory

“…However, since accurate reference data can only be obtained for systems with tens of atoms, it is just not possible to obtain reference data for DNA or a protein directly and fragments of the large molecules are used to build test sets of binding energies and geometries instead. One such test set [112][113][114] is the popular S22 data set of Jurečka et al 22 It is useful since it contains 22 different dimers with a range of weak bonding types and with a wide range of interaction energies. Results for some of the methods are reported in Table II; specifically, we report mean absolute deviations (MAD) and mean absolute percentage deviations (MAPD).…”

Higher-accuracy van der Waals density functional

“…2, we summarize the calculated binding energies at equilibrium separation, at equilibrium separation plus 1 Å, and the equilibrium separations themselves, with each quantity given as a deviation from that implied by the reference calculations. [31][32][33] Each subfigure clearly shows one of the three major improvements. ͑i͒ Hydrogen-bond strengths.…”

“…Figure 1 shows a typical PEC for each kind of interaction. To make a direct comparison to the QC results, the PECs are calculated at the same geometry of those of the CCSD͑T͒ PEC calculations 33 ͑shown as dashed-dotted lines with circles͒, where each molecule is kept in its S22 geometry 31 and moved along the line defined by the center-of-mass coordinates of two molecules without any rotation. Overall, the vdW-DF2 PECs ͑solid lines͒ show a remarkable agreement with QC ones for all separations and for all three types of interactions.…”