MP2-F12 Basis Set Convergence for the S66 Noncovalent Interactions Benchmark: Transferability of the Complementary Auxiliary Basis Set (CABS)

Complementary auxiliary basis sets for F12 explicitly correlated calculations appear to be more transferable between orbital basis sets than has been generally assumed. We also find that aVnZ-F12 basis sets, originally developed with anionic systems in mind, appear to be superior for noncovalent interactions as well, and propose a suitable CABS sequence for them.Comment: AIP Conference Proceedings, in press (ICCMSE-2017 proceedings), 4 page

The S66 noncovalent interactions benchmark reconsidered using explicitly correlated methods near the basis set limit

The S66 benchmark for noncovalent interactions has been re-evaluated using explicitly correlated methods with basis sets near the one-particle basis set limit. It is found that post-MP2 "high-level corrections" are treated adequately well using a combination of CCSD(F12*) with (aug-)cc-pVTZ-F12 basis sets on the one hand, and (T) extrapolated from conventional CCSD(T)/heavy-aug-cc-pV{D,T}Z on the other hand. Implications for earlier benchmarks on the larger S66x8 problem set in particular, and for accurate calculations on noncovalent interactions in general, are discussed. At a slight cost in accuracy, (T) can be considerably accelerated by using sano-V{D,T}Z+ basis sets, while half-counterpoise CCSD(F12*)(T)/cc-pVDZ-F12 offers the best compromise between accuracy and computational cost.Comment: Australian Journal of Chemistry, in press [Graham S. Chandler special issue

Toward Simple, Predictive Understanding of Protein-Ligand Interactions: Electronic Structure Calculations Join Forces with the Chemist’s Intuition

Contemporary efforts for modeling protein-ligand interactions entail a painful tradeoff – as reliable information on both noncovalent binding factors and the dynamic behavior of a protein-ligand complex is often beyond practical limits. In the following paper, we demonstrate that information drawn exclusively from static molecular structures can be used for the semi-quantitative prediction of experimentally-measured binding affinities for protein-ligand complexes. In the particular case considered here, inhibition constants (Ki) were calculated for eight different ligands of torpedo californica acetylcholinesterase using a simple, multiple-linearregression-based model. The latter, incorporating five informative and independent variables – drawn from QM cluster, DLPNO-CCSD(T) calculations and LED analyses on the eight complexes – is shown to recover no-lessthan 96% of the sum of squares for measured Ki values, and used to predict the inhibition potential for yet another ligand (E20, for which no Ki values are available in the literature). This thus challenges the widespread assumption that “static pictures” are inadequate for predicting reactivity properties of flexible and dynamic protein-ligand systems

2019-nCoV vs. SARS-CoV: Which Truly Has a Higher ACE2 Affinity? A Quantum Chemical Perspective on Virus-Receptor Noncovalent Interactions

Noncovalent interaction energetics associated with ACE2 affinity differences are investigated using electronic structure methods; Our results were found to challenge previous predictions – claiming a higher affinity for 2019-nCoV compared to SARS-CoV based merely on "chemical intuition". In addition, we demonstrate that a broadly-used classical molecular dynamics force field – MMFF94 – is clearly incapable of reproducing DFT-based noncovalent interaction energetics for the systems at hand (despite being specifically parameterized for van der Waals interactions)

Probing the Basis Set Limit for Thermochemical Contributions of Inner-Shell Correlation: Balance of Core-Core and Core-Valence Contributions

The inner-shell correlation contributions to the total atomization energies of the W4-17 computational thermochemistry benchmark have been determined at the CCSD(T) level near the basis set limit using several families of core correlation basis sets, such as aug-cc-pCVnZ (n=3-6), aug-cc-pwCVnZ (n=3-5), and nZaPa-CV (n=3-5). The three families of basis sets agree very well with each other (0.01 kcal/mol RMS) when extrapolating from the two largest available basis sets: however, there are considerable differences in convergence behavior for the smaller basis sets. nZaPa-CV is superior for the core-core term and awCVnZ for the core-valence term. While the aug-cc-pwCV(T+d)Z basis set of Yockel and Wilson is superior to aug-cc-pwCVTZ, further extension of this family proved unproductive. The best compromise between accuracy and computational cost, in the context of high-accuracy computational thermochemistry methods such as W4 theory, is CCSD(T)/awCV{T,Q}Z, where the {T,Q} notation stands for extrapolation from the awCVTZ and awCVQZ basis set pair. For lower-cost calculations, a previously proposed combination of CCSD-F12b/cc-pCVTZ-F12 and CCSD(T)/pwCVTZ(no f) appears to ‘give the best bang for the buck’. While core-valence correlation accounts for the lion’s share of the inner shell contribution in first-row molecules, for second-row molecules core-core contributions may become important, particularly in systems like P4and S4with multiple adjacent second-row atoms.[In memory of Dieter Cremer, 1944-2017]</div