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An impressive collection of accurate two-body interaction energies for small complexes has been assembled into benchmark databases and used to improve the performance of multiple density functional, semiempirical, and machine learning methods. Similar benchmark data on nonadditive three-body energies in molecular trimers are comparatively scarce, and the existing ones are practically limited to homotrimers. In this work, we present a benchmark dataset of 20 equilibrium noncovalent interaction energies for a small but diverse selection of 10 heteromolecular trimers. The new 3BHET dataset presents complexes that combine different interactions including π-π, anion-π, cation-π, and various motifs of hydrogen and halogen bonding in each trimer. A detailed symmetry-adapted perturbation theory (SAPT)-based energy decomposition of the two- and three-body interaction energies shows that 3BHET consists of electrostatics- and dispersion-dominated complexes. The nonadditive three-body contribution is dominated by induction, but its influence on the overall bonding type in the complex (as exemplified by its position on the ternary diagram) is quite small. We also tested the extended SAPT (XSAPT) approach which is capable of including some nonadditive interactions in clusters of any size. The resulting three-body dispersion term (obtained from the many-body dispersion formalism) is mostly in good agreement with the supermolecular CCSD(T)-MP2 values and the nonadditive induction term is similar to the three-body SAPT(DFT) data, but the overall three-body XSAPT energies are not very accurate as they are missing the first-order exchange terms.
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Intramolecular symmetry-adapted perturbation theory (ISAPT) is a method to compute and decompose the noncovalent interaction energy between two molecular fragments A and B covalently connected via a linker C. However, the existing ISAPT algorithm displays several issues for many fragmentation patterns (that is, specific assignments of atoms to the A/B/C subsystems), including an artificially repulsive electrostatic energy (even when the fragments are hydrogen-bonded) and very large and mutually cancelling induction and exchange-induction terms. We attribute those issues to the presence of artificial dipole moments at the interfragment boundary, as the atoms of A and B directly connected to C are missing electrons on one of their hybrid orbitals. Therefore, we propose several new partitioning algorithms which reassign one electron, on a singly occupied link hybrid orbital, from C to each of A/B. Once the contributions from these link orbitals are added to fragment density matrices, the computation of ISAPT electrostatic, induction, and dispersion energies proceeds exactly as normal, and the exchange energy expressions need only minor modifications. Among the link partitioning algorithms introduced, the so-called ISAPT(SIAO1) approach (in which the link orbital is obtained by a projection onto the intrinsic atomic orbitals (IAOs) of a given fragment followed by orthogonalization to this fragment's occupied space) leads to reasonable values of all ISAPT corrections for all fragmentation patterns, and exhibits a fast and systematic basis set convergence. This improvement is made possible by a significant reduction in magnitude (even though not a complete elimination) of the unphysical dipole moments at the interfragment boundaries. We demonstrate the utility of the improved ISAPT partitioning by examining intramolecular interactions in several pentanediol isomers, examples of linear and branched alkanes, and the open and closed conformations of a family of N-arylimide molecular torsion balances.
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A dispersion function Das in the form of a damped atom-atom asymptotic expansion fitted to ab initio dispersion energies from symmetry-adapted perturbation theory was improved and extended to systems containing heavier halogen atoms. To illustrate its performance, the revised Das function was implemented in the multipole first-order electrostatic and second-order dispersion (MED) scoring model. The extension has allowed applications to a much larger set of biocomplexes than it was possible with the original Das. A reasonable correlation between MED and experimentally determined inhibitory activities was achieved in a number of test cases, including structures featuring nonphysically shortened intermonomer distances, which constitute a particular challenge for binding strength predictions. Since the MED model is also computationally efficient, it can be used for reliable and rapid assessment of the ligand affinity or multidimensional scanning of amino acid side-chain conformations in the process of rational design of novel drugs or biocatalysts.
Asunto(s)
Biocatálisis , Diseño de Fármacos , Halógenos/química , Ligandos , Electricidad EstáticaRESUMEN
The exchange terms in symmetry-adapted perturbation theory (SAPT) are normally calculated within the so-called S2 or single exchange approximation, which approximates the all-electron antisymmetrizer by interchanges of at most one electron pair between the interacting molecules. This approximation is typically very accurate at the van der Waals minimum separation and at larger intermolecular distances but begins to deteriorate at short range. Nonapproximated expressions for the second-order SAPT exchange corrections have been derived some time ago by Schäffer and Jansen [Mol. Phys. 111, 2570 (2013)]. In this work, we extend Schäffer and Jansen's formalism to derive and implement a nonapproximated expression for the third-order exchange-induction correction. Numerical tests on several representative noncovalent databases show that the S2 approximation underestimates the exchange-induction contributions in both second and third orders. This underestimation is very similar in relative terms, but the larger absolute values of the third-order exchange-induction effects, and their near complete cancellation with the corresponding induction energies, make the third-order errors more severe. In the worst-case scenario of interactions involving ions, the breakdown of the S2 approximation can result in a qualitatively wrong, attractive character of SAPT total energies at short range {as first observed by Lao and Herbert [J. Phys. Chem. A 116, 3042 (2012)]}. As expected, the inclusion of the full third-order exchange-induction energy in place of its S2-approximated counterpart restores the correct, repulsive short-range behavior of the SAPT potential energy curves computed through the third order.
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The interactions between carbon dioxide and cluster models of coordinatively unsaturated metal-organic frameworks (MOFs) were studied using a variety of ab initio methods. Three metal species and three organic linkers in four structures were considered in these models as a representation of the tunable nature of MOFs and the potential multireference character of such systems. Common single-reference methods, such as MP2 and CCSD(T), were compared with multireference methods based on complete active space self-consistent field theory, going as far as multireference configuration interaction with single and double excitations (MRCISD). Special consideration is taken to avoid issues of size inconsistency in the CI results, where an alternate reference is used in the interaction energy definition. The benchmark values are used to judge the adequacy of a selection of density functionals for the current systems. Symmetry-adapted perturbation theory (SAPT) decomposition was performed to elucidate the important effects that comprise the binding interactions. The systems proved to have very limited multireference character, and MP2 values were closer to the CCSD(T) benchmark than the more difficult MRCISD results. Though the SAPT total energies prove to be relatively poor approximations to the benchmark interaction energies, they reveal (in most cases) the correct trends with respect to the choice of the metal. The SAPT energy decompositions indicate that the CO2 binding is primarily driven by electrostatics, but induction and dispersion also provide sizable, and quite similar, attractive contributions. Importantly, the small diformate model provides a faithful representation of complexes with large aromatic linkers, both in terms of the total interaction energy and the SAPT decomposition.
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Chiral discrimination, the ability of a chiral molecule to exhibit different weak intermolecular interactions than its mirror image, is investigated for dimers of oxiranemethanol (glycidol). In this regard, high-level ab initio calculations were performed to study the chiral recognition effects in the homochiral and heterochiral dimers of glycidol. Fourteen dimer structures, seven homochiral and seven heterochiral, were studied: they all feature two intermolecular O-H···O hydrogen bonds. These structures have been determined with the second-order Møller-Plesset perturbation theory (MP2) using the aug-cc-pVTZ basis set and verified to pertain to actual local minima. The benchmark interaction energy values were computed using MP2 extrapolated from the aug-cc-pVQZ and aug-cc-pV5Z bases with a higher-level correction from a coupled-cluster calculation in the aug-cc-pVTZ basis. The global minimum structure is a homochiral one, with the two hydrogen bonds forming a part of a ring with eight heavy atoms. A similar heterochiral structure has a binding energy smaller by about 0.6 kcal/mol. The largest diastereomeric energy difference is about 1.0 kcal/mol. Further insight into the origins of chiral discrimination was provided by symmetry-adapted perturbation theory (SAPT) and a functional-group SAPT (F-SAPT) difference analysis to investigate the direct and indirect effects of two -H/-CH2OH substitutions leading from an achiral ethylene oxide dimer to the chiral glycidol dimer. Last but not least, harmonic frequency shifts relative to a noninteracting glycidol molecule were calculated and analyzed for all conformations to get insight into the origins of chiral discrimination. It is found that the largest frequency shifts are related to the effect of hydrogen bonding on the O-H stretch mode, the stability of the ring involving both hydrogen bonds, and the transition between two nonequivalent minima of the glycidol molecule.
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PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree-Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4's core functionalities via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSCHEMA data format, facilitating interoperability. A rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCARCHIVE INFRASTRUCTURE project, makes the latest version of PSI4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.
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We elucidate the subtle energetic effects that give rise to chiral recognition in the propylene oxide dimer. Specifically, we investigate six homochiral (RRx) and six heterochiral (RSx) structures of this complex, with the RRn-RSn pair sharing the same pattern of weak O···H-C hydrogen bonds but subtly differing in energy due to chiral effects. The interaction energies for the 12 structures are computed at various levels of electronic structure theory and basis set up to the complete basis set limit of the coupled-cluster approach with single, double, and perturbative triple excitations (CCSD(T)). These benchmark interaction energies are compared to the results of various approximate approaches, both density functional theory-based and wave function-based. We find that while the RRn-RSn diastereomeric energy differences exhibit a great deal of error cancellation between the individual interaction energies, most approximate methods have a hard time even reproducing the correct signs of these differences consistently. The origins of the RRn-RSn differences are elucidated by several symmetry-adapted perturbation theory (SAPT) analyses ranging from ordinary intermolecular SAPT to a functional-group SAPT (F-SAPT) decomposition of direct and indirect H â CH3 substitution effects leading from achiral ethylene oxide complexes to chiral propylene oxide ones. It is shown that the largest diastereomeric energy differences are correlated to the variations in the electrostatic and dispersion SAPT contributions. Finally, the effect of chiral interactions on the vibrational frequencies of a propylene oxide molecule is investigated, showing that the interaction results in largest frequency shifts, splittings, and chiral discrimination effects in the lowest, torsional vibrational mode of the noninteracting monomer.
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High-accuracy noncovalent interaction energies are indispensable as data points for potential energy surfaces and as benchmark values for improving and testing more approximate approaches. The preferred algorithm (the gold standard) for computing these energies has been the coupled-cluster method with singles, doubles, and perturbative triples [CCSD(T)] converged to the complete basis set (CBS) limit. However, gold-standard calculations are expensive as correlated interaction energies converge slowly with the basis set size, and establishing the CBS limit to better than 0.05 kcal/mol typically requires a CCSD(T) calculation in a basis set of at least triple-zeta quality. If an even higher accuracy is required (for example, for the assignment of complicated high-resolution spectra), establishing a superior platinum standard requires both a precisely converged CCSD(T)/CBS limit and the corrections for the core correlation, relativistic effects, and higher-order coupled-cluster terms at least through the perturbative quadruple excitations. On the other hand, if a triple-zeta CCSD(T) calculation is not feasible but a double-zeta one is, it is worthwhile to look for a silver standard that provides the most accurate and consistent approximation to the gold standard at a reduced computational cost. We review the recent developments aimed at (i) increasing the breadth and diversity of the available collection of gold-standard benchmark interaction energies, (ii) evaluating the best computational strategies for platinum-standard calculations and producing beyond-CCSD(T) potential energy surfaces for spectroscopic and scattering applications of the highest precision, and (iii) improving the accuracy of the silver-standard, double-zeta-level CCSD(T)/CBS estimates through the use of explicit correlation and midbond basis functions. We also outline the remaining challenges in the accurate ab initio calculations of noncovalent interaction energies.
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The recently proposed spin-flip symmetry-adapted perturbation theory (SF-SAPT) first-order exchange energy [Patkowski et al., J. Chem. Phys. 148, 164110 (2018)] enables the standard open-shell SAPT approach to treat arbitrary spin states of the weakly interacting complex. Here, we further extend first-order SF-SAPT beyond the single-exchange approximation to a complete treatment of the exchanges of electrons between monomers. This new form of the exchange correction replaces the single-exchange approximation with a more moderate single-spin-flip approximation. The newly developed expressions are applied to a number of small test systems to elucidate the quality of both approximations. They are also applied to the singlet-triplet splittings in pancake bonded dimers. The accuracy of the single-exchange approximation deteriorates at short intermolecular separations, especially for systems with few electrons and for the high-spin state of the complex. In contrast, the single-spin-flip approximation is exact for interactions involving a doublet molecule and remains highly accurate for any number of unpaired electrons. Because the single-exchange approximation affects the high-spin and low-spin states of pancake bonded complexes evenly, the resulting splitting values are of similar accuracy to those produced by the formally more accurate single-spin-flip approximation.
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We present a symmetry-adapted perturbation theory (SAPT) for the interaction of two high-spin open-shell molecules (described by their restricted open-shell Hartree-Fock determinants) resulting in low-spin states of the complex. The previously available SAPT formalisms, except for some system-specific studies for few-electron complexes, were restricted to the high-spin state of the interacting system. Thus, the new approach provides, for the first time, a SAPT-based estimate of the splittings between different spin states of the complex. We have derived and implemented the lowest-order SAPT term responsible for these splittings, that is, the first-order exchange energy. We show that within the so-called S2 approximation commonly used in SAPT (neglecting effects that vanish as fourth or higher powers of intermolecular overlap integrals), the first-order exchange energies for all multiplets are linear combinations of two matrix elements: a diagonal exchange term that determines the spin-averaged effect and a spin-flip term responsible for the splittings between the states. The numerical factors in this linear combination are determined solely by the Clebsch-Gordan coefficients: accordingly, the S2 approximation implies a Heisenberg Hamiltonian picture with a single coupling strength parameter determining all the splittings. The new approach is cast into both molecular-orbital and atomic-orbital expressions: the latter enable an efficient density-fitted implementation. We test the newly developed formalism on several open-shell complexes ranging from diatomic systems (Liâ¯H, Mnâ¯Mn, ) to the phenalenyl dimer.
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We have developed a new krypton-krypton interaction-induced isotropic dipole polarizability curve based on high-level ab initio methods. The determination was carried out using the coupled-cluster singles and doubles plus perturbative triples method with very large basis sets up to augmented correlation-consistent sextuple zeta as well as the corrections for core-core and core-valence correlation and relativistic effects. The analytical function of polarizability and our recently constructed reference interatomic potential [J. M. Waldrop et al., J. Chem. Phys. 142, 204307 (2015)] were used to predict the thermophysical and electromagnetic properties of krypton gas. The second pressure, acoustic, and dielectric virial coefficients were computed for the temperature range of 116 K-5000 K using classical statistical mechanics supplemented with high-order quantum corrections. The virial coefficients calculated were compared with the generally less precise available experimental data as well as with values computed from other potentials in the literature {in particular, the recent highly accurate potential of Jäger et al. [J. Chem. Phys. 144, 114304 (2016)]}. The detailed examination in this work suggests that the present theoretical prediction can be applied as reference values in disciplines involving thermophysical and electromagnetic properties of krypton gas.
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We assessed the performance of a large variety of modern density functional theory approaches for the adsorption of carbon dioxide on molecular models of pyridinic N-doped graphene. Specifically, we selected eight polyheterocyclic aromatic compounds ranging from pyridine and pyrazine to 1,6-diazacoronene and investigated their complexes with CO2 for a large range of intermolecular distances and including both in-plane and stacked orientations. The benchmark interaction energies were computed at the complete-basis-set limit MP2 level plus a CCSD(T) coupled-cluster correction in a moderate but carefully selected basis set. Using a set of 96 benchmark CCSD(T)-level interaction energies as a reference, we investigated the accuracy of DFT-based approaches as a function of the density functional, the dispersion correction, the basis set, and the counterpoise correction or lack thereof. While virtually all DFT variants exhibit some deterioration of accuracy for distances slightly shorter than the van der Waals minima, we were able to identify several schemes such as B2PLYP-D3 and M05-2X-D3 whose average errors on the entire benchmark data set are in the 5-10% range. The top DFT performers were subsequently used to investigate the energy profile for a carbon dioxide transition through model N-doped graphene pores. All investigated methods confirmed that the largest, N4H4 pore allows for a barrierless CO2 transition to the other side of a graphene sheet.
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A new highly accurate potential energy curve for the krypton dimer was constructed using coupled-cluster calculations up to the singles, doubles, triples, and perturbative quadruples level, including corrections for core-core and core-valence correlation and for relativistic effects. The ab initio data points were fitted to an analytic potential which was used to compute the most important transport properties of the krypton gas. The viscosity, thermal conductivity, self-diffusion coefficient, and thermal diffusion factor were calculated by the kinetic theory at low density and temperatures from 116 to 5000 K. The comparisons with literature experimental data as well as with values from other pair potentials indicate that our new potential is superior to all previous ones. The transport property values computed in this work are recommended as standard values over the complete temperature range.
RESUMEN
An accurate 2D ab initio potential energy surface of the He-C3 collisional system is calculated using the supermolecular coupled-cluster method with up to perturbative quadruple excitations, CCSDT(Q). This interaction potential is then incorporated in full close-coupling calculations of rotational excitation/de-excitation cross sections in He + C3 collisions for rotational levels j = 0, 2, ..., 10 and collision energies up to 1000 cm(-1). Corresponding rate coefficients are reported for temperature between 1 and 100 K. Results are found to be in excellent agreement with available theoretical data that were restricted to the temperature range of 5-15 K. Implications of the computed rate coefficients to astrophysical models of C3 and carbon clusters in interstellar and circumstellar environments are discussed.
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Interaction energies for seven weakly bound dimers involving helium, argon, water, and methane are computed using large correlation-consistent basis sets augmented with bond functions. The estimates of the coupled-cluster singles, doubles, and noniterative triples [CCSD(T)] complete basis set limit are obtained using both the conventional approach and several variants of the explicitly correlated CCSD(T)-F12 method. It is shown that both bond functions and the F12 approach significantly speed up the convergence of the CCSD(T)/aug-cc-pVXZ interaction energies with the basis set cardinal number X. However, the extent of improvement provided by each technique varies with the character of the interactions-the F12 method works best for polar, electrostatics-bound dimers, while for dispersion-dominated complexes the addition of bond functions is more efficient. The convergence rate afforded by different coupled-cluster variants is fairly consistent across the entire attractive region of the potential curve, while the improvement provided by the F12 correction increases along the repulsive wall. The use of large basis sets and the agreement between conventional and explicitly correlated approaches allow us to assess the importance of different residual approximations present in the popular CCSD(T)-F12 implementations.
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A new highly accurate interaction potential is constructed for the He-H2 van der Waals complex. This potential is fitted to 1900 ab initio energies computed at the very large-basis coupled-cluster level and augmented by corrections for higher-order excitations (up to full configuration interaction level) and the diagonal Born-Oppenheimer correction. At the vibrationally averaged H-H bond length of 1.448736 bohrs, the well depth of our potential, 15.870 ± 0.065 K, is nearly 1 K larger than the most accurate previous studies have indicated. In addition to constructing our own three-dimensional potential in the van der Waals region, we present a reparameterization of the Boothroyd-Martin-Peterson potential surface [A. I. Boothroyd, P. G. Martin, and M. R. Peterson, J. Chem. Phys. 119, 3187 (2003)] that is suitable for all configurations of the triatomic system. Finally, we use the newly developed potentials to compute the properties of the lone bound states of (4)He-H2 and (3)He-H2 and the interaction second virial coefficient of the hydrogen-helium mixture.
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The basis set convergence of weak interaction energies for dimers of noble gases helium through krypton is studied for six variants of the explicitly correlated, frozen geminal coupled-cluster singles, doubles, and noniterative triples [CCSD(T)-F12] approach: the CCSD(T)-F12a, CCSD(T)-F12b, and CCSD(T)(F12*) methods with scaled and unscaled triples. These dimers were chosen because CCSD(T) complete-basis-set (CBS) limit benchmarks are available for them to a particularly high precision. The dependence of interaction energies on the auxiliary basis sets has been investigated and it was found that the default resolution-of-identity sets cc-pVXZ/JKFIT are far from adequate in this case. Overall, employing the explicitly correlated approach clearly speeds up the basis set convergence of CCSD(T) interaction energies, however, quite surprisingly, the improvement is not as large as the one achieved by a simple addition of bond functions to the orbital basis set. Bond functions substantially improve the CCSD(T)-F12 interaction energies as well. For small and moderate bases with bond functions, the accuracy delivered by the CCSD(T)-F12 approach cannot be matched by conventional CCSD(T). However, the latter method in the largest available bases still delivers the CBS limit to a better precision than CCSD(T)-F12 in the largest bases available for that approach. Our calculations suggest that the primary reason for the limited accuracy of the large-basis CCSD(T)-F12 treatment are the approximations made at the CCSD-F12 level and the non-explicitly correlated treatment of triples. In contrast, the explicitly correlated second-order Mo̸ller-Plesset perturbation theory (MP2-F12) approach is able to pinpoint the complete-basis-set limit MP2 interaction energies of rare gas dimers to a better precision than conventional MP2. Finally, we report and analyze an unexpected failure of the CCSD(T)-F12 method to deliver the core-core and core-valence correlation corrections to interaction energies consistently and accurately.
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The leading-order dispersion and exchange-dispersion terms in symmetry-adapted perturbation theory (SAPT), Edisp(20) and Eexch-disp(20), suffer from slow convergence to the complete basis set limit. To alleviate this problem, explicitly correlated variants of these corrections, Edisp(20)-F12 and Eexch-disp(20)-F12, have been proposed recently. However, the original formalism (M., Kodrycka , J. Chem. Theory Comput. 2019, 15, 5965-5986), while highly successful in terms of improving convergence, was not competitive to conventional orbital-based SAPT in terms of computational efficiency due to the need to manipulate several kinds of two-electron integrals. In this work, we eliminate this need by decomposing all types of two-electron integrals using robust density fitting. We demonstrate that the error of the density fitting approximation is negligible when standard auxiliary bases such as aug-cc-pVXZ/MP2FIT are employed. The new implementation allowed us to study all complexes in the A24 database in basis sets up to aug-cc-pV5Z, and the Edisp(20)-F12 and Eexch-disp(20)-F12 values exhibit vastly improved basis set convergence over their conventional counterparts. The well-converged Edisp(20)-F12 and Eexch-disp(20)-F12 numbers can be substituted for conventional Edisp(20) and Eexch-disp(20) ones in a calculation of the total SAPT interaction energy at any level (SAPT0, SAPT2+3, ...). We show that the addition of F12 terms does not improve the accuracy of low-level SAPT treatments. However, when the theory errors are minimized in high-level SAPT approaches such as SAPT2+3(CCD)δMP2, the reduction of basis set incompleteness errors thanks to the F12 treatment substantially improves the accuracy of small-basis calculations.
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The set of interaction energies for 22 systems of biological importance, developed by Jurecka et al. [Phys. Chem. Chem. Phys., 2006, 8, 1985] and called S22, became an often used benchmark for evaluating the performance of various computational methods. As the quality of such methods improves, the uncertainties of the S22 energies are becoming too large to enable meaningful comparisons. We therefore improved the benchmarks by performing calculations in larger basis sets than used by Jurecka et al. The basis extensions included additions of higher angular momentum, diffuse, and midbond functions. The percentage deviations of the original S22 interaction energies from our values are up to 15.4%. We have estimated that the average (unsigned) uncertainty of our results should be about 1.0%. This estimate includes contributions from basis set truncation, frozen-core approximation, and neglected electron excitations.