Blind test of density-functional-based methods on intermolecular interaction energies

Ab Initio Extended Hartree-Fock plus Dispersion Method Applied to Dimers with Hundreds of Atoms

The Hartree-Fock plus dispersion plus first-order correlation (HFDc⁽¹⁾) method consists in augmenting the HF interaction energy by the correlation part of the first-order interaction energy and the second-order dispersion and exchange-dispersion energies. All of the augmentation terms are computed using the symmetry-adapted perturbation theory based on density functional theory description of monomers [SAPT(DFT)]; thus, HFDc⁽¹⁾ is a fully ab initio method. A partly empirical version of this method, HFD_asc⁽¹⁾, uses a damped asymptotic expansion for the dispersion plus exchange-dispersion term fitted to SAPT(DFT) ab initio values. The HFDc⁽¹⁾ interaction energies for dimers in the S22, S66, S66x8, NCCE31, IonHB, and UD-ARL benchmark data sets are more accurate than those given by most ab initio methods with comparable costs. HFDc⁽¹⁾ can be used routinely for dimers with nearly 200 atoms, such as included in the S12L benchmark set, giving results comparable to those obtained by the most expensive methods applicable.

Theoretical investigation of the ORR on boron-silicon nanotubes (B-SiNTs) as acceptable catalysts in fuel cells

Here, the potential of boron doped silicon nanotubes (7, 0) as ORR catalysts is examined. Acceptable paths for the ORR on studied catalysts are examined through DFT. The optimum mechanism of the ORR on the surface of B2-SiNT (7, 0) is shown. The ORR on the surface of B2-SiNTs (7, 0) can continue through LH and ER mechanisms. The calculated beginning voltage for the ORR on B2-SiNTs (7, 0) is 0.37 V and it is smaller than the beginning voltage (0.45 V) for platinum-based catalysts. In the acidic solution the beginning voltage for the oxygen reduction process can be evaluated to be 0.97 V, which corresponds to 0.37 V as a minimum overvoltage for the ORR. The B2-SiNTs (7, 0) are suggested as an ORR catalyst in acidic environments.

Soft experimental constraints for soft interactions: a spectroscopic benchmark data set for weak and strong hydrogen bonds

An experimental benchmark data base on rotational constants, vibrational properties and energy differences for weakly and more strongly hydrogen-bonded complexes and their constituents from the spectroscopic literature is assembled. It is characterized in detail and finally contracted to a more compact, discriminatory set (ENCH-51, for Experimental Non-Covalent Harmonic with 51 entries). The meeting points between theory and experiment consist of equilibrium rotational constants and harmonic frequencies and energies, which are back-corrected from experimental observables and are very easily accessible by quantum chemical calculations. The relative performance of B3LYP-D3, PBE0-D3 and M06-2X density functional theory predictions with a quadruple-zeta basis set is used to illustrate systematic errors, error compensation and selective performance for structural, vibrational and energetical observables. The current focus is on perspectives and different benchmarking methodologies, rather than on a specific theoretical method or a specific class of compounds. Extension of the data base in chemical, observable and quantum chemical method space is encouraged.

Range-separated double-hybrid density-functional theory with coupled-cluster and random-phase approximations

We construct range-separated double-hybrid (RSDH) schemes which combine coupled-cluster or random-phase approximations (RPAs) with a density functional based on a two-parameter Coulomb-attenuating-method-like decomposition of the electron-electron interaction. We find that the addition of a fraction of short-range electron-electron interaction in the wave-function part of the calculation is globally beneficial for the RSDH scheme involving a variant of the RPA with exchange terms. Even though the latter scheme is globally as accurate as the corresponding scheme employing only second-order Møller-Plesset perturbation theory for atomization energies, reaction barrier heights, and weak intermolecular interactions of small molecules, it is more accurate for the more complicated case of the benzene dimer in the stacked configuration. The present RSDH scheme employing a RPA thus represents a new member in the family of double hybrids with minimal empiricism which could be useful for general chemical applications.

Nine questions on energy decomposition analysis

The paper collects the answers of the authors to the following questions: Is the lack of precision in the definition of many chemical concepts one of the reasons for the coexistence of many partition schemes? Does the adoption of a given partition scheme imply a set of more precise definitions of the underlying chemical concepts? How can one use the results of a partition scheme to improve the clarity of definitions of concepts? Are partition schemes subject to scientific Darwinism? If so, what is the influence of a community's sociological pressure in the "natural selection" process? To what extent does/can/should investigated systems influence the choice of a particular partition scheme? Do we need more focused chemical validation of Energy Decomposition Analysis (EDA) methodology and descriptors/terms in general? Is there any interest in developing common benchmarks and test sets for cross-validation of methods? Is it possible to contemplate a unified partition scheme (let us call it the "standard model" of partitioning), that is proper for all applications in chemistry, in the foreseeable future or even in principle? In the end, science is about experiments and the real world. Can one, therefore, use any experiment or experimental data be used to favor one partition scheme over another? © 2019 Wiley Periodicals, Inc.

Dispersion Energy from Local Polarizability Density

A simple nonlocal functional for calculation of dispersion energies is proposed. Compared to a similar formula used earlier, we introduced a regularization to remove its singularities and used a dynamic polarizability density similar to those in the so-called van der Waals density functionals. The performance of the new functional is tested on dispersion energies for a set of representative dimers, and it is found that it is significantly more accurate than published nonlocal functionals.

A generally applicable atomic-charge dependent London dispersion correction

The so-called D4 model is presented for the accurate computation of London dispersion interactions in density functional theory approximations (DFT-D4) and generally for atomistic modeling methods. In this successor to the DFT-D3 model, the atomic coordination-dependent dipole polarizabilities are scaled based on atomic partial charges which can be taken from various sources. For this purpose, a new charge-dependent parameter-economic scaling function is designed. Classical charges are obtained from an atomic electronegativity equilibration procedure for which efficient analytical derivatives with respect to nuclear positions are developed. A numerical Casimir-Polder integration of the atom-in-molecule dynamic polarizabilities then yields charge- and geometry-dependent dipole-dipole dispersion coefficients. Similar to the D3 model, the dynamic polarizabilities are precomputed by time-dependent DFT and all elements up to radon (Z = 86) are covered. The two-body dispersion energy expression has the usual sum-over-atom-pairs form and includes dipole-dipole as well as dipole-quadrupole interactions. For a benchmark set of 1225 molecular dipole-dipole dispersion coefficients, the D4 model achieves an unprecedented accuracy with a mean relative deviation of 3.8% compared to 4.7% for D3. In addition to the two-body part, three-body effects are described by an Axilrod-Teller-Muto term. A common many-body dispersion expansion was extensively tested, and an energy correction based on D4 polarizabilities is found to be advantageous for larger systems. Becke-Johnson-type damping parameters for DFT-D4 are determined for more than 60 common density functionals. For various standard energy benchmark sets, DFT-D4 slightly but consistently outperforms DFT-D3. Especially for metal containing systems, the introduced charge dependence of the dispersion coefficients improves thermochemical properties. We suggest (DFT-)D4 as a physically improved and more sophisticated dispersion model in place of DFT-D3 for DFT calculations as well as other low-cost approaches like semi-empirical models.

The Good, the Bad, and the Ugly: "HiPen", a New Dataset for Validating (S)QM/MM Free Energy Simulations

Indirect (S)QM/MM free energy simulations (FES) are vital to efficiently incorporating sufficient sampling and accurate (QM) energetic evaluations when estimating free energies of practical/experimental interest. Connecting between levels of theory, i.e., calculating Δ A l o w → h i g h , remains to be the most challenging step within an indirect FES protocol. To improve calculations of Δ A l o w → h i g h , we must: (1) compare the performance of all FES methods currently available; and (2) compile and maintain datasets of Δ A l o w → h i g h calculated for a wide-variety of molecules so that future practitioners may replicate or improve upon the current state-of-the-art. Towards these two aims, we introduce a new dataset, "HiPen", which tabulates Δ A g a s M M → 3 o b (the free energy associated with switching from an M M to an S C C - D F T B molecular description using the 3ob parameter set in gas phase), calculated for 22 drug-like small molecules. We compare the calculation of this value using free energy perturbation, Bennett's acceptance ratio, Jarzynski's equation, and Crooks' equation. We also predict the reliability of each calculated Δ A g a s M M → 3 o b by evaluating several convergence criteria including sample size hysteresis, overlap statistics, and bias metric ( Π ). Within the total dataset, three distinct categories of molecules emerge: the "good" molecules, for which we can obtain converged Δ A g a s M M → 3 o b using Jarzynski's equation; "bad" molecules which require Crooks' equation to obtain a converged Δ A g a s M M → 3 o b ; and "ugly" molecules for which we cannot obtain reliably converged Δ A g a s M M → 3 o b with either Jarzynski's or Crooks' equations. We discuss, in depth, results from several example molecules in each of these categories and describe how dihedral discrepancies between levels of theory cause convergence failures even for these gas phase free energy simulations.

Halogen bonds and σ-holes

The models behind simple bonding theory and the origins of some components often proposed to be involved in weak intermolecular bonds are described with special reference to σ-hole bonding, of which halogen bonds are a subset. A protocol for the analysis of weak intermolecular interactions is proposed on the basis of sound physical principles. This protocol uses three different levels of interaction; "permanent" Coulomb interactions between unperturbed monomers, relaxed Coulomb interactions and dispersion. Of the three, only dispersion is not a real, measurable quantity. It is, however, included in order to describe interactions that cannot be treated entirely by the first two levels.

Strained hydrogen bonding in imidazole trimer: a combined infrared, Raman, and theory study

This is not how three imidazole molecules prefer to arrange, as a combined IR, Raman and computational analysis unambiguously shows.

Do Semilocal Density-Functional Approximations Recover Dispersion Energies at Small Intermonomer Separations?

The methods that add dispersion energies to interaction energies computed using density-functional theory (DFT), known as DFT+D methods, taper off the dispersion energies at distances near van der Waals minima and smaller based on an assumption that DFT starts to reproduce the dispersion energies there. We show that this assumption is not correct as the alleged contribution behaves unphysically and originates to a large extent from nonexchange-correlation terms. Thus, dispersion functions correct DFT in this region for deficiencies unrelated to dispersion interactions.

Range-Separated Double-Hybrid Functional from Nonempirical Constraints

On the basis of our previous developments in the field of nonempirical double hybrids, we present here a new exchange-correlation functional based on a range-separated model for the exchange part and integrating a nonlocal perturbative correction to the electron correlation contribution. Named RSX-QIDH, the functional is free from any kind of empirical parametrization. Its range-separation parameter is set to recover the total energy of the hydrogen atom, thus eliminating the self-interaction error for this one-electron system. Subsequent tests on some relevant benchmark data sets confirm that the self-interaction error is particularly low for RSX-QIDH. This new functional provides also correct dissociation profiles for charged rare-gas dimers and very accurate ionization potentials directly from Kohn-Sham orbital energies. Above all, these good results are not obtained at the expense of other properties. Indeed, further tests on standard benchmarks show that RSX-QIDH is competitive with the more empirical ωB97X-2 double hybrid and outperforms the parent LC-PBE long-range corrected hybrid, thus underlining the important role of the nonlocal perturbative correlation.

A three-armed cryptand with triazine and pyridine units: synthesis, structure and complexation with polycyclic aromatic compounds

The aromatic nucleophilic substitution reaction based synthesis of a three-armed cryptand displaying 2,4,6-triphenyl-1,3,5-triazine units as caps and pyridine rings in the bridges, along with NMR, MS and molecular modelling-based structural analysis of this compound are reported. Appropriate NMR and molecular modelling investigations proved the formation of 1:1 host–guest assemblies between the investigated cryptand and some polynuclear aromatic hydrocarbons or their derivatives.

A Systematic Protocol for Benchmarking Guest-Host Interactions by First-Principles Computations: Capturing CO2 in Clathrate Hydrates

Clathrate hydrates of CO₂ have been proposed as potential molecular materials in tackling important environmental problems related to greenhouse gases capture and storage. Despite the increasing interest in such hydrates and their technological applications, a molecular-level understanding of their formation and properties is still far from complete. Modeling interactions is a challenging and computationally demanding task, essential to reliably determine molecular properties. First-principles calculations for the CO₂ guest in all sI, sII, and sH clathrate cages were performed, and the nature of the guest-host interactions, dominated by both hydrogen-bond and van der Waals forces, was systematically investigated. Different families of density functionals, as well as pairwise CO₂ @H₂ O model potentials versus wavefunction-based quantum approaches were studied for CO₂ clathrate-like systems. Benchmark energies for new distance-dependent datasets, consisting of potential energy curves sampling representative configurations of the systems at the repulsive, near-equilibrium, and asymptotic/long-range regions of the full-dimensional surface, were generated, and a general protocol was proposed to assess the accuracy of such conventional and modern approaches at minimum and non-minimum orientations. Our results show that dispersion interactions are important in the guest-host stabilization energies of such clathrate cages, and the encapsulation of the CO₂ into guest-free clathrate cages is always energetically favorable. In addition, the orientation of CO₂ inside each cage was explored, and the ability of current promising approaches to accurately describe non-covalent CO₂ @H₂ O guest-host interactions in sI, sII, and sH clathrates was discussed, providing information for their applicability to future multiscale computer simulations.

A general range-separated double-hybrid density-functional theory

A range-separated double-hybrid (RSDH) scheme which generalizes the usual range-separated hybrids and double hybrids is developed. This scheme consistently uses a two-parameter Coulomb-attenuating-method (CAM)-like decomposition of the electron-electron interaction for both exchange and correlation in order to combine Hartree-Fock exchange and second-order Møller-Plesset (MP2) correlation with a density functional. The RSDH scheme relies on an exact theory which is presented in some detail. Several semi-local approximations are developed for the short-range exchange-correlation density functional involved in this scheme. After finding optimal values for the two parameters of the CAM-like decomposition, the RSDH scheme is shown to have a relatively small basis dependence and to provide atomization energies, reaction barrier heights, and weak intermolecular interactions globally more accurate or comparable to range-separated MP2 or standard MP2. The RSDH scheme represents a new family of double hybrids with minimal empiricism which could be useful for general chemical applications.

Extension of the D3 dispersion coefficient model

A new model, termed D4, for the efficient computation of molecular dipole-dipole dispersion coefficients is presented. As in the related, well established D3 scheme, these are obtained as a sum of atom-in-molecule dispersion coefficients over atom pairs. Both models make use of dynamic polarizabilities obtained from first-principles time-dependent density functional theory calculations for atoms in different chemical environments employing fractional atomic coordination numbers for interpolation. Different from the D3 model, the coefficients are obtained on-the-fly by numerical Casimir-Polder integration of the dynamic, atomic polarizabilities α(iω). Most importantly, electronic density information is now incorporated via atomic partial charges computed at a semi-empirical quantum mechanical tight-binding level, which is used to scale the polarizabilities. Extended statistical measures show that errors for dispersion coefficients with the proposed D4 method are significantly lower than with D3 and other, computationally more involved schemes. Alongside, accurate isotropic charge and hybridization dependent, atom-in-molecule static polarizabilities are obtained with an unprecedented efficiency. Damping function parameters are provided for three standard density functionals, i.e., TPSS, PBE0, and B3LYP, allowing evaluation of the new DFT-D4 model for common non-covalent interaction energy benchmark sets.

Mechanisms of acetylcholinesterase protection against sarin and soman by adenosine A1 receptor agonist N6-cyclopentyladenosine

Organophosphorus nerve agents (NAs) irreversibly inhibit acetylcholinesterase (AChE), the enzyme responsible for breaking down the neurotransmitter acetylcholine (ACh). The over accumulation of ACh after NA exposure leads to cholinergic toxicity, seizure, and death. Current medical countermeasures effectively mitigate peripheral symptoms, however; the brain is often unprotected. Alternative acute treatment with the adenosine A₁ receptor agonist N⁶-cyclopentyladensosine (CPA) has previously been demonstrated to prevent AChE inhibition as well as to suppress neuronal activity. The mechanism of AChE protection is unknown. To elucidate the feasibility of potential CPA-AChE interaction mechanisms, we applied a truncated molecular model approach and density functional theory. The candidate mechanisms studied are reversible enzyme inhibition, enzyme reactivation, and NA blocking prior to enzyme conjugation. Our thermodynamic data suggest that CPA can compete with the NAs sarin and soman for the active site of AChE, but may, in contrast to NAs, undergo back-reaction. We found a strong interaction between CPA and NA conjugated AChE, making enzyme reactivation unlikely but possibly allowing for CPA protection through the prevention of NA aging. The data also indicates that there is an affinity between CPA and unbound NAs. The results from this study support the hypothesis that CPA counters NA toxicity via multiple mechanisms and is a promising therapeutic strategy that warrants further development.

2-Ethynylpyridine dimers: IR spectroscopic and computational study

2-ethynylpyridine (2-EP) presents a multifunctional system capable of participation in hydrogen-bonded complexes utilizing hydrogen bond donating (CH, Aryl-H) and hydrogen bond accepting functions (N-atom, CC and pyridine π-systems). In this work, IR spectroscopy and theoretical calculations are used to study possible 2-EP dimer structures as well as their distribution in an inert solvent such as tetrachloroethene. Experimentally, the CH stretching vibration of the 2-EP monomer absorbs close to 3300 cm^-1, whereas a broad band with maximum around 3215 cm^-1 emerges as the concentration rises, indicating the formation of hydrogen-bonded complexes involving the CH moiety. The CC stretching vibration of monomer 2-EP close to 2120 cm^-1 is, using derivative spectroscopy, resolved from the signals of the dimer complexes with maximum around 2112 cm^-1. Quantum chemical calculations using the B3LYP + D3 model with counterpoise correction predict that the two most stable dimers are of the π-stacked variety, closely followed by dimers with intermolecular CH⋯N hydrogen bonding; the predicted red shifts of the CH stretching wavenumbers due to hydrogen bonding are in the range 54-120 cm^-1. No species with obvious hydrogen bonding involving the CC or pyridine π-systems as acceptors are predicted. Dimerization constant at 25 °C is estimated to be K₂ = 0.13 ± 0.01 mol^-1 dm³.

Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems

pH is a critical parameter for biological and technological systems directly related with electrical charges. It can give rise to peculiar electrostatic phenomena, which also makes them more challenging. Due to the quantum nature of the process, involving the forming and breaking of chemical bonds, quantum methods should ideally by employed. Nevertheless, due to the very large number of ionizable sites, different macromolecular conformations, salt conditions, and all other charged species, the CPU time cost simply becomes prohibitive for computer simulations, making this a quite complex problem. Simplified methods based on Monte Carlo sampling have been devised and will be reviewed here, highlighting the updated state-of-the-art of this field, advantages, and limitations of different theoretical protocols for biomolecular systems (proteins and nucleic acids). Following a historical perspective, the discussion will be associated with the applications to protein interactions with other proteins, polyelectrolytes, and nanoparticles.

Benchmarking Quantum Chemical Methods: Are We Heading in the Right Direction?

Theoreticians and experimentalists should work together more closely to establish reliable rankings and benchmarks for quantum chemical methods. Comparison to carefully designed experimental benchmark data should be a priority. Guidelines to improve the situation for experiments and calculations are proposed.

Quantum confinement of molecular deuterium clusters in carbon nanotubes: ab initio evidence for hexagonal close packing

This study shows ab initio evidence for hexagonal close packing of D₂ molecules in carbon nanotubes, with a = 3.6 Å and .

A look at the density functional theory zoo with the advanced GMTKN55 database for general main group thermochemistry, kinetics and noncovalent interactions

We present the updated and extended GMTKN55 benchmark database for more accurate and extensive energetic evaluation of density functionals and other electronic structure methods with detailed guidelines for method users.