Theory cracks old data: Rovibrational energy levels of orthoH2-CO derived from experiment.

Measurements of rovibrational spectra of clusters provide physical insight only if spectral lines can be assigned to pairs of quantum states, and further insight is obtained if one can deduce the quantitative energy-level pattern. Both steps can be so difficult that some measured spectra remain unassigned, one example is orthoH2-CO. To extend the scope of spectroscopic insights, we propose to use theoretical information in interpretation of spectra. We first performed high accuracy, full-dimensional calculations of the orthoH2-CO spectrum, at the highest practically achievable levels of electronic structure theory and quantum nuclear dynamics. Then, an iterative, theory-guided method developed here allowed us to fully interpret the spectrum of orthoH2-CO, extending the range of van der Waals clusters for which spectroscopy can provide physical insights.

Physical mechanisms of intermolecular interactions from symmetry-adapted perturbation theory.

Symmetry-adapted perturbation theory (SAPT) is a method for computational studies of noncovalent interactions between molecules. This method will be discussed here from the perspective of establishing the paradigm for understanding mechanisms of intermolecular interactions. SAPT interaction energies are obtained as sums of several contributions. Each contribution possesses a clear physical interpretation as it results from some specific physical process. It also exhibits a specific dependence on the intermolecular separation R. The four major contributions are the electrostatic, induction, dispersion, and exchange energies, each due to a different mechanism, valid at any R. In addition, at large R, SAPT interaction energies are seamlessly connected with the corresponding terms in the asymptotic multipole expansion of interaction energy in inverse powers of R. Since such expansion explicitly depends on monomers' multipole moments and polarizabilities, this connection provides additional insights by rigorously relating interaction energies to monomers' properties.

Reliable crystal structure predictions from first principles.

An inexpensive and reliable method for molecular crystal structure predictions (CSPs) has been developed. The new CSP protocol starts from a two-dimensional graph of crystal's monomer(s) and utilizes no experimental information. Using results of quantum mechanical calculations for molecular dimers, an accurate two-body, rigid-monomer ab initio-based force field (aiFF) for the crystal is developed. Since CSPs with aiFFs are essentially as expensive as with empirical FFs, tens of thousands of plausible polymorphs generated by the crystal packing procedures can be optimized. Here we show the robustness of this protocol which found the experimental crystal within the 20 most stable predicted polymorphs for each of the 15 investigated molecules. The ranking was further refined by performing periodic density-functional theory (DFT) plus dispersion correction (pDFT+D) calculations for these 20 top-ranked polymorphs, resulting in the experimental crystal ranked as number one for all the systems studied (and the second polymorph, if known, ranked in the top few). Alternatively, the polymorphs generated can be used to improve aiFFs, which also leads to rank one predictions. The proposed CSP protocol should result in aiFFs replacing empirical FFs in CSP research.

Factors influencing hydrogen peroxide versus water inclusion in molecular crystals.

Hydrate formation is often unavoidable during crystallization, leading to performance degradation of pharmaceuticals and energetics. In some cases, water molecules trapped within crystal lattices can be substituted for hydrogen peroxide, improving the solubility of drugs and detonation performance of explosives. The present work compares hydrates and hydrogen peroxide solvates in two ways: (1) analyzing structural motifs present in crystal structures accessed from the Cambridge Structural Database and (2) developing potential energy surfaces for water and hydrogen peroxide interacting with functional groups of interest at geometries relevant to the solid state. By elucidating fundamental differences in local interactions that can be formed with molecules of hydrogen peroxide and/or water, the analyses presented here provide a foundation for the design and selection of candidate molecules for the formation of hydrogen peroxide solvates.

Ammonia dimer: extremely fluxional but still hydrogen bonded.

In the 1980s, Nelson, Fraser, and Klemperer (NFK) published an experimentally derived structure of the ammonia dimer dramatically different from the structure determined computationally, which led these authors to the question "Does ammonia hydrogen bond?". This question has not yet been answered satisfactorily. To answer it, we have developed an ab initio potential energy surface (PES) for this dimer at the limits of the current computational capabilities and performed essentially exact six-dimensional calculations of the vibration-rotation-tunneling (VRT) spectra of NH3-NH3 and ND3-ND3, obtaining an unprecedented agreement with experimental spectra. In agreement with other recent electronic structure calculations, the global minimum on the PES is in a substantially bent hydrogen-bonded configuration. Since the bottom of the PES is exceptionally flat, the dimer is extremely fluxional and the probability of finding it in configurations that are not hydrogen bonded is high. Nevertheless, the probability of hydrogen-bonded configurations is large enough to consider the ammonia dimer to be hydrogen bonded. We also show that NFK's inference that the ammonia dimer is nearly rigid actually results from unusual cancellations between quantum effects that generate differences in spectra of different isotopologues.

Extension of an Atom-Atom Dispersion Function to Halogen Bonds and Its Use for Rational Design of Drugs and Biocatalysts.

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.

SAPT codes for calculations of intermolecular interaction energies.

Symmetry-adapted perturbation theory (SAPT) is a method for calculations of intermolecular (noncovalent) interaction energies. The set of SAPT codes that is described here, the current version named SAPT2020, includes virtually all variants of SAPT developed so far, among them two-body SAPT based on perturbative, coupled cluster, and density functional theory descriptions of monomers, three-body SAPT, and two-body SAPT for some classes of open-shell monomers. The properties of systems governed by noncovalent interactions can be predicted only if potential energy surfaces (force fields) are available. SAPT is the preferred approach for generating such surfaces since it is seamlessly connected to the asymptotic expansion of interaction energy. SAPT2020 includes codes for automatic development of such surfaces, enabling generation of complete dimer surfaces with a rigid monomer approximation for dimers containing about one hundred atoms. These codes can also be used to obtain surfaces including internal degrees of freedom of monomers.

Automatic Generation of Flexible-Monomer Intermolecular Potential Energy Surfaces.

A method is developed for automatic generation of nonreactive intermolecular two-body potential energy surfaces (PESs) including intramonomer degrees of freedom. This method, called flex-autoPES, is an extension of the autoPES method developed earlier, which assumes rigid monomers. In both cases, the whole PES development proceeds without any human intervention. The functional form used is a sum of products of site-site functions (both atomic and off-atomic sites can be used). The leading terms with sites involving different monomers are of physically motivated form. The long-range part of a PES is computed from monomer properties without using any dimer information. The close-range part is fitted to dimer interaction energies computed using electronic structure methods. Virtually any method can be used in such calculations, but the use of symmetry-adapted perturbation theory provides a seamless connection to the long-range part of the PES. The performance of the flex-autoPES code was tested by developing a full-dimensional PES for the water dimer and PESs including only some soft intramonomer degrees of freedom for the ethylene glycol dimer and for the ethylene glycol-water dimer. In the case of the water dimer, the root-mean-square error (RMSE) of the PES from the data points with negative total energies is 0.03 kcal/mol, and we expect this PES to be more accurate than any previously published PES of this type. For the ethylene glycol dimer and the ethylene glycol-water dimers, the analogous RMSEs are 0.25 and 0.1 kcal/mol, respectively.

A statistically guided grid generation method and its application to intermolecular potential energy surfaces.

We present a method for the generation of points in space needed to create training data for fitting of nonlinear parametric models. This method uses statistical information extracted from an initial fit on a sparse grid to select optimal grid points in an iterative manner and is, therefore, called the iterative variance minimizing grid approach. We demonstrate the method in the case of six-dimensional intermolecular potential energy surfaces (PESs) fitted to ab initio computed interaction energies. The number of required grid points is reduced by roughly a factor of two in comparison to alternative systematic sampling methods. The method is not limited to fitting PESs and can be applied to any cases of fitting parametric models where data points may be chosen freely but are expensive to obtain.

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, HFDasc(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.

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.

Molecular dimers of methane clathrates: ab initio potential energy surfaces and variational vibrational states.

Motivated by the energetic and environmental relevance of methane clathrates, highly accurate ab initio potential energy surfaces (PESs) have been developed for the three possible dimers of the methane and water molecules: (H2O)2, CH4·H2O, and (CH4)2. While only a single monomer geometry was used for each monomer in the ab initio calculations, the PES parameterization makes it possible to produce distinct surfaces for all isotopologues within the rigid-monomer approximation. The PESs were fitted to computations at the frozen-core coupled-cluster level with single, double, and non-iterative triple excitations, employing basis sets of augmented triple- and quadruple-zeta quality plus bond functions, followed by extrapolations to the complete basis set limit. The long-range parts of the PESs are computed using the asymptotic version of symmetry-adapted perturbation theory based on a density-functional description of the monomers. All PESs are polarizable, i.e., in cluster or condensed-phase applications they approximate many-body effects by the induced dipole polarization model. The PESs were developed in a fully automated procedure applying the autoPES method, which is used for the first time to generate near-spectroscopic quality surfaces. The stationary points (SPs) on the PESs have been determined and compared with literature data. For CH4·H2O, previously unknown SPs have been identified and the first detailed study of the (CH4)2 potential energy landscape has been carried out. The PESs were used in variational quantum nuclear motion computations. For the water dimer, the resulting vibrational transitions are in excellent agreement with available high-resolution spectroscopic data. For (CH4)2, the intermonomer vibrational states are reported for the first time.

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.

Does a pair of methane molecules aggregate in water?

Molecular dynamics (MD) simulations of methane-water mixtures were performed using ab initio force fields for the CH4-H2O, H2O-H2O, and CH4-CH4 interactions. Both methane and water molecules were polarizable. From these calculations, the potential of mean force (PMF) between two methane molecules was extracted. Our results are compared with PMFs from a density-functional-theory (DFT) based Born-Oppenheimer type MD (BOMD) simulation, from a Monte Carlo (MC) simulation with ab initio-based force fields, and from MD simulations with empirical force fields. Our PMF is qualitatively similar to that obtained from the simulations with empirical force fields but differs significantly from those resulting from the DFT-BOMD and MC simulations. The depth of the PMF global minimum obtained in the present work is in a much better agreement with the experimental estimate than the result of the DFT-BOMD simulation, possibly due to the inability of DFT to describe the dispersion interactions and the lack of extensive sampling in the BOMD simulations. Our work indicates that, for a pair of methane molecules, there are configurations where the solvent increases the attraction between the solutes, but there are also conformations in which the solvent causes a weak net repulsion. On average, the methane molecules are more likely to be in the configuration where they are separated by a water molecule than in the one in which they are in contact even though the minimum of the PMF at the latter configuration is deeper than that at the former. Finally, we found that the water structure around methane solutes does not show a greater tetrahedral ordering than in neat bulk water.

Fully quantum calculation of the second and third virial coefficients of water and its isotopologues from ab initio potentials.

Path-Integral Monte Carlo methods were applied to calculate the second, B(T), and the third, C(T), virial coefficients for water. A fully quantum approach and state-of-the-art flexible-monomer pair and three-body potentials were used. Flexible-monomer potentials allow calculations for any isotopologue; we performed calculations for both H2O and D2O. For B(T) of H2O, the quantum effect contributes 25% of the value at 300 K and is not entirely negligible even at 1000 K, in accordance with recent literature findings. The effect of monomer flexibility, while not as large as some claims in the literature, is significant compared to the experimental uncertainty. It is of opposite sign to the quantum effect, smaller in magnitude than the latter below 500 K, and varies from 2% at 300 K to 10% at 700 K. When monomer flexibility is accounted for, results from the CCpol-8sf pair potential are in excellent agreement with the available experimental data and provide reliable B(T) values at temperatures outside the range of experimental data. The flexible-monomer MB-pol pair potential yields B(T) values that are slightly too high compared to experiment. For C(T), our calculations confirm earlier findings that the use of three-body potential is necessary for meaningful predictions. However, due to various uncertainties of the potentials used, especially the three-body ones, we were not able to establish benchmark values of C(T), although our results are in qualitative agreement with available experimental data. The quantum effect, never before included for water, reduces the magnitude of the classical value for H2O by a factor of 2.5 at 300 K and is not entirely negligible even at 1000 K.

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.