Predicting crystal form stability under real-world conditions.

The physicochemical properties of molecular crystals, such as solubility, stability, compactability, melting behaviour and bioavailability, depend on their crystal form1. In silico crystal form selection has recently come much closer to realization because of the development of accurate and affordable free-energy calculations2-4. Here we redefine the state of the art, primarily by improving the accuracy of free-energy calculations, constructing a reliable experimental benchmark for solid-solid free-energy differences, quantifying statistical errors for the computed free energies and placing both hydrate crystal structures of different stoichiometries and anhydrate crystal structures on the same energy landscape, with defined error bars, as a function of temperature and relative humidity. The calculated free energies have standard errors of 1-2 kJ mol-1 for industrially relevant compounds, and the method to place crystal structures with different hydrate stoichiometries on the same energy landscape can be extended to other multi-component systems, including solvates. These contributions reduce the gap between the needs of the experimentalist and the capabilities of modern computational tools, transforming crystal structure prediction into a more reliable and actionable procedure that can be used in combination with experimental evidence to direct crystal form selection and establish control5.

The first microsolvation step for furans: New experiments and benchmarking strategies.

The site-specific first microsolvation step of furan and some of its derivatives with methanol is explored to benchmark the ability of quantum-chemical methods to describe the structure, energetics, and vibrational spectrum at low temperature. Infrared and microwave spectra in supersonic jet expansions are used to quantify the docking preference and some relevant quantum states of the model complexes. Microwave spectroscopy strictly rules out in-plane docking of methanol as opposed to the top coordination of the aromatic ring. Contrasting comparison strategies, which emphasize either the experimental or the theoretical input, are explored. Within the harmonic approximation, only a few composite computational approaches are able to achieve a satisfactory performance. Deuteration experiments suggest that the harmonic treatment itself is largely justified for the zero-point energy, likely and by design due to the systematic cancellation of important anharmonic contributions between the docking variants. Therefore, discrepancies between experiment and theory for the isomer abundance are tentatively assigned to electronic structure deficiencies, but uncertainties remain on the nuclear dynamics side. Attempts to include anharmonic contributions indicate that for systems of this size, a uniform treatment of anharmonicity with systematically improved performance is not yet in sight.

The furan microsolvation blind challenge for quantum chemical methods: First steps.

Herein we present the results of a blind challenge to quantum chemical methods in the calculation of dimerization preferences in the low temperature gas phase. The target of study was the first step of the microsolvation of furan, 2-methylfuran and 2,5-dimethylfuran with methanol. The dimers were investigated through IR spectroscopy of a supersonic jet expansion. From the measured bands, it was possible to identify a persistent hydrogen bonding OH-O motif in the predominant species. From the presence of another band, which can be attributed to an OH-π interaction, we were able to assert that the energy gap between the two types of dimers should be less than or close to 1 kJ/mol across the series. These values served as a first evaluation ruler for the 12 entries featured in the challenge. A tentative stricter evaluation of the challenge results is also carried out, combining theoretical and experimental results in order to define a smaller error bar. The process was carried out in a double-blind fashion, with both theory and experimental groups unaware of the results on the other side, with the exception of the 2,5-dimethylfuran system which was featured in an earlier publication.

Can dispersion corrections annihilate the dispersion-driven nano-aggregation of non-polar groups? An ab initio molecular dynamics study of ionic liquid systems.

In this study, we aim at understanding the influence of dispersion correction on the ab initio molecular dynamics simulations of ionic liquid (IL) systems. We investigated a large bulk system of the 1-butyl-3-methylimidazolium triflate IL and a small cluster system of ethylamine in ethylammonium nitrate both under periodic boundary conditions. The large system displays several changes upon neglect of dispersion correction, the most striking one is the surprising decrease of the well-known microheterogeneity which is accompanied by an increase of side chain hydrogen atom-anion interplay. For the diffusion coefficient, we observe a correction towards experimental behavior in terms of the cation becoming faster than the anion with dispersion correction. Changes in the electronic structure upon dispersion correction are reflected in larger/smaller dipole moments for anions/cations also seen in the calculated IR spectrum. The energetics of different ion pair dimer subsystems (polar and non-polar) are in accordance with the analysis of the trajectories: A detailed balance in the ionic liquid system determines its particular behavior. While the overall interaction terms for dispersion-corrected calculations are higher, the decrease in microheterogeneity upon inclusion of dispersion interaction becomes obvious due to the relation between all contributions to polar-polar terms. For the small system, we clearly observe the well known behavior that the hybrid functionals show higher reaction barriers than the pure generalized gradient approximation (GGA) functionals. The correction of dispersion reduces the discrepancies in some cases. Accounting for the number of jumps, we observe that dispersion correction reduces the discrepancies from 50% to less than 10%.

Computer-Aided Design of Ionic Liquids as CO2 Absorbents.

Ionic liquids (ILs), vary strongly in their interaction with CO2. We suggest simple theoretical approach to predict the CO2 absorption behavior of ILs. Strong interaction of the CO2 with the IL anions corresponds to chemical absorption whereas weak interaction indicates physical absorption. A predictive estimate with a clear distinction between physical and chemical absorption can be simply obtained according to geometries optimized in the presence of a solvation model instead of optimizing it only in gas phase as has been done to date. The resulting Gibbs free energies compare very well with experimental values and the energies were correlated with experimental capacities. Promising anions, for ionic liquids with reversible CO2 absorption properties can be defined by a reaction Gibbs free energy of absorption in the range of -30 to 16 kJ mol(-1).

An abnormal N-heterocyclic carbene-carbon dioxide adduct from imidazolium acetate ionic liquids: the importance of basicity.

In the reaction of 1-ethyl-3-methylimidazolium acetate [C2C1Im][OAc] ionic liquid with carbon dioxide at 125 °C and 10 MPa, not only the known N-heterocyclic carbene (NHC)-CO2 adduct I, but also isomeric aNHC-CO2 adducts II and III were obtained. The abnormal NHC-CO2 adducts are stabilized by the presence of the polarizing basic acetate anion, according to static DFT calculations and ab initio molecular dynamics studies. A further possible reaction pathway is facilitated by the high basicity of the system, deprotonating the initially formed NHC-CO2 adduct I, which can then be converted in the presence of the excess of CO2 to the more stable 2-deprotonated anionic abnormal NHC-CO2 adduct via the anionic imidazolium-2,4-dicarboxylate according to DFT calculations on model compounds. This suggests a generalizable pathway to abnormal NHC complex formation.

From `crystallographic accuracy' to `thermodynamic accuracy': a redetermination of the crystal structure of calcium atorvastatin trihydrate (Lipitor®).

With ever-improving quantum-mechanical computational methods, the accuracy requirements for experimental crystal structures increase. The crystal structure of calcium atorvastatin trihydrate, which has 56 degrees of freedom when determined with a real-space algorithm, was determined from powder diffraction data by Hodge et al. [Powder Diffr. (2020), 35, 136-143]. The crystal structure was a good fit to the experimental data, indicating that the electron density had been captured essentially correctly, but two independent quantum-mechanical calculations disagreed with the experimental structure and with each other. Using the same experimental data, the crystal structure was redetermined from scratch and it was shown that it can be reproduced within a root-mean-square Cartesian displacement of 0.1 Šby two independent quantum-mechanical calculations. The consequences for the calculated energies and solubilities are described.

The seventh blind test of crystal structure prediction: structure ranking methods.

A seventh blind test of crystal structure prediction has been organized by the Cambridge Crystallographic Data Centre. The results are presented in two parts, with this second part focusing on methods for ranking crystal structures in order of stability. The exercise involved standardized sets of structures seeded from a range of structure generation methods. Participants from 22 groups applied several periodic DFT-D methods, machine learned potentials, force fields derived from empirical data or quantum chemical calculations, and various combinations of the above. In addition, one non-energy-based scoring function was used. Results showed that periodic DFT-D methods overall agreed with experimental data within expected error margins, while one machine learned model, applying system-specific AIMnet potentials, agreed with experiment in many cases demonstrating promise as an efficient alternative to DFT-based methods. For target XXXII, a consensus was reached across periodic DFT methods, with consistently high predicted energies of experimental forms relative to the global minimum (above 4 kJ mol-1 at both low and ambient temperatures) suggesting a more stable polymorph is likely not yet observed. The calculation of free energies at ambient temperatures offered improvement of predictions only in some cases (for targets XXVII and XXXI). Several avenues for future research have been suggested, highlighting the need for greater efficiency considering the vast amounts of resources utilized in many cases.

The seventh blind test of crystal structure prediction: structure generation methods.

A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems of varying complexity: a silicon and iodine-containing molecule, a copper coordination complex, a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this first of two parts focusing on structure generation methods, many crystal structure prediction (CSP) methods performed well for the small but flexible agrochemical compound, successfully reproducing the experimentally observed crystal structures, while few groups were successful for the systems of higher complexity. A powder X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully determining a crystal structure from a low-quality PXRD pattern. The use of CSP in the prediction of likely cocrystal stoichiometry was also explored, demonstrating multiple possible approaches. Crystallographic disorder emerged as an important theme throughout the test as both a challenge for analysis and a major achievement where two groups blindly predicted the existence of disorder for the first time. Additionally, large-scale comparisons of the sets of predicted crystal structures also showed that some methods yield sets that largely contain the same crystal structures.

Improved electronic excitation energies from shape-corrected semilocal Kohn-Sham potentials.

We propose a general method for obtaining accurate valence and Rydberg excitation energies from standard density-functional approximations in adiabatic linear-response time-dependent density-functional theory. The method consists in modeling the sum of Hartree (Coulomb) and exchange-correlation potentials, v(HXC)(r), by the Hartree-exchange-correlation potential of the corresponding partially ionized system in which a fraction of electron charge (δ = 0.15 to 0.30, depending on the functional) is removed from the highest occupied Kohn-Sham orbital level. The model potential is less repulsive and closer to exact in valence and near asymptotic regions, so it yields more accurate Kohn-Sham orbitals and orbital eigenvalues. By applying this scheme to conventional local, semilocal, and hybrid density-functional approximations, we improve their accuracy for Rydberg excitations by almost an order of magnitude without sacrificing the already good performance for valence transitions.

Efficient Crystal Structure Prediction for Structurally Related Molecules with Accurate and Transferable Tailor-Made Force Fields.

Crystal structure prediction (CSP) is generally used to complement experimental solid form screening and applied to individual molecules in drug development. The fast development of algorithms and computing resources offers the opportunity to use CSP earlier and for a broader range of applications in the drug design cycle. This study presents a novel paradigm of CSP specifically designed for structurally related molecules, referred to as Quick-CSP. The approach prioritizes more accurate physics through robust and transferable tailor-made force fields (TMFFs), such that significant efficiency gains are achieved through the reduction of expensive ab initio calculations. The accuracy of the TMFF is increased by the introduction of electrostatic multipoles, and the fragment-based force field parameterization scheme is demonstrated to be transferable for a family of chemically related molecules. The protocol is benchmarked with structurally related compounds from the Bromodomain and Extraterminal (BET) domain inhibitors series. A new convergence criterion is introduced that aims at performing only as many ab initio optimizations of crystal structures as required to locate the bottom of the crystal energy landscape within a user-defined accuracy. The overall approach provides significant cost savings ranging from three- to eight-fold less than the full-CSP workflow. The reported advancements expand the scope and utility of the underlying CSP building blocks as well as their novel reassembly to other applications earlier in the drug design cycle to guide molecule design and selection.

Pressure-Dependent Rate Constant Predictions Utilizing the Inverse Laplace Transform: A Victim of Deficient Input Data.

k(E) can be calculated either from the Rice-Ramsperger-Kassel-Marcus theory or by inverting macroscopic rate constants k(T). Here, we elaborate the inverse Laplace transform approach for k(E) reconstruction by examining the impact of k(T) data fitting accuracy. For this approach, any inaccuracy in the reconstructed k(E) results from inaccurate/incomplete k(T) description. Therefore, we demonstrate how an improved mathematical description of k(T) data leads to accurate k(E) data. Refitting inaccurate/incomplete k(T), hence, allows for recapturing k(T) information that yields more accurate k(E) reconstructions. The present work suggests that accurate representation of experimental and theoretical k(T) data in a broad temperature range could be used to obtain k(T,p). Thus, purely temperature-dependent kinetic models could be converted into fully temperature- and pressure-dependent kinetic models.

Basic Phosphonium Ionic Liquids as Wittig Reagents.

The possibility of designing a solvent/reagent for Wittig reactions from basic phosphonium salts is explored theoretically. In the suggested R4P+PhO- and Ph3PR+PhO- ionic liquids (ILs), the phenolate anion is prone to remove the α-proton from the alkyl chains, forming a phosphorous ylide. Significant hydrogen bonding between the oxygen atoms of the anions and α-hydrogen atoms of the cations were found by molecular dynamics simulations of these substances; therefore, proton transfer between the two ions is inherently supported by the structure of the liquid as well. The subsequent steps of the Wittig reaction from the phosphorous ylide were also found to be energetically possible. The mesoscopic structure of these materials exhibits a significant segregation into polar and nonpolar domains, which may also allow an easy dissolution of the substrates. The formation of a pentacoordinated phosphorous derivative through P-O bond formation was found to be also possible in the gas phase for both kind of compounds. Accordingly, having such basic anions in phosphonium-based ILs may produce such a neutral and therefore volatile species, which may hold further significant applications for these solvents in ion-exchange and separation techniques and in synthesis.

Tuning the Carbon Dioxide Absorption in Amino Acid Ionic Liquids.

One of the possible solutions to prevent global climate change is the reduction of CO2 emissions, which is highly desired for the sustainable development of our society. In this work, the chemical absorption of carbon dioxide in amino acid ionic liquids was studied through first-principles methods. The use of readily accessible and biodegradable amino acids as building blocks for ionic liquids makes them highly promising replacements for the widely applied hazardous aqueous solutions of amines. A detailed insight into the reaction mechanism of the CO2 absorption was obtained through state-of-the-art theoretical methods. This allowed us to determine the reason for the specific CO2 capacities found experimentally. Moreover, we have also conducted a theoretical design of ionic liquids to provide valuable insights into the precise tuning of the energetic and kinetic parameters of the CO2 absorption.

SO2 Solvation in the 1-Ethyl-3-Methylimidazolium Thiocyanate Ionic Liquid by Incorporation into the Extended Cation-Anion Network.

We have carried out an ab initio molecular dynamics study on the sulfur dioxide (SO2) solvation in 1-ethyl-3-methylimidazolium thiocyanate for which we have observed that both cations and anions play an essential role in the solvation of SO2. Whereas, the anions tend to form a thiocyanate- and much less often an isothiocyanate-SO2 adduct, the cations create a "cage" around SO2 with those groups of atoms that donate weak interactions like the alkyl hydrogen atoms as well as the heavy atoms of the [Formula: see text]-system. Despite these similarities between the solvation of SO2 and CO2 in ionic liquids, an essential difference was observed with respect to the acidic protons. Whereas CO2 avoids accepting hydrogen bonds form the acidic hydrogen atoms of the cations, SO2 can from O(SO2)-H(cation) hydrogen bonds and thus together with the strong anion-adduct it actively integrates in the hydrogen bond network of this particular ionic liquid. The fact that SO2 acts in this way was termed a linker effect by us, because the SO2 can be situated between cation and anion operating as a linker between them. The particular contacts are the H(cation)[Formula: see text]O(SO2) hydrogen bond and a S(anion)-S(SO2) sulfur bridge. Clearly, this observation provides a possible explanation for the question of why the SO2 solubility in these ionic liquids is so high.

Ion pairing in ionic liquids.

In the present article we briefly review the extensive discussion in literature about the presence or absence of ion pair-like aggregates in ionic liquids. While some experimental studies point towards the presence of neutral subunits in ionic liquids, many other experiments cannot confirm or even contradict their existence. Ion pairs can be detected directly in the gas phase, but no direct method is available to observe such association behavior in the liquid, and the corresponding indirect experimental proofs are based on such assumptions as unity charges at the ions. However, we have shown by calculating ionic liquid clusters of different sizes that assuming unity charges for ILs is erroneous, because a substantial charge transfer is taking place between the ionic liquid ions that reduce their total charge. Considering these effects might establish a bridge between the contradicting experimental results on this matter. Beside these results, according to molecular dynamics simulations the lifetimes of ion-ion contacts and their joint motions are far too short to verify the existence of neutral units in these materials.

Carbene formation in ionic liquids: spontaneous, induced, or prohibited?

We present a theoretical study of carbene formation from the 1-ethyl-3-methylimidazolium acetate ionic liquid in the absence and presence of CO2 in gas and liquid phase. Although CO2 physisorption constitutes a precursory step of chemisorption (the CO2's reaction with carbenes, which forms from cations via proton abstraction by anions), it also enables a very stable CO2-anion associate. However, this counteracts the chemical absorption by reducing the basicity of the anion and the electrophilicity of the CO2, which is reflected by charge transfer. Accordingly, the observable carbene formation in the gas phase is hindered in the presence of CO2. In the neat liquid, the carbene formation is also suppressed by the charge screening compared to the case of the gas phase; nevertheless, indications for carbene incidents appear. Interestingly, in the CO2-containing liquid we detect more carbene-like incidents than in the neat one, which is caused by the way CO2 is solvated. Despite the weakness of the CO2-cation interaction, the CO2-anion associate is distorted by cations, which can be seen in longer associate distances and reduced "binding" energies. While the single solvating anion is shifted away from CO2, many more solvating cations approach it compared to the case of the gas phase. This leads to the conclusion that while the ionic liquid effect stabilizes charged species, introducing neutral species such as CO2 provides an opposite trend, leading to an inverse ionic liquid effect with the facilitation of carbene formation and thus of chemical absorption.