van der Waals dispersion interactions in molecular materials: beyond pairwise additivity

Efficient Electron Injection into Graphullerene Enables Reversible NaC2 Sodium Storage

Sodium-ion batteries are emerging as promising alternatives to conventional lithium-based technology, offering solutions to challenges in large-scale grid storage. However, the capacity of conventional graphite-based anodes for storing Na-ions is inherently limited by suboptimal thermodynamic interactions and irreversible structural changes that occur in the anode during charge-discharge cycles. Herein, we present a computational design that explores the potential of graphullerene, a two-dimensional framework with interconnected fullerene moieties, for the reversible storage of Na-ions. A unique aspect of this design is the electron injection capacity into the graphullerene anode, reaching 15 electrons per fullerene moiety, which is the highest limit to date. This advancement enables large-scale Na-ion storage up to the stoichiometry of NaC2, exhibiting specific capacity of 551 mAhg-1 and averaged open circuit voltage of 0.18 V vs Na/Na+. In addition, the multilayered arrangement of stored Na-ions enhances the Na-ion diffusivity on the graphullerene surface, leading to rapid insertion and extraction kinetics. Thus, raising the electron injection limit offers a promising strategy to transform carbon-based anodes into suitable candidates for reversible Na-ion storage, without relying on artificial defect introduction or doping.

Unprecedented Packing Polymorphism of Oxindole: An Exploration Inspired by Crystal Structure Prediction

Crystal polymorphism, characterized by different packing arrangements of the same compound, strongly ties to the physical properties of a molecule. Determining the polymorphic landscape is complex and time-consuming, with the number of experimentally observed polymorphs varying widely from molecule to molecule. Furthermore, disappearing polymorphs, the phenomenon whereby experimentally observed forms cannot be reproduced, pose a significant challenge for the pharmaceutical industry. Herein, we focused on oxindole (OX), a small rigid molecule with four known polymorphs, including a reported disappearing form. Using crystal structure prediction (CSP), we assessed OX solid-state landscape and thermodynamic stability by comparing predicted structures with experimentally known forms. We then performed melt and solution crystallization in bulk and nanoconfinement to validate our predictions. These experiments successfully reproduced the known forms and led to the discovery of four novel polymorphs. Our approach provided insights into reconstructing disappearing polymorphs and building more comprehensive polymorph landscapes. These results also establish a new record of packing polymorphism for rigid molecules.

Computational predictions of cocrystal formation: A benchmark study of 28 assemblies comparing five methods from high-throughput to advanced models

Cocrystals are assemblies of more than one type of molecule stabilized through noncovalent interactions. They are promising materials for improved drug formulation in which the stability, solubility, or biocompatibility of the active pharmaceutical ingredient (API) is improved by including a coformer. In this work, a range of density functional theory (DFT) and density functional tight binding (DFTB) models are systematically compared for their ability to predict the lattice enthalpy of a broad range of existing pharmaceutically relevant cocrystals. These range from cocrystals containing model compounds 4,4'-bipyridine and oxalic acid to those with the well benchmarked APIs of aspirin and paracetamol, all tested with a large set of alternative coformers. For simple cocrystals, there is a general consensus in lattice enthalpy calculated by the different DFT models. For the cocrystals with API coformers the cocrystals, enthalpy predictions depend strongly on the DFT model. The significantly lighter DFTB models predict unrealistic values of lattice enthalpy even for simple cocrystals.

Perhalogenated Anilines as Bifunctional Donors of Hydrogen and Halogen Bonds in Cocrystals with Ditopic Nitrogen-Containing Acceptors

In this study, we examine the experimental and theoretical capabilities of two perhalogenated anilines, 2,3,5,6-tetrafluoro-4-bromoaniline (btfa) and 2,3,5,6-tetrafluoro-4-iodoaniline (itfa) as hydrogen and halogen bond donors. A series of 11 cocrystals derived from the two anilines and selected ditopic nitrogen-containing acceptors (4,4'-bipyridine, 1,2-bis(4-pyridyl)ethane, and 1,4-diazabicyclo[2.2.2]octane) in 1:1 and 2:1 stoichiometries were prepared by liquid-assisted grinding and crystallization from solution. Crystallographic analysis revealed bifunctional donor properties in both anilines. The dominant supramolecular interaction in four cocrystals of btfa is the N-H···Nacceptor hydrogen bond between btfa and acceptor molecules, while in the one remaining cocrystal, donor and acceptor molecules are connected via the N-H···Nacceptor hydrogen bond and the Br···Nacceptor halogen bond. In two cocrystals of itfa, the dominant supramolecular interaction is the I···Nacceptor halogen bond between itfa and acceptor molecules, while in the remaining four cocrystals, donor and acceptor molecules are additionally connected by the N-H···Nacceptor hydrogen bond. Periodic density-functional theory (DFT) calculations have been conducted to assess the formation energies of these cocrystals and the strengths of the established halogen and hydrogen bonds. Molecular DFT calculations on btfa and itfa indicate that the differences in electrostatic potential between the competing sites on the molecules are 261.6 and 157.0 kJ mol-1 e-1, respectively. The findings suggest that itfa, with a smaller electrostatic potential difference between donor sites, is more predisposed to act as a bifunctional donor.

System-Specific Parameter Optimization for Nonpolarizable and Polarizable Force Fields

The accuracy of classical force fields (FFs) has been shown to be limited for the simulation of cation-protein systems despite their importance in understanding the processes of life. Improvements can result from optimizing the parameters of classical FFs or by extending the FF formulation by terms describing charge transfer (CT) and polarization (POL) effects. In this work, we introduce our implementation of the CTPOL model in OpenMM, which extends the classical additive FF formula by adding CT and POL. Furthermore, we present an open-source parametrization tool, called FFAFFURR, that enables the (system-specific) parametrization of OPLS-AA and CTPOL models. The performance of our workflow was evaluated by its ability to reproduce quantum chemistry energies and by molecular dynamics simulations of a zinc-finger protein.

Water Electric Field Induced Modulation of the Wetting of Hexagonal Boron Nitride: Insights from Multiscale Modeling of Many-Body Polarization

Understanding the behavior of water contacting two-dimensional materials, such as hexagonal boron nitride (hBN), is important in practical applications, including seawater desalination and energy harvesting. Water, being a polar solvent, can strongly polarize the hBN surface via the electric fields that it generates. However, there is a lack of molecular-level understanding about the role of polarization effects at the hBN/water interface, including its effect on the wetting properties of water. In this study, we develop a theoretical framework that introduces an all-atomistic polarizable force field to accurately model the interactions of water molecules with hBN surfaces. The force field is then utilized to self-consistently describe the water-induced polarization of hBN using the classical Drude oscillator model, including predicting the hBN-water binding energies which are found to be in excellent agreement with diffusion Monte Carlo (DMC) predictions. By carrying out molecular dynamics (MD) simulations, we demonstrate that the polarizable force field yields a water contact angle on multilayered hBN which is in close agreement with the recent experimentally reported values. Conversely, an implicit modeling of the hBN-water polarization energy utilizing a Lennard-Jones (LJ) potential, a commonly utilized approximation in previous MD simulation studies, leads to a considerably lower water contact angle. This difference in the predicted contact angles is attributed to the significant energy-entropy compensation resulting from the incorporation of polarization effects at the hBN-water interface. Our work highlights the importance of self-consistently modeling the hBN-water polarization energy and offers insights into the wetting-related interfacial phenomena of water on polarizable materials.

Multimer Embedding Approach for Molecular Crystals up to Harmonic Vibrational Properties

Accurate calculations of molecular crystals are crucial for drug design and crystal engineering. However, periodic high-level density functional calculations using hybrid functionals are often prohibitively expensive for the relevant systems. These expensive periodic calculations can be circumvented by the usage of embedding methods in which, for instance, the periodic calculation is only performed at a lower-cost level and then monomer energies and dimer interactions are replaced by those of the higher-level method. Herein, we extend such a multimer embedding approach to enable energy corrections for trimer interactions and the calculation of harmonic vibrational properties up to the dimer level. We evaluate this approach for the X23 benchmark set of molecular crystals by approximating a periodic hybrid density functional (PBE0+MBD) by embedding multimers into less expensive calculations using a generalized-gradient approximation functional (PBE+MBD). We show that trimer interactions are crucial for accurately approximating lattice energies within 1 kJ/mol and might also be needed for further improvement of lattice constants and hence cell volumes. Finally, the vibrational properties are already very well captured at the monomer and dimer level, making it possible to approximate vibrational free energies at room temperature within 1 kJ/mol.

libMBD: A general-purpose package for scalable quantum many-body dispersion calculations

Many-body dispersion (MBD) is a powerful framework to treat van der Waals (vdW) dispersion interactions in density-functional theory and related atomistic modeling methods. Several independent implementations of MBD with varying degree of functionality exist across a number of electronic structure codes, which both limits the current users of those codes and complicates dissemination of new variants of MBD. Here, we develop and document libMBD, a library implementation of MBD that is functionally complete, efficient, easy to integrate with any electronic structure code, and already integrated in FHI-aims, DFTB+, VASP, Q-Chem, CASTEP, and Quantum ESPRESSO. libMBD is written in modern Fortran with bindings to C and Python, uses MPI/ScaLAPACK for parallelization, and implements MBD for both finite and periodic systems, with analytical gradients with respect to all input parameters. The computational cost has asymptotic cubic scaling with system size, and evaluation of gradients only changes the prefactor of the scaling law, with libMBD exhibiting strong scaling up to 256 processor cores. Other MBD properties beyond energy and gradients can be calculated with libMBD, such as the charge-density polarization, first-order Coulomb correction, the dielectric function, or the order-by-order expansion of the energy in the dipole interaction. Calculations on supramolecular complexes with MBD-corrected electronic structure methods and a meta-review of previous applications of MBD demonstrate the broad applicability of the libMBD package to treat vdW interactions.

Elucidating mechanochemical reactivity of a ternary halogen-bonded cocrystal system by computational and calorimetric studies

Discovery of a halogen-bonded ternary cocrystal of 1,3,5-trifluoro-2,4,6-triiodobenzene with pyrazine and triphenylphosphine sulfide has revealed a complex landscape of multicomponent phases, all achievable by mechanochemical interconversion. The observed solid-state reaction pathways were explained by periodic density-functional calculations and comprehensive intermolecular interaction analysis, supported by dissolution calorimetry measurements.

Experimental and Theoretical Evaluation of the Thermodynamics of the Carbonation Reaction of ZIF-8 and Its Close-Packed Polymorph with Carbon Dioxide

We report the first experimental and theoretical evaluation of the thermodynamic driving force for the reaction of metal-organic framework (MOF) materials with carbon dioxide, leading to a metal-organic carbonate phase. Carbonation upon exposure of MOFs to CO2 is a significant concern for the design and deployment of such materials in carbon storage technologies, and this work shows that the formation of a carbonate material from the popular SOD-topology framework material ZIF-8, as well as its dense-packed dia-topology polymorph, is significantly exothermic. With knowledge of the crystal structure of the starting and final phases in the carbonation reaction, we have also identified periodic density functional theory approaches that most closely reproduce the measured reaction enthalpies. This development now permits the use of advanced theoretical calculations to calculate the driving forces behind the carbonation of zeolitic imidazolate frameworks with reasonable accuracy.

London Dispersion Interactions Imitate Pressure for Molecular Crystals

The packing of molecular crystals, in which the constituent molecular units have no directional forces, is primarily controlled by weak London dispersion (LD) forces. These forces assist in stabilizing the system by bringing the molecular units into the proximity of each other. In this paper, the same effect is shown to be externally induced by pressure. The minimal pressure required to correctly describe the crystal structure without LD interactions (P_LD) provides a quantifiable measure for the weak intermolecular interactions. LD forces are shown to be essential for an accurate description of the pressure-induced phase transitions across examples of linear, trigonal-planar, square-planar, tetrahedral, trigonal bipyramidal, and octahedral molecules.

Optimized Quantum Drude Oscillators for Atomic and Molecular Response Properties

The quantum Drude oscillator (QDO) is an efficient yet accurate coarse-grained approach that has been widely used to model electronic and optical response properties of atoms and molecules as well as polarization and dispersion interactions between them. Three effective parameters (frequency, mass, and charge) fully characterize the QDO Hamiltonian and are adjusted to reproduce response properties. However, the soaring success of coupled QDOs for many-atom systems remains fundamentally unexplained, and the optimal mapping between atoms/molecules and oscillators has not been established. Here we present an optimized parametrization (OQDO) where the parameters are fixed by using only dipolar properties. For the periodic table of elements as well as small molecules, our model accurately reproduces atomic (spatial) polarization potentials and multipolar dispersion coefficients, elucidating the high promise of the presented model in the development of next-generation quantum-mechanical force fields for (bio)molecular simulations.

The Realm of Unconventional Noncovalent Interactions in Proteins: Their Significance in Structure and Function

Proteins and their assemblies are fundamental for living cells to function. Their complex three-dimensional architecture and its stability are attributed to the combined effect of various noncovalent interactions. It is critical to scrutinize these noncovalent interactions to understand their role in the energy landscape in folding, catalysis, and molecular recognition. This Review presents a comprehensive summary of unconventional noncovalent interactions, beyond conventional hydrogen bonds and hydrophobic interactions, which have gained prominence over the past decade. The noncovalent interactions discussed include low-barrier hydrogen bonds, C5 hydrogen bonds, C-H···π interactions, sulfur-mediated hydrogen bonds, n → π* interactions, London dispersion interactions, halogen bonds, chalcogen bonds, and tetrel bonds. This Review focuses on their chemical nature, interaction strength, and geometrical parameters obtained from X-ray crystallography, spectroscopy, bioinformatics, and computational chemistry. Also highlighted are their occurrence in proteins or their complexes and recent advances made toward understanding their role in biomolecular structure and function. Probing the chemical diversity of these interactions, we determined that the variable frequency of occurrence in proteins and the ability to synergize with one another are important not only for ab initio structure prediction but also to design proteins with new functionalities. A better understanding of these interactions will promote their utilization in designing and engineering ligands with potential therapeutic value.

Interaction energy of Cl2 and Br2 with H2 O: Exchange, dispersion and density the crucial ingredients

Modern Density Functional Theory models are now suitable for many molecular and condensed phase studies. The study of noncovalent interactions, a well-known drawback, is no longer an insurmountable obstacle through design and empirical corrections. However, using empirical corrections as in the DFT-D methods might not be an all-in-one solution. This work uses a simple system, X₂ -H₂ O with X = Cl or Br, with two different interactions, halogen-bonded (XB) and hydrogen-halogen (HX), to investigate the capability of current density functional approximations (DFA) in predicting interaction energies with eight different exchange-correlation functionals. SAPT(DFT) provides, for all the studied cases, better predictions than the widely used supermolecular approach. In addition, the components of the interaction energy suggest where some of the shortcomings originate in each DFA. The analysis of the functionals used confirms that PBE0 and ω-B97X-D have a physically correct behavior. Using SAPT(DFT) and PBE0, and ω-B97X-D, we obtained the interaction energy of Cl₂ and Br₂ inside different clathrate cages and satisfactorily compared with wavefunction results; hence, the lower and upper limits of this value are defined: Cl₂ @5¹² , -5.3 ± 0.3 kcal/mol; Cl₂ @5¹² 6² , -5.5 ± 0.1 kcal/mol; Br₂ @5¹² 6² , -7.6 ± 1.0 kcal/mol; Br₂ @5¹² 6³ , -10.6 ± 1.0 kcal/mol; Br₂ @5¹² 6⁴ , -10.9 ± 0.8 kcal/mol.

Discriminating and understanding molecular crystal polymorphism

Polymorph discrimination for a molecular crystal has long been a challenging task, which, nonetheless, is a major concern in the pharmaceutical industry. In this work, we have investigated polymorph discrimination on three different molecular crystals, tetrolic acid, oxalic acid, and oxalyl dihydrazide, covering both packing polymorphism and conformational polymorphism. To gain more understanding, we have performed energy decomposition analysis based on many-body expansion, and have compared the results from the XO-PBC method, that is, the eXtended ONIOM method (XO) with the periodic boundary condition (PBC), with those from some commonly used dispersion corrected density functional theory (DFT-D) methods. It is shown here that, with the XYG3 doubly hybrid functional chosen as the target high level to capture the intra- and short-range intermolecular interactions, and the periodic PBE as the basic low level to take long range interactions into account, the XO-PBC(XYG3:PBE) method not only obtains the correct experimental stability orderings, but also predicts reasonable polymorph energy ranges for all three cases. Our results have demonstrated the usefulness of the present theoretical methods, in particular XO-PBC, while highlighted the importance of a better treatment of different kinds of interactions to be beneficial to polymorph control.

Stable Crystalline Nanohoop Radical and Its Self-Association Promoted by van der Waals Interactions

A stable nanohoop radical (OR3) combining the structures of cycloparaphenylene and an olympicenyl radical is synthesized and isolated in the crystalline state. X-ray crystallographic analysis reveals that OR3 forms a unique head-to-tail dimer that further aggregates into a one-dimensional chain in the solid state. Variable-temperature NMR and concentration-dependent absorption measurements indicate that the π-dimer is not formed in solution. An energy decomposition analysis indicates that van der Waals interactions are the driving force for the self-association process, in contrast with other olympicenyl derivatives that favor π-dimerization. The physical properties in solution phase have been studied, and the stable cationic species obtained by one-electron chemical oxidation. This study offers a new molecular design to modulate the self-association of organic radicals for overcoming the spin-Peierls transition, and to prepare novel nanohoop compounds with spin-related properties.

Toward Pair Atomic Density Fitting for Correlation Energies with Benchmark Accuracy

Pair atomic density fitting (PADF) has been identified as a promising strategy to reduce the scaling with system size of quantum chemical methods for the calculation of the correlation energy like the direct random-phase approximation (RPA) or second-order Møller-Plesset perturbation theory (MP2). PADF can however introduce large errors in correlation energies as the two-electron interaction energy is not guaranteed to be bounded from below. This issue can be partially alleviated by using very large fit sets, but this comes at the price of reduced efficiency and having to deal with near-linear dependencies in the fit set. One posibility is to use global density fitting (DF), but in this work, we introduce an alternative methodology to overcome this problem that preserves the intrinsically favorable scaling of PADF. We first regularize the Fock matrix by projecting out parts of the basis set which gives rise to orbital products that are hard to describe by PADF. After having thus obtained a reliable self-consistent field solution, we then also apply this projector to the orbital coefficient matrix to improve the precision of PADF-MP2 and PADF-RPA. We systematically assess the accuracy of this new approach in a numerical atomic orbital framework using Slater type orbitals (STO) and correlation consistent Gaussian type basis sets up to quintuple-ζ quality for systems with more than 200 atoms. For the small and medium systems in the S66 database we show the maximum deviation of PADF-MP2 and PADF-RPA relative correlation energies to DF-MP2 and DF-RPA reference results to be 0.07 and 0.14 kcal/mol, respectively. When the new projector method is used, the errors only slightly increase for large molecules and also when moderately sized fit sets are used the resulting errors are well under control. Finally, we demonstrate the computational efficiency of our algorithm by calculating the interaction energies of large, non-covalently bound complexes with more than 1000 atoms and 20000 atomic orbitals at the RPA@PBE/CC-pVTZ level of theory.

Experimentally Validated Ab Initio Crystal Structure Prediction of Novel Metal-Organic Framework Materials

First-principles crystal structure prediction (CSP) is the most powerful approach for materials discovery, enabling the prediction and evaluation of properties of new solid phases based only on a diagram of their underlying components. Here, we present the first CSP-based discovery of metal-organic frameworks (MOFs), offering a broader alternative to conventional techniques, which rely on geometry, intuition, and experimental screening. Phase landscapes were calculated for three systems involving flexible Cu(II) nodes, which could adopt a potentially limitless number of network topologies and are not amenable to conventional MOF design. The CSP procedure was validated experimentally through the synthesis of materials whose structures perfectly matched those found among the lowest-energy calculated structures and whose relevant properties, such as combustion energies, could immediately be evaluated from CSP-derived structures.

The Halogen Bond in Weakly Bonded Complexes and the Consequences for Aromaticity and Spin-Orbit Coupling

The halogen bond complexes CF3X⋯Y and C2F3X⋯Y, with Y = furan, thiophene, selenophene and X = Cl, Br, I, have been studied by using DFT and CCSD(T) in order to understand which factors govern the interaction between the halogen atom X and the aromatic ring. We found that PBE0-dDsC/QZ4P gives an adequate description of the interaction energies in these complexes, compared to CCSD(T) and experimental results. The interaction between the halogen atom X and the π-bonds in perpendicular orientation is stronger than the interaction with the in-plane lone pairs of the heteroatom of the aromatic cycle. The strength of the interaction follows the trend Cl < Br < I; the chalcogenide in the aromatic ring nor the hybridization of the C−X bond play a decisive role. The energy decomposition analysis shows that the interaction energy is dominated by all three contributions, viz., the electrostatic, orbital, and dispersion interactions: not one factor dominates the interaction energy. The aromaticity of the ring is undisturbed upon halogen bond formation: the π-ring current remains equally strong and diatropic in the complex as it is for the free aromatic ring. However, the spin-orbit coupling between the singlet and triplet π→π* states is increased upon halogen bond formation and a faster intersystem crossing between these states is therefore expected.

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

Crystal structure prediction (CSP) his 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.

Functionalisation of Inorganic Material Surfaces with Staphylococcus Protein A: A Molecular Dynamics Study

Staphylococcus protein A (SpA) is found in the cell wall of Staphylococcus aureus bacteria. Its ability to bind to the constant Fc regions of antibodies means it is useful for antibody extraction, and further integration with inorganic materials can lead to the development of diagnostics and therapeutics. We have investigated the adsorption of SpA on inorganic surface models such as experimentally relevant negatively charged silica, as well as positively charged and neutral surfaces, by use of fully atomistic molecular dynamics simulations. We have found that SpA, which is itself negatively charged at pH7, is able to adsorb on all our surface models. However, adsorption on charged surfaces is more specific in terms of protein orientation compared to a neutral Au (111) surface, while the protein structure is generally well maintained in all cases. The results indicate that SpA adsorption is optimal on the siloxide-rich silica surface, which is negative at pH7 since this keeps the Fc binding regions free to interact with other species in solution. Due to the dominant role of electrostatics, the results are transferable to other inorganic materials and pave the way for new diagnostic and therapeutic designs where SpA might be used to conjugate antibodies to nanoparticles.

Harnessing Deep Learning for Optimization of Lennard-Jones Parameters for the Polarizable Classical Drude Oscillator Force Field

The outcomes of computational chemistry and biology research, including drug design, are significantly influenced by the underlying force field (FF) used in molecular simulations. While improved FF accuracy may be achieved via inclusion of explicit treatment of electronic polarization, such an extension must be accompanied by optimization of van der Waals (vdW) interactions, in the context of the Lennard-Jones (LJ) formalism in the present study. This is particularly challenging due to the extensive nature of chemical space combined with the correlated nature of LJ parameters. To address this challenge, a deep learning (DL)-based parametrization framework is developed, allowing for sampling of wide ranges of LJ parameters targeting experimental condensed phase thermodynamic properties. The present work utilizes this framework to develop the LJ parameters for atoms associated with four distinct groups covering 10 different atom types. Final parameter selection was facilitated by quantum mechanical data on rare-gas interactions with the training set molecules. The chosen parameters were then validated through experimental hydration free energies and condensed phase thermodynamic properties of validation set molecules to confirm transferability. The ultimate outcome of utilizing this framework is a set of LJ parameters in the context of the polarizable Drude FF, which demonstrated improvement in the reproduction of both experimental pure solvent and crystal properties and hydration free energies of the molecules compared to the additive CHARMM General FF (CGenFF) including the ability of the Drude FF to accurately reproduce both experimental pure solvent properties and hydration free energies. The study also shows how correlations between difference in the reproduction of condensed phase data between model compounds may be used to direct the selection of new atom types and training set molecules during FF development.

Molecular Interactions Induced by a Static Electric Field in Quantum Mechanics and Quantum Electrodynamics

By means of quantum mechanics and quantum electrodynamics applied to coupled harmonic Drude oscillators, we study the interaction between two neutral atoms or molecules subject to a uniform static electric field. Our focus is to understand the interplay between leading contributions to field-induced electrostatics/polarization and dispersion interactions, as considered within the employed Drude model for both non-retarded and retarded regimes. For the first case, we present an exact solution for two coupled oscillators obtained by diagonalizing the corresponding quantum-mechanical Hamiltonian and demonstrate that the external field can control the strength of different intermolecular interactions and relative orientations of the molecules. In the retarded regime described by quantum electrodynamics, our analysis shows that field-induced electrostatic and polarization energies remain unchanged (in isotropic and homogeneous vacuum) compared to the non-retarded case. For interacting species modeled by quantum Drude oscillators, the developed framework based on quantum mechanics and quantum electrodynamics yields the leading contributions to molecular interactions under the combined action of external and vacuum fields.

Rationalising the difference in crystallisability of two sulflowers using efficient in silico methods

The molecular structures of the first and second generation sulflowers, sulflower and persulfurated coronene (PSC), are remarkably similar: carbon ring structures decorated with sulfur atoms, without any additional moiety.

Tuning the quasi-harmonic treatment of crystalline ionic liquids within the density functional theory

Five ionic liquids are selected for benchmarking the performance of quasi-harmonic density functional theory (DFT) calculations of structural, phonon, and thermodynamic properties of their crystals. Data predicted by individual computational setups are sorted, establishing a distinct hierarchy among the first-principles approaches. PBE-D3 and B3LYP-D3 functionals are coupled with various plane wave and Gaussian-type orbital (GTO) basis sets. Propagation of the basis set superposition error and of the imperfections of both functionals into finite-temperature properties is discussed in detail. PBE-D3 together with a triple-zeta GTO basis set often yields the most accurate predictions of predicted molar volume and heat capacity with errors at 1% and 8%, respectively, representing the state-of-the-art for quasi-harmonic DFT calculations for crystalline ionic liquids. Fortuitous error cancellation between the basis-set superposition (overbinding) and PBE imperfection (overexpanding) strongly affects the overall accuracy, unlike the case of B3LYP/GTO calculations, impeding systematic convergence of the methodology towards higher accuracy.

Simplifying and expanding the scope of boron imidazolate framework (BIF) synthesis using mechanochemistry

Mechanochemistry enables rapid access to boron imidazolate frameworks (BIFs), including ultralight materials based on Li and Cu(i) nodes, as well as new, previously unexplored systems based on Ag(i) nodes. Compared to solution methods, mechanochemistry is faster, provides materials with improved porosity, and replaces harsh reactants (e.g. n-butylithium) with simpler and safer oxides, carbonates or hydroxides. Periodic density-functional theory (DFT) calculations on polymorphic pairs of BIFs based on Li⁺, Cu⁺ and Ag⁺ nodes reveals that heavy-atom nodes increase the stability of the open SOD-framework relative to the non-porous dia-polymorph.

Understanding stress-induced disorder and breakage in organic crystals: beyond crystal structure anisotropy

Crystal engineering has advanced the strategies for design and synthesis of organic solids with the main focus being on customising the properties of the materials. Research in this area has a significant impact on large-scale manufacturing, as industrial processes may lead to the deterioration of such properties due to stress-induced transformations and breakage. In this work, we investigate the mechanical properties of structurally related labile multicomponent solids of carbamazepine (CBZ), namely the dihydrate (CBZ·2H2O), a cocrystal of CBZ with 1,4-benzoquinone (2CBZ·BZQ) and the solvates with formamide and 1,4-dioxane (CBZ·FORM and 2CBZ·DIOX, respectively). The effect of factors that are external (e.g. impact stressing) and/or internal (e.g. phase transformations and thermal motion) to the crystals are evaluated. In comparison to the other CBZ multicomponent crystal forms, CBZ·2H2O crystals tolerate less stress and are more susceptible to breakage. It is shown that this poor resistance to fracture may be a consequence of the packing of CBZ molecules and the orientation of the principal molecular axes in the structure relative to the cleavage plane. It is concluded, however, that the CBZ lattice alone is not accountable for the formation of cracks in the crystals of CBZ·2H2O. The strength and the temperature-dependence of electrostatic interactions, such as hydrogen bonds between CBZ and coformer, appear to influence the levels of stress to which the crystals are subjected that lead to fracture. Our findings show that the appropriate selection of coformer in multicomponent crystal forms, targetting superior mechanical properties, needs to account for the intrinsic stress generated by molecular vibrations and not solely by crystal anisotropy. Structural defects within the crystal lattice, although highly influenced by the crystallisation conditions and which are especially difficult to control in organic solids, may also affect breakage.

Mechanochemical Synthesis and Physicochemical Characterization of Previously Unreported Praziquantel Solvates with 2-Pyrrolidone and Acetic Acid

Two new solvates of the widely used anthelminthic Praziquantel (PZQ) were obtained through mechanochemical screening with different liquid additives. Specifically, 2-pyrrolidone and acetic acid gave solvates with 1:1 stoichiometry (PZQ-AA and PZQ-2P, respectively). A wide-ranging characterization of the new solid forms was carried out by means of powder X-ray diffraction, differential scanning calorimetry, FT-IR, solid-state NMR and biopharmaceutical analyses (solubility and intrinsic dissolution studies). Besides, the crystal structures of the two new solvates were solved from their Synchrotron-PXRD pattern: the solvates are isostructural, with equivalent triclinic packing. In both structures acetic acid and 2-pyrrolidone showed a strong interaction with the PZQ molecule via hydrogen bond. Even though previous studies have shown that PZQ is conformationally flexible, the same syn conformation as the PZQ Form A of the C=O groups of the piperazinone-cyclohexylcarbonyl segment is involved in these two new solid forms. In terms of biopharmaceutical properties, PZQ-AA and PZQ-2P exhibited water solubility and intrinsic dissolution rate much greater than those of anhydrous Form A.

Can We Predict the Isosymmetric Phase Transition? Application of DFT Calculations to Study the Pressure Induced Transformation of Chlorothiazide

Isosymmetric structural phase transition (IPT, type 0), in which there are no changes in the occupation of Wyckoff positions, the number of atoms in the unit cell, and the space group symmetry, is relatively uncommon. Chlorothiazide, a diuretic agent with a secondary function as an antihypertensive, has been proven to undergo pressure-induced IPT of Form I to Form II at 4.2 GPa. For that reason, it has been chosen as a model compound in this study to determine if IPT can be predicted in silico using periodic DFT calculations. The transformation of Form II into Form I, occurring under decompression, was observed in geometry optimization calculations. However, the reverse transition was not detected, although the calculated differences in the DFT energies and thermodynamic parameters indicated that Form II should be more stable at increased pressure. Finally, the IPT was successfully simulated using ab initio molecular dynamics calculations.

Classical threshold law for the formation of van der Waals molecules

We study the role of pairwise long-range interactions in the formation of van der Waals molecules through direct three-body recombination processes A + B + B → AB + B, based on a classical trajectory method in hyperspherical coordinates developed in our earlier works [J. Pérez-Ríos et al., J. Chem. Phys. 140, 044307 (2014); M. Mirahmadi and J. Pérez-Ríos, J. Chem. Phys. 154, 034305 (2021)]. In particular, we find the effective long-range potential in hyperspherical coordinates with an exact expression in terms of dispersion coefficients of pairwise potentials. Exploiting this relation, we derive a classical threshold law for the total cross section and the three-body recombination rate yielding an analytical expression for the three-body recombination rate as a function of the pairwise long-range coefficients of the involved partners.

Fourier transform infrared absorption (FTIR) on dry stratum corneum, corneocyte-lipid interfaces: experimental and vibrational spectroscopy calculations

Many questions concerning the biophysical and physiological properties of skin are still open. Skin aging, permeability, dermal absorption, hydration, and drug transdermal delivery, are few examples of processes with unveiled underlying mechanisms. In this work, it is presented a comparison between Fourier transform infrared absorption (FTIR) of dry stratum corneum and stratum corneum under lipase action supported by first-principles density functional vibrational calculations. The molecular structure of stratum corneum was modeled by an archetype of its hygroscopic proteic portion inside the corneocytes, the natural moisturizing factor, coupled to glycerol molecules which represent the lipid fraction of stratum corneum. Vibrational spectra were calculated and compared to experimental data obtained on the animal model of stratum corneum. The experimental results indicated prominent spectral differences between dry and lipase-treated stratum corneum. Principal components analysis and hyerarchical clustering indicated that 1200, 1650, and 1695 cm^-1 bands are the most influential on the discrimination. It is noticed that bands in the fingerprint region (800-1800 cm^-1) were correctly assigned. Moreover, the calculations revealed the existence of two coupled vibration between the hydroxyl group of lipid and methylene (1120 and 1160 cm^-1), which are of special interest since they probe the lipid-amino acid coupling. The model was also able to predict the shear modulus of dry stratum corneum in excellent agreement with the reported values from the literature. Other physical/chemical properties could be calculated exploring the chemical accuracy and molecular resolution of this model. Research in dermatology, cosmetology, and biomedical engineering in the specific topics of drug delivery and/or mechanical properties of skin are examples of fields that would potentially take advantage of this approach.

Prediction of lattice energy of benzene crystals: A robust theoretical approach

We present an inexpensive and robust theoretical approach based on the fragment molecular orbital methodology and the spin-ratio scaled second-order Møller-Plesset perturbation theory to predict the lattice energy of benzene crystals within 2 kJ⋅mol^-1 . Inspired by the Harrison method to estimate the Madelung constant, the proposed approach calculates the lattice energy as a sum of two- and three-body interaction energies between a reference molecule and the surrounding molecules arranged in a sphere. The lattice energy converges rapidly at a radius of 13 Å. Adding the corrections to account for a higher correlated level of theory and basis set superposition for the Hartree Fock (HF) level produced a lattice energy of -57.5 kJ⋅mol^-1 for the benzene crystal structure at 138 K. This estimate is within 1.6 kJ⋅mol^-1 off the best theoretical prediction of -55.9 kJ⋅mol^-1 . We applied this approach to calculate lattice energies of the crystal structures of phase I and phase II-polymorphs of benzene-observed at a higher temperature of 295 K. The stability of these polymorphs was correctly predicted, with phase II being energetically preferred by 3.7 kJ⋅mol^-1 over phase I. The proposed approach gives a tremendous potential to predict stability of other molecular crystal polymorphs.

Structural and electronic properties of layered nanoporous organic nanocrystals

In this work, we present the optimized geometric stacking of several layered nanoporous organic nanocrystals (NONs) and the stacking effect on their electronic structure. Hexagonal layered structures, C₁₂H₆-h2D, B₆N₆H₆-h2D and C₆N₆-h2D are built from aromatic organic molecular units benzene, borazine and 1,3,5-triazine, respectively while oblique structures, C₁₀N₂H₄-o2D, C₈N₄H₂-o2D, C₁₀P₂H₄-o2D and C₁₀As₂H₄-o2D, are built from pyridine, 1,3-diazine, phosphinine and arsinine, respectively. Our density functional theory calculations show stacking energy profiles of NONs that are similar to graphene in both the stand-alone and bulk C₁₂H₆-h2D and B₆N₆H₆-h2D structures while the rest of the studied layered materials deviate from the perfect AB stacking. The number of layers as well as the stacking configuration significantly influence the electronic properties of these materials. Indirect to direct band gap crossovers from the bulk to monolayers are observed in all of the NONs except in C₆N₆-h2D which exhibits a direct band gap in both the monolayer, isolated few-layers, and bulk. Furthermore, it is observed that the electronic nature of C₁₀As₂H₄-o2D changes from a semiconducting character in the isolated monolayer to a metallic character in the bulk. The porous nature and the stability of these layered NONs combined with the electronic properties observed in this work point at them as valuable materials for potential applications in nanoelectronics and gas separation membranes, as well as deep ultraviolet optoelectronics and laser devices.

The effect of dispersion interactions on the geometric and electronic properties of novel porous organic nanocrystals.

Crystal structure prediction of energetic materials and a twisted arene with Genarris and GAtor

A molecular crystal structure prediction workflow, based on the random structure generator, Genarris, and the genetic algorithm (GA), GAtor, is successfully applied to two energetic materials and a chiral arene.

The inactivation mechanism of chemical disinfection against SARS-CoV-2: from MD and DFT perspectives

Exploring effective disinfection methods and understanding their mechanisms on the new coronavirus is becoming more active due to the outbreak of novel coronavirus pneumonia (COVID-19) caused by severe acute respiratory coronavirus 2 (SARS-CoV-2). By combining molecular dynamics and first-principles calculations, we investigate the interaction mechanism of chemical agents with 3CL hydrolase of SARS-CoV-2. The radial distribution functions indicate that the biocidal ingredients are sensitive to the unsaturated oxygen atoms of 3CL hydrolase and their interactions remarkably depend on the concentration of the biocidal ingredients. Besides, we find that the adsorption performance of the active ingredients for the unsaturated oxygen atoms is superior to other styles of atoms. These computational results not only decipher the inactivation mechanism of chemical agents against SARS-CoV-2 from the molecule-level perspective, but also provide a theoretical basis for the development and application of new chemical methods with a high disinfection efficiency.

Challenging the Ostwald rule of stages in mechanochemical cocrystallisation

Mechanochemistry provides an efficient, but still poorly understood route to synthesize and screen for polymorphs of organic solids. We present a hitherto unexplored effect of the milling assembly on the polymorphic outcome of mechanochemical cocrystallisation, tentatively related to the efficiency of mechanical energy transfer to the milled sample. Previous work on mechanochemical cocrystallisation has established that introducing liquid or polymer additives to milling systems can be used to direct polymorphic behavior, leading to extensive studies how the amount and nature of grinding additive affect reaction outcome and polymorphism. Here, focusing on a model pharmaceutical cocrystal of nicotinamide and adipic acid, we demonstrate that changes to the choice of milling media (i.e. number and material of milling balls) and/or the choice of milling assembly (i.e. jar material) can be used to direct polymorphism of mechanochemical cocrystallisation, enabling the selective synthesis, and even reversible and repeatable interconversion of cocrystal polymorphs. While real-time mechanistic studies of mechanochemical transformations of metal–organic materials have previously suggested that reactions follow a path described by Ostwald's rule of stages, i.e. from metastable to increasingly more stable product structures, the herein presented systematic study presents an exception to that rule, revealing that modification of energy input in the mechanochemical system, combined with a small energy difference between polymorphs, permits the selective synthesis of either the more stable room temperature form, or the new metastable high-temperature form, of the target cocrystal.

The choice of milling assembly (jar and ball material, number and size of balls) can be used to direct polymorphism in mechanochemical cocrystallisation, enabling the selective synthesis, and even reversible interconversion of cocrystal polymorphs.

Mechanochemical reactions of cocrystals: comparing theory with experiment in the making and breaking of halogen bonds in the solid state

Mechanochemical re-investigation of the halogen-bonded cocrystallisation of 1,4-diazabicyclo[2.2.2]-octane and 1,2-diiodotetrafluorobenzene revealed an unexpectedly complex system with three distinct cocrystal compositions, one of which also exhibits temperature-dependent polymorphism. This provided an opportunity to experimentally test the ability of dispersion-corrected periodic density functional theory (DFT) to not only explain the formation, but also predict the interconversion between halogen-bonded cocrystals of different stoichiometries.

XO-PBC: An Accurate and Efficient Method for Molecular Crystals

In this work, we propose the XO-PBC method, which combines the eXtended ONIOM method (XO) with the periodic boundary condition (PBC) for the description of molecular crystals. XO-PBC tries to embed a finite cluster cut out from the solid into the periodic environment, making it feasible to employ advanced molecular quantum chemistry methods, which are usually prohibitively expensive for direct PBC calculations. In particular, XO-PBC utilizes the results from force calculations to design the scheme to fragment the molecule when crystals are made of large molecules and to select cluster model systems automatically consisting of dimer up to tetramer interactions for embedding. By applying an appropriate theory to each model, a satisfactory accuracy for the system under study is ensured, while a high efficiency is achieved with massively parallel computing by distributing model systems onto different processors. A comparison of the XO-PBC calculations with the conventional direct PBC calculations at the B3LYP level demonstrates its accuracy at substantially low cost for the description of molecular crystals. The usefulness of the XO-PBC method is further exemplified, showing that XO-PBC is able to predict the lattice energies of various types of molecular crystals within chemical accuracy (<4 kJ/mol) when the doubly hybrid density functional XYG3 is used as the target high level and the periodic PBE as the basic low level. The XO-PBC method provides a general protocol that brings the great predictive power of advanced electronic structure methods from molecular systems to the extended solids.

NMR crystallography of molecular organics

Developments of NMR methodology to characterise the structures of molecular organic structures are reviewed, concentrating on the previous decade of research in which density functional theory-based calculations of NMR parameters in periodic solids have become widespread. With a focus on demonstrating the new structural insights provided, it is shown how "NMR crystallography" has been used in a spectrum of applications from resolving ambiguities in diffraction-derived structures (such as hydrogen atom positioning) to deriving complete structures in the absence of diffraction data. As well as comprehensively reviewing applications, the different aspects of the experimental and computational techniques used in NMR crystallography are surveyed. NMR crystallography is seen to be a rapidly maturing subject area that is increasingly appreciated by the wider crystallographic community.

Contributions of IQA electron correlation in understanding the chemical bond and non-covalent interactions

The quantum topological energy partitioning method Interacting Quantum Atoms (IQA) has been applied for over a decade resulting in an enlightening analysis of a variety of systems. In the last three years we have enriched this analysis by incorporating into IQA the two-particle density matrix obtained from Møller–Plesset (MP) perturbation theory. This work led to a new computational and interpretational tool to generate atomistic electron correlation and thus topologically based dispersion energies. Such an analysis determines the effects of electron correlation within atoms and between atoms, which covers both bonded and non-bonded “through -space” atom–atom interactions within a molecule or molecular complex. A series of papers published by us and other groups shows that the behavior of electron correlation is deeply ingrained in structural chemistry. Some concepts that were shown to be connected to bond correlation are bond order, multiplicity, aromaticity, and hydrogen bonding. Moreover, the concepts of covalency and ionicity were shown not to be mutually excluding but to both contribute to the stability of polar bonds. The correlation energy is considerably easier to predict by machine learning (kriging) than other IQA terms. Regarding the nature of the hydrogen bond, correlation energy presents itself in an almost contradicting way: there is much localized correlation energy in a hydrogen bond system, but its overall effect is null due to internal cancelation. Furthermore, the QTAIM delocalization index has a connection with correlation energy. We also explore the role of electron correlation in protobranching, which provides an explanation for the extra stabilization present in branched alkanes compared to their linear counterparts. We hope to show the importance of understanding the true nature of the correlation energy as the foundation of a modern representation of dispersion forces for ab initio, DFT, and force field calculations.

Quantum mechanics of proteins in explicit water: The role of plasmon-like solute-solvent interactions

Quantum-mechanical van der Waals dispersion interactions play an essential role in intraprotein and protein-water interactions-the two main factors affecting the structure and dynamics of proteins in water. Typically, these interactions are only treated phenomenologically, via pairwise potential terms in classical force fields. Here, we use an explicit quantum-mechanical approach of density-functional tight-binding combined with the many-body dispersion formalism and demonstrate the relevance of many-body van der Waals forces both to protein energetics and to protein-water interactions. In contrast to commonly used pairwise approaches, many-body effects substantially decrease the relative stability of native states in the absence of water. Upon solvation, the protein-water dispersion interaction counteracts this effect and stabilizes native conformations and transition states. These observations arise from the highly delocalized and collective character of the interactions, suggesting a remarkable persistence of electron correlation through aqueous environments and providing the basis for long-range interaction mechanisms in biomolecular systems.

Effects of atomic species and interatomic distance on the interactions in one-dimensional nanomaterials

Noncovalent van der Waals (vdW) interactions are significant for the constitution of nanomaterials; however, they are not well understood in one-dimensional materials. Herein, we employ density functional theory (DFT) methods to address this issue and find that the many-body effects of vdW interactions within the one-dimensional wires composed of atoms chosen from the second period (B, C, N, O, F) vary with the interatomic distance of the wires. Furthermore, the atomic species effectively regulate the transition threshold of the many-body effects of vdW interactions. In the case of the adsorption of n-heptane (C7H16) on the wires, the atomic species alters the interactions between the wires and the molecule by modulating the coupling vibration between wires and C7H16 molecules. Correspondingly, replacing a portion of Pb with Tl atoms could contribute to the stability of the organic-inorganic hybrid halide perovskites with one-dimensional structures. Our findings not only contribute to the understanding of vdW interactions in one-dimensional structures with second-period atoms (B, C, N, O, F) but also provide clues for improving the stability of perovskites with one-dimensional structures.