Interactions In Molecular Crystals Research Articles

On the predictability of supramolecular interactions in molecular cocrystals – the view from the bench

A series of cocrystals involving theophylline and fluorobenzoic acids highlights the difficulty of predicting supramolecular interactions in molecular crystals.

Giant electron-phonon interactions in molecular crystals and the importance of nonquadratic coupling

We investigate electron-phonon coupling in the molecular crystals ${\mathrm{CH}}_{4}, {\mathrm{NH}}_{3}, {\mathrm{H}}_{2}\mathrm{O}$, and HF, using first-principles quantum mechanical calculations. We find vibrational corrections to the electronic band gaps at zero temperature of $\ensuremath{-}1.97$ eV, $\ensuremath{-}1.01$ eV, $\ensuremath{-}1.52$ eV, and $\ensuremath{-}1.62$ eV, respectively, which are comparable in magnitude to those from electron-electron correlation effects. Microscopically, the strong electron-phonon coupling arises in roughly equal measure from the almost dispersionless high-frequency molecular modes and from the lower-frequency lattice modes. We also highlight the limitations of the widely used Allen-Heine-Cardona theory, which gives significant discrepancies compared to our more accurate treatment.

Exploration of Supramolecular Architecture in Complexes with 1-Substituted-1H-[1,2,3]-triazole-4-carboxylic Acid: Structural Elucidation and Hirshfeld Surface Analysis

Two new complexes [Cu(HL)2(H2O)2] (1) and [AgHL]n (2) (where H2L is 5-methyl-1-(1H-pyrazol-3-yl)-1H-1,2,3-triazole-4-carboxylic acid) have been synthesized at room temperature and structurally characterized by elemental analysis, IR spectroscopy, and single crystal X-ray diffraction. Intermolecular, compounds 1 displays a 2D network containing 10-number and 4-number rings forming by intermolecular hydrogen bond O–H···O. Complex 2 is a Ag(I) polymer and exists C–H···Ag interactions forming the 2D layers into supermolecule. Intermolecular interactions in molecular crystal of 2 was explored by hirshfeld surface analysis, and the 2D fingerprint plots reveal that the main intermolecular contact is N···H/H···N contact with proportion of 22.9 %.

Accurate and Efficient Model Energies for Exploring Intermolecular Interactions in Molecular Crystals.

The energy of interaction between molecules is commonly expressed in terms of four key components: electrostatic, polarization, dispersion, and exchange-repulsion. Using monomer wave functions to obtain accurate estimates of electrostatic, polarization, and repulsion energies along with Grimme's dispersion corrections, a series of energy models are derived by fitting to dispersion-corrected DFT energies for a large number of molecular pairs extracted from organic and inorganic molecular crystals. The best performing model reproduces B3LYP-D2/6-31G(d,p) counterpoise-corrected energies with a mean absolute deviation (MAD) of just over 1 kJ mol(-1) but in considerably less computation time. It also performs surprisingly well against benchmark CCSD(T)/CBS energies, with a MAD of 2.5 kJ mol(-1) for a combined data set including Hobza's X40, S22, A24, and S66 dimers. Two of these energy models, the most accurate and the fastest, are expected to find widespread application in investigations of molecular crystals.

Incisive probing of intermolecular interactions in molecular crystals: core level spectroscopy combined with density functional theory.

The α-form of crystalline para-aminobenzoic acid (PABA) has been examined as a model system for demonstrating how the core level spectroscopies X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine-structure (NEXAFS) can be combined with CASTEP density functional theory (DFT) to provide reliable modeling of intermolecular bonding in organic molecular crystals. Through its dependence on unoccupied valence states NEXAFS is an extremely sensitive probe of variations in intermolecular bonding. Prediction of NEXAFS spectra by CASTEP, in combination with core level shifts predicted by WIEN2K, reproduced experimentally observed data very well when all significant intermolecular interactions were correctly taken into account. CASTEP-predicted NEXAFS spectra for the crystalline state were compared with those for an isolated PABA monomer to examine the impact of intermolecular interactions and local environment in the solid state. The effects of the loss of hydrogen-bonding in carboxylic acid dimers and intermolecular hydrogen bonding between amino and carboxylic acid moieties are evident, with energy shifts and intensity variations of NEXAFS features arising from the associated differences in electronic structure and bonding.

Intermolecular interactions in molecular crystals and glasses

The local structure of materials may not be apparent from Bragg crystallography, but emerges naturally from refinement against a pair distribution function (PDF). In molecular systems, the most prominent features in the PDF are the low-r peaks corresponding to the intramolecular interactions, yet these features are often the least interesting. The domination of the PDF by intramolecular interactions makes it difficult in the case of molecular materials to investigate the more interesting intermolecular interactions. In particular, few amorphous framework materials or molecular glasses have been characterized in any detail. Using reverse Monte Carlo (RMC) refinement against total neutron and x-ray scattering data we have studied the intermolecular interactions in two families of molecular materials, each including both crystalline and glassy phases. To overcome the problem posed by intramolecular interactions prior chemical knowledge of the molecular structure is incorporated into the refinement using empirical intramolecular potentials. One family consists of three phases of ZIF-4, a metal-organic framework consisting of tetrahedrally coordinated Zn2+ ions connected by imidazolate rings. In this material, we identify the molecular motion responsible for the greater flexibility shown by the amorphous phase compared to two crystalline phases [1]. The other family consists of the isomeric molecules para- and ortho-terphenyl (PTP/OTP). OTP is a paradigmatic glass-former, with a critical cooling rate of less than 0.1 K/min. PTP, on the other hand, is a crystalline material that undergoes an order-disorder phase transition at 178 K. We have characterized these materials' flexibility with the aid of molecular dynamics simulations. Our results demonstrate that RMC refinement with appropriate intramolecular potentials is capable of elucidating the intermolecular interactions of molecular systems, revealing new structural details in glassy and amorphous structures.

Structural elucidation and contribution of intermolecular interactions in O-hydroxy acyl aromatics: Insights from X-ray and Hirshfeld surface analysis

An O-hydroxy acyl aromatics, namely 1,1′,1″-(2,4,6-trihydroxybenzene-1,3,5-triyl) triethanone (1) was synthesized and characterized by spectroscopic and single crystal X-ray structural studies with a detailed scrutiny of visualizing and exploring intermolecular interactions in molecular crystals through Hirshfeld surface. The crystal packing of (1) exhibits intermolecular π–π stacking interactions to generate a one-dimensional parallel stacked ribbon propagating along (001) direction. Hirshfeld surface analysis for visually analyzing intermolecular interactions in crystal structures employing molecular surface contours and 2D fingerprint plots have been used to scrutinize molecular shapes. Crystal structure analysis supported with the Hirshfeld surface and fingerprint plots enabled the identification of the significant intermolecular interactions.

Structure and interactions in benzamide molecular crystals

In this study, we resolved discrepancies concerning the experimentally determined structure of benzamide molecular crystals from dispersion-corrected density functional calculations. A clear energy ranking was obtained for the two candidates of the stable (P1) modification of benzamide. This was rationalised by subtle differences of the molecular interactions in the molecular crystal. The potential energy of the different structures was dominated by the interplay of intermolecular attraction and molecular torsion/deformation to accommodate favourable hydrogen-bonded networks. Using suitable proxies arranged in pseudo-crystalline set-ups, we discriminated the contribution of electrostatics, π–π interactions and intra-molecular interactions to the lattice energies.

Understanding the role of vibrations, exact exchange, and many-body van der Waals interactions in the cohesive properties of molecular crystals

The development and application of computational methods for studying molecular crystals, particularly density-functional theory (DFT), is a large and ever-growing field, driven by their numerous applications. Here we expand on our recent study of the importance of many-body van der Waals interactions in molecular crystals [A. M. Reilly and A. Tkatchenko, J. Phys. Chem. Lett. 4, 1028 (2013)], with a larger database of 23 molecular crystals. Particular attention has been paid to the role of the vibrational contributions that are required to compare experiment sublimation enthalpies with calculated lattice energies, employing both phonon calculations and experimental heat-capacity data to provide harmonic and anharmonic estimates of the vibrational contributions. Exact exchange, which is rarely considered in DFT studies of molecular crystals, is shown to have a significant contribution to lattice energies, systematically improving agreement between theory and experiment. When the vibrational and exact-exchange contributions are coupled with a many-body approach to dispersion, DFT yields a mean absolute error (3.92 kJ/mol) within the coveted "chemical accuracy" target (4.2 kJ/mol). The role of many-body dispersion for structures has also been investigated for a subset of the database, showing good performance compared to X-ray and neutron diffraction crystal structures. The results show that the approach employed here can reach the demanding accuracy of crystal-structure prediction and organic material design with minimal empiricism.

Revealing Non‐covalent Interactions in Molecular Crystals through Their Experimental Electron Densities

Non-covalent interactions (NCI) define the rules underlying crystallisation, self-assembly and drug-receptor docking processes. A novel NCI descriptor, based on the reduced electron density gradient (RDG), that enables easy visualisation of the zones of the electron density (ED) involved in either the supposedly attractive (dispersive, hydrogen bonding) or allegedly repulsive (steric) intermolecular interactions, was recently developed by Johnson et al. Here, it is applied for the first time to EDs derived from single-crystal X-ray diffraction data. A computer code handling both experimental and ab initio EDs in the RDG-NCI perspective was purposely written. Three cases spanning a wide range of NCI classes were analysed: 1) benzene, as the prototype of stacking and weak CH···π interactions; 2) austdiol, a heavily functionalised fungal metabolite with a complex hydrogen-bonding network; 3) two polymorphs of the heteroatom-rich anti-ulcer drug famotidine, with van der Waals and hydrogen-bond contacts between N- and S-containing groups. Even when applied to experimental EDs, the RDG index is a valuable NCI descriptor that can highlight their different nature and strength and provide results of comparable quality to ab initio approaches. Combining the RDG-NCI study with Bader's ED approach was a key step forward, as the RDG index can depict inherently delocalised interactions in terms of extended and flat RDG isosurfaces, in contrast to the bond path analysis, which is often bounded to a too localised and possibly discontinuous (yes/no) description. Conversely, the topological tool can provide quantitative insight into the simple, qualitative NCI picture offered by the RDG index. Hopefully, this study may pave the way to a deeper analysis of weak interactions in proteins using structural and ED information from experiment.

Effect of dipolar interaction in molecular crystals

In this paper we investigate the ground state and the nature of the transition from an orientational ordered phase at low temperature to the disordered state at high temperature in a molecular crystal. Our model is a Potts model which takes into account the exchange interaction J between nearest-neighbor molecules and a dipolar interaction between molecular axes in three dimensions. The dipolar interaction is characterized by two parameters: its amplitude D and the cutoff distance rc. If the molecular axis at a lattice site has three orientations, say the x, y or z axes, then when D = 0, the system is equivalent to the 3-state Potts model: the transition to the disordered phase is known to be of first order. When D ≠ 0, the ground-state configuration is shown to be composed of two independent interpenetrating layered subsystems which form a sandwich whose periodicity depends on D and rc. We show by extensive Monte Carlo simulation with a histogram method that the phase transition remains of first order at relatively large values of rc.

Structures and lattice energies of molecular crystals using density functional theory: Assessment of a local atomic potential approach

Lattice parameters and lattice energies of twelve selected molecular crystals are computed by using density functional theory (DFT) with different treatments of dispersion correction, including the local atomic potential (LAP) and three popular DFT-D methods. Inclusion of LAPs improves the description of intermolecular interactions in molecular crystals over standard DFT calculations. The DFT+LAP approach provides accurate structural parameters and lattice energies that are comparable to the PBE-Grimme scheme. Our results suggest that the DFT+LAP approach is a promising alternative for efficient and accurate quantum simulations on molecular crystals and other systems involving noncovalent interactions.

Hydrogen-Bonding Networks from First-Principles: Exploring the Guanidine Crystal

Hydrogen bonding is among the most important interactions in molecular crystals, and examples are abundant. As a consequence of such interactions, many molecules crystallize in complex but intriguing structures, in contrast to the relatively simple packing principles of metallic or ionic solids. In this work, we present a computational approach based on plane-wave density-functional theory (DFT) and supercell techniques, aiming to understand and quantify hydrogen-bonded networks in the solid state and in two-, one-, and zero-dimensional fragments derived from the molecular crystal. With such methodology at hand, we investigate guanidine, a fitting example of a molecular crystal and an important compound for inorganic and organic chemistry alike. On the basis of our computations, we discuss the initially proposed layered structure of guanidine and identify both stabilizing and destabilizing cooperative interactions in the three crystalline dimensions.

Atoms‐in‐molecules analysis of the effect of intermolecular interactions on dielectric properties in hydrogen‐bonded material 5‐bromo‐9‐hydroxyphenalenone

AbstractIntermolecular interactions in molecular crystal of 5‐bromo‐9‐hydroxyphenalenone are analyzed by means of Bader's theory of atoms in molecules. A set of criteria to ascertain the presence of a hydrogen bond is applied to two candidates of intermolecular contacts suggested by our previous work [Otaki and Ando,Phys. Chem. Chem. Phys.2011,13, 10719]. It is shown that they almost satisfy the criteria to confirm the existence of intermolecular CH···O hydrogen bond. In addition to the hydrogen bonding, other types of interactions, such as H···H and H···Br, are found in one of the candidates. The discussions are extended to explain how the molecular dipole moment is induced by surrounding molecules. It is also found that the bias in the atomic charges due to the electrophilicity of the oxygen atom is strongly correlated with the induced dipole moment. © 2012 Wiley Periodicals, Inc.

Charge Density Analysis of Heterohalogen (Cl···F) and Homohalogen (F···F) Intermolecular Interactions in Molecular Crystals: Importance of the Extent of Polarizability

Experimental charge density distribution in 2-chloro-4-fluorobenzoic acid and 4-fluorobenzamide has been carried out using high resolution X-ray diffraction data collected at 100 K using Hansen-Coppens multipolar formalism of electron density. These compounds display short Cl···F and F···F interactions, respectively. The experimental results are compared with the theoretical charge densities using theoretical structure factors obtained from periodic quantum calculation at the B3LYP/6-31G** level. The topological features were derived from Bader’s “atoms in molecules” (AIM) approach. Intermolecular Cl···F interaction in 2-chloro-4-fluorobenzoic acid is attractive in nature (type II interaction) while the nature of F···F interactions in 4-fluorobenzamide shows indication of a minor decrease in repulsion (type I interaction), though the extent of polarization on the fluorine atom is arguably small.

Yadernyi magnitnyi rezonans v van-flekovskikh magnetikakh i mezhmolekulyarnye vzaimodeistviya v molekulyarnykh kristallakh i fazakh Shevryolya

Ядерный магнитный резонанс в ван-флековских магнетиках и межмолекулярные взаимодействия в молекулярных кристаллах и фазах Шеврёля, Габуда С.П., Козлова С.Г., Лундин А.Г.

Application of the short and long consecutive pairs model to the triplet-doublet interaction in molecular crystals

We have adapted the model of two consecutive pairs to the study of the triplet-doublet (T-D) interaction in molecular crystals. We have applied this model to the modulation of the photoconductivity in crystalline anthracene by a static magnetic field (MFE) and a microwave field (PDMR). We were able to reproduce, for the first time, quite perfectly two types of experiments with the same set of kinetic constants.

On quantitative structural and electron-density studies of interactions in molecular crystals

On quantitative structural and electron-density studies of interactions in molecular crystals

Application of an empirical dispersion potential to van der Waals binding in nitromethane, pentaerythritol, and pentaerythritol tetranitrate

The use of an empirical dispersion potential to accurately represent the van der Waals interaction in molecular crystals is discussed. Results for nitromethane, pentaerythritol (PE), and pentaerythritol tetranitrate (PETN) are presented for equilibrium volumes using a variety of basis sets ranging in quality in the Crystal program. Agreement with experiment for equilibrium volumes is found to be within a few percent when the Grimme potential and a high-quality basis set is used.

Organic Nanoclusters on Inorganic Nanostructures for Tailoring the Emission Properties of Organic Materials

AbstractInorganic nanostructures have been intensively studied because of their size‐dependent emission color as a result of quantum confinement effects. In contrast, no significant size dependence of the optical properties is expected for organic nanostructures owing to the weak nearest‐neighbor interactions in molecular crystals; however, the optical properties of organic materials can be significantly affected by aggregation and molecular packing, which can result in large differences between the emission spectra of solutions and thin films. Thus, the emission spectra of organic nanostructures may differ considerably from the bulk material despite the absence of quantum confinement effects. We demonstrate that 3,4,9,10‐perylenetetracarboxylicdiimide (PTCDI) nanoclusters grown on ZnO nanorods exhibit an intense blue‐white photoluminescence, different from the weak red emission of PTCDI films. Light emitting diodes consisting of ZnO nanorods and PTCDI nanoclusters also exhibited white emission.