Organic Molecular Crystals Research Articles

First-principle simulation of solid nitrobenzene under uniaxial compression

Energetic materials (EMs) including explosives, propellants and pyrotechnics have been widely used for the military and many other purposes. Solid nitrobenzene (an organic molecular crystal) could be considered as a prototype of energetic material. Up to now, numerous studies have been devoted to crystal structures, spectrum properties and decomposition mechanisms for solid nitrobenzene experimentally and theoretically. However there has been a lack of the comprehensive understanding of the anisotropic characteristics under different loading conditions. Thus we investigate the hydrostatic and uniaxial compressions along three different lattice directions to determine this anisotropic effect. In this work, the density functional theory calculations are performed based on Cambridge Sequential Total Energy Package (CASTEP) code using normconserving pseudo potentials and a kinetic energy cutoff of 700 eV. The generalized gradient approximation with the Perdew-Burke-Ernzerhof parameterization is used. Monkhorst-Pack k-point meshes with a density of 0.05 -1 are used for Brillouin-zone integration. The empirical dispersion correction by Grimme is taken to account for week intermolecular interactions. The hydrostatic compressions are applied from 0 GPa to 20 GPa. Cell volume, lattice shape and coordinates of the atoms could be fully relaxed. while uniaxial compression is applied up to 70% of the equilibrium cell volume in steps of 2% along their lattice directions respectively. At each compression step, only atomic coordinates are allowed to relax, with the lattice fixed. The equilibrium lattice structures under hydrostatic compressions are obtained by full relaxation at 0 K temperature. In ambient condition, the calculated volume and parameter of the unit cell are underestimated compared with the experimental data, and corresponding errors are -2.98%, 0.01%, -4.39%, 5.71% respectively. In contrast, the calculated lattice energy is overestimated compared with the range of experimental results with 5.71% of the error. In high pressure condition, the volume and cell parameter of the unit cell as a function of compression ratio are plotted and compared with the experimental data. The theoretical and experimental values are close with the increase of the pressure, for instant, the error decreases from -4.39% at 0 GPa to -1.93% at 4 GPa. On the other hand, the uniaxial compression is applied along the directions of three lattice vectors. The changes of stress tensor, band gap, energy per atom as a function of compression ratio are also plotted and discussed, which can characterize the anisotropic effect of solid nitrobenzene. The most noticeable effect of anisotropy in solid nitrobenzene is the metallization at V/V0=0.76 compressed along the X axis, while the solid nitrobenzene under hydrostatic pressure or other uniaxial compressions up to V/V0=0.76 remains semiconductor with band gap larger than 1.591 eV. By analyzing the local density of states and charge density distribution of nitrobenzene crystal, we confirm that the metallization is caused by the overlap of the electron from benzene ring. Through calculating different physical parameters, we find that X axis is the most sensitive direction of nitrobenzene crystal. The studies of anisotropic effects are expected to shed light on the physical and chemical properties of solid nitrobenzene on an atomistic scale and provide several insights for experiments.

Unusual physical behaviour and polymorphic phase transitions in crystalline bicyclic anhydrides

Bicyclic anhydrides function as versatile building blocks for polymeric materials, but molecular crystals of these monomeric units demonstrate interesting physicochemical properties. Here, we investigate two pairs of crystalline bicyclic anhydrides, where each pair contains a saturated and unsaturated component. One pair (RTM3/RTM4) is built around bicyclo[2.2.2]octane-2-endo,3-endo-dicarboxylic acid anhydride (BA) and another pair (BCA1/BCA2) consists of a BA-core with alkyl substituents. Differential scanning calorimetry (DSC), powder X-ray diffraction (PXRD) and reflective melting point determination shows that both components in the RTM3/RTM4 pair undergo reversible, polymorphic temperature-induced phase transitions to the same space group while the BCA1/BCA2 pair does not. The melting point (MP) behavior of the BCA1/BCA2 pair is interesting because it contradicts typical alkane/alkene MP trends, as the un-saturated component (BCA1) has the higher MP. Lattice enthalpies calculated via dispersion inclusive density functional theory (DFT+vdW) help to elucidate this unusual MP behavior. In addition, Hirshfeld surface analysis of both pairs demonstrates that variations in the intermolecular close contacts may have an effect as to whether the saturated or unsaturated component will exhibit the higher MP. Finally, BCA1 is found to possess unique liquid–solid phase transition properties for a single component organic molecular crystal (OMC), as it is supercoolable over a ∼60 K range.

АНАЛИЗ НЕКОТОРЫХ ПРИБЛИЖЕНИЙ ДЛЯ ОПИСАНИЯ ТЕПЛОВОЙ ЧАСТИ УРАВНЕНИЙ СОСТОЯНИЯ МОЛЕКУЛЯРНЫХ КРИСТАЛЛОВ

The paper deals with the analysis of available approximations to describe the dependence of heat capacity at constant volume on the temperature of a molecular crystal. The information on the dependence of heat capacity at constant volume on the molecular crystal’s temperature plays an important role in construction of molecular crystal state equations. Molecular crystals are closing relations of mathematical models, which describe shock wave propagation, initiation of detonation in molecular crystals, etc. It is shown that the examined in the paper Debye and Einstein approximations, widely used for description of thermodynamic properties of monoatomic crystals, do not enable us to sufficiently describe the dependence of heat capacity at constant volume on the temperature of molecular crystals of nitro compounds. The suggestion by A.I. Kitaygorosky to divide crystal vibration frequency into intramolecular and vibration of a molecule as a whole (three vibrations of the molecule’s center of gravity and three vibrations of Euler angles), well-proven when calculating thermodynamic functions of a number of organic molecular crystals with planar molecules, doesn’t make it possible to adequately describe the dependence of heat capacity at constant volume on the temperature of molecular crystals of nitro compounds. The obtained in this work results highlight the necessity for development of special approximations, which provide an opportunity to adequately describe both low-frequency and high-frequency parts of a vibration spectrum of molecular crystals of nitro compounds, the dependence of heat capacity at constant volume on the crystal’s temperature and the Gruneisen function, which is a link between heat and cold components of the molecular crystal state equation.

Nanoparticles of organic nonlinear optical molecular crystals synthesized by laser ablation in liquid

In this work, nanoparticles of nonlinear optical organic molecular cocrystal DAST (4-dimethylamino-N-methylstilbazolium p-toluenesulfonate) were obtained by pulsed laser ablation in liquid monomer isodecyl acrylate (IDA). Sizes of obtained nanoparticles were determined by scanning electron microscope and were about 200 nm in width. Laser ablation does not lead to photocuring or photodegradation of liquid monomer. Ablation processes was similar to the processes in classical liquids (water, organic solvents). Since in this case the nanoparticles were synthesized directly in the liquid medium of the surfactant monomer, so they are stabilized in it. Nanocomposites films were synthesized on the basis of these stable colloid solution by photocuring. For aliphatic polymer IDA long molecules cross-linking 1,6-Hexandiol diacrylate was used (DIOL). Optical properties of colloid solution and nanocomposites were investigated. It was found that obtained nanoparticles are amorphous form of DAST cocrystal and have a rod-like shape. Also dodecane and polyphenelene ether were tried in this work as liquids with different viscosity to find its effect on size and shape of nanoparticles.

Inorganic bromine in organic molecular crystals: Database survey and four case studies

We present a Cambridge Structural Database and experimental study of multicomponent molecular crystals containing bromine. The CSD study covers supramolecular behaviour of bromide and tribromide anions as well as halogen bonded dibromine molecules in crystal structures of organic salts and cocrystals, and a study of the geometries and complexities in polybromide anion systems. In addition, we present four case studies of organic structures with bromide, tribromide and polybromide anions as well as the neutral dibromine molecule. These include the first observed crystal with diprotonated phenazine, a double salt of phenazinium bromide and tribromide, a cocrystal of 4-methoxypyridine with the neutral dibromine molecule as a halogen bond donor, as well as bis(4-methoxypyridine)bromonium polybromide. Structural features of the four case studies are in the most part consistent with the statistically prevalent behaviour indicated by the CSD study for given bromine species, although they do exhibit some unorthodox structural features and in that indicate possible supramolecular causes for aberrations from the statistically most abundant (and presumably most favourable) geometries.

An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics.

We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%.

Application of discrete solvent reaction field to second-order susceptibility of organic molecular crystal

This article presents an assessment of methods to study the second harmonic generation (SHG) response of organic molecular crystal. We incorporated the discrete solvent reaction field model, density functional theory, and the local field approximation (designated as the LF-DRF/DFT) to investigate the SHG susceptibilities of the chromophore of 2-carboxylic acid-4-nitropyridine-1-oxide (POA). In experiment, the POA appears in two different polymorphic crystal structures easily identified by noticeable differences in the melting points and SHG susceptibilities. In this work, we tried to utilize the LF-DRF/DFT in a supermolecular framework to differentiate the two crystals. While focusing on the ratio of the calculated SHG susceptibilities for the two crystals, at optical wavelength of 1064 nm, the S12 g and SSB-D exchange–correlation functionals within a 5 × 5 × 5 extended architecture produced 2.16 and 2.08, differing from the experimental estimate of 2.16 by 0 and 3.7 %, respectively.

In Situ Tailor-Made Additives for Molecular Crystals: A Simple Route to Morphological Crystal Engineering

We report on a new morphological crystal engineering technique introducing in situ tailor-made additives for organic molecular crystals. In the crystal growing process, phenolic substrate molecules are transformed to in situ tailor-made phenolate additives by adding a small amount of base, without any additional synthetic and purification processes. To demonstrate the in situ tailor-made additive technique, phenolic OH1 (2-(3-(4-hydroxystyryl)-5,5-dimethylcyclohex-2-enylidene)malononitrile) crystal, exhibiting highly efficient nonlinear optical and terahertz generation responses, is chosen as substrate crystal. The in situ tailor-made additive molecules containing a phenolate group exhibit considerably different stereoselective interactions with specific crystal surfaces of phenolic substrate OH1 crystals compared to analogous conventional tailor-made additives. The stereospecific interactions result in a morphological change of the grown OH1 crystal more optimal for photonic applications. To show the use...

Ionization Energies, Electron Affinities, and Polarization Energies of Organic Molecular Crystals: Quantitative Estimations from a Polarizable Continuum Model (PCM)-Tuned Range-Separated Density Functional Approach.

We propose a new methodology for the first-principles description of the electronic properties relevant for charge transport in organic molecular crystals. This methodology, which is based on the combination of a nonempirical, optimally tuned range-separated hybrid functional with the polarizable continuum model, is applied to a series of eight representative molecular semiconductor crystals. We show that it provides ionization energies, electron affinities, and transport gaps in very good agreement with experimental values, as well as with the results of many-body perturbation theory within the GW approximation at a fraction of the computational costs. Hence, this approach represents an easily applicable and computationally efficient tool to estimate the gas-to-crystal phase shifts of the frontier-orbital quasiparticle energies in organic electronic materials.

Communication: Charge-population based dispersion interactions for molecules and materials.

We introduce a system-independent method to derive effective atomic C6 coefficients and polarizabilities in molecules and materials purely from charge population analysis. This enables the use of dispersion-correction schemes in electronic structure calculations without recourse to electron-density partitioning schemes and expands their applicability to semi-empirical methods and tight-binding Hamiltonians. We show that the accuracy of our method is en par with established electron-density partitioning based approaches in describing intermolecular C6 coefficients as well as dispersion energies of weakly bound molecular dimers, organic crystals, and supramolecular complexes. We showcase the utility of our approach by incorporation of the recently developed many-body dispersion method [Tkatchenko et al., Phys. Rev. Lett. 108, 236402 (2012)] into the semi-empirical density functional tight-binding method and propose the latter as a viable technique to study hybridorganic-inorganic interfaces.

High performance organic field-effect transistors using ambient deposition of tetracene single crystals

Organic molecular crystals (OMCs) are of significant interest due to their potential use in transistors, photovoltaic devices, light emitting diodes, and other applications. However, conventional vacuum-based methods of growing crystalline OMC films are costly and provide limited control over crystal growth. In this study, we present a new method for preparing high performance single-crystal tetracene field-effect transistors under near-ambient conditions using organic vapor-liquid-solid (OVLS) deposition. We find that the mobility of OVLS-grown tetracene is comparable to high quality crystalline films prepared by physical vapor deposition. These results establish OVLS deposition as a relatively low cost, low substrate temperature, and ambient pressure method for growing high quality OMC films for device applications.

Structural changes in perylene from UV Raman spectroscopy up to 1 GPa

Vibrational properties and structural changes under pressure of a highly luminescent molecular organic crystal have been investigated by ultraviolet resonant Raman spectroscopy with a 244-nm excitation. Resonant Raman modes of α-perylene crystal up to 1GPa were followed under hydrostatic pressure in an anvil cell with a sapphire window transparent to ultraviolet light. Nonlinear evolution of intra-molecular modes is induced by pressure. Abrupt shifts of Raman wavenumbers suggest structural and planar modifications of the molecules in the crystal. We interpret these shifts as a first-order phase transition to a lower volume of unit cell. The luminescence of perylene crystal is gradually modified as a consequence of these structural changes. The present experimental setup allows investigating with Raman spectroscopy very luminescent molecules involved in chemical reactions and molecular organic crystals under relatively high pressure (up to 1GPa). Copyright © 2016 John Wiley & Sons, Ltd.

Thermodynamic assessment of binary systems Tris(hydroxymethyl)aminomethane-Pentaglycerine (TRIS-PG) and 2-amino-2-methyl-1,3-propanediol-Pentaglycerine (AMPL-PG) phase diagrams

Solid state phase change materials are considered as potential candidates for thermal energy storage. Among the solid–solid heat storage materials, the most promising heat storage materials are organic polyalcohol globular tetrahedral molecular crystals such as (CH3)C(CH2OH)3 for PG, (NH2)C(CH2OH)3 for TRIS, and (CH3)(NH2)C(CH2OH)2 for AMPL, which store a large amount of thermal energy in their solid state high temperature phases with orientationally disorder crystal structure. In this study, we obtained the Gibbs energies of pure PG and pure TRIS derived utilizing the available experimental data including temperature-dependency of heat capacity, enthalpy, and transitions temperatures, as well as obtained optimized binary phase diagrams of TRIS-PG and AMPL-PG by CALPHAD calculations. The phase boundaries are verified by in-situ X-ray diffraction (XRD). Optimized database of these two binaries will allow exploration of ternary and higher order systems using CALPHAD methodology that will provide a wider selection of materials for practical thermal energy storage applications. Regular and sub-regular solution models are used for calculations in which the excess Gibbs energies are expressed by the Redlich–Kister–Muggianu polynomial. A set of self-consistent interaction parameters formulating the Gibbs energies of various phases in binary systems are obtained. The TRIS-PG binary phase diagram was calculated from room temperature to the liquid phase temperature, the modeled phase diagram and the experimental data from our work are in good agreement. We also used experimental data of TRIS-PG from the literature which shows a good agreement between the two data sets. Our optimized TRIS-PG phase diagrams show a wider solid-state two phase region, where there is de-mixing of phases, whereas the calculations from the literature show a very narrow region. We also present optimized AMPL-PG binary phase diagram using PARROT module in Thermal-Calc software. The calculated phase diagrams for the two systems mentioned above are presented along with the experimental data.

Computational identification of organic porous molecular crystals

Most nanoporous solids, such as metal–organic frameworks and zeolites, are composed of extended three-dimensional covalent or coordination bond networks. Nevertheless, an increasing number of porous molecular crystals have been reported that display surface areas and separation efficiencies rivaling those of conventional porous materials. In this investigation, a geometry-based analysis and molecular simulations were used to screen over 150000 organic molecular crystal structures, resulting in the identification of 481 potential organic porous molecular crystals, a testament to the rarity of these materials. Subsequently, we have computed the surface area and pore dimensions of these structures. This computer-generated database has been used to uncover a number of trends and properties that had not previously been quantified due to the limited number of reported porous molecular crystals. Finally, we have used machine learning to show that the van der Waals surface area and other related descriptors of molecular size are the molecular properties best able to predict a crystal's propensity to form structural voids, which are strong indicators of permanent porosity. We posit that the identified database is a promising resource for discovering candidate structures for gas-separation applications and providing general design guidelines for the production of new porous crystals.

Accurate force fields and methods for modelling organic molecular crystals at finite temperatures.

We present an assessment of the performance of several force fields for modelling intermolecular interactions in organic molecular crystals using the X23 benchmark set. The performance of the force fields is compared to several popular dispersion corrected density functional methods. In addition, we present our implementation of lattice vibrational free energy calculations in the quasi-harmonic approximation, using several methods to account for phonon dispersion. This allows us to also benchmark the force fields' reproduction of finite temperature crystal structures. The results demonstrate that anisotropic atom-atom multipole-based force fields can be as accurate as several popular DFT-D methods, but have errors 2-3 times larger than the current best DFT-D methods. The largest error in the examined force fields is a systematic underestimation of the (absolute) lattice energy.

Toward polarizable AMOEBA thermodynamics at fixed charge efficiency using a dual force field approach: application to organic crystals.

First principles prediction of the structure, thermodynamics and solubility of organic molecular crystals, which play a central role in chemical, material, pharmaceutical and engineering sciences, challenges both potential energy functions and sampling methodologies. Here we calculate absolute crystal deposition thermodynamics using a novel dual force field approach whose goal is to maintain the accuracy of advanced multipole force fields (e.g. the polarizable AMOEBA model) while performing more than 95% of the sampling in an inexpensive fixed charge (FC) force field (e.g. OPLS-AA). Absolute crystal sublimation/deposition phase transition free energies were determined using an alchemical path that grows the crystalline state from a vapor reference state based on sampling with the OPLS-AA force field, followed by dual force field thermodynamic corrections to change between FC and AMOEBA resolutions at both end states (we denote the three step path as AMOEBA/FC). Importantly, whereas the phase transition requires on the order of 200 ns of sampling per compound, only 5 ns of sampling was needed for the dual force field thermodynamic corrections to reach a mean statistical uncertainty of 0.05 kcal mol-1. For five organic compounds, the mean unsigned error between direct use of AMOEBA and the AMOEBA/FC dual force field path was only 0.2 kcal mol-1 and not statistically significant. Compared to experimental deposition thermodynamics, the mean unsigned error for AMOEBA/FC (1.4 kcal mol-1) was more than a factor of two smaller than uncorrected OPLS-AA (3.2 kcal mol-1). Overall, the dual force field thermodynamic corrections reduced condensed phase sampling in the expensive force field by a factor of 40, and may prove useful for protein stability or binding thermodynamics in the future.

Vibrational properties of organic donor-acceptor molecular crystals: Anthracene-pyromellitic-dianhydride (PMDA) as a case study.

We establish a reliable quantum-mechanical approach to evaluate the vibrational properties of donor-acceptor molecular crystals. The anthracene-PMDA (PMDA = pyromellitic dianhydride) crystal, where anthracene acts as the electron donor and PMDA as the electron acceptor, is taken as a representative system for which experimental non-resonance Raman spectra are also reported. We first investigate the impact that the amount of nonlocal Hartree-Fock exchange (HFE) included in a hybrid density functional has on the geometry, normal vibrational modes, electronic coupling, and electron-vibrational (phonon) couplings. The comparison between experimental and theoretical Raman spectra indicates that the results based on the αPBE functional with 25%-35% HFE are in better agreement with the experimental results compared to those obtained with the pure PBE functional. Then, taking αPBE with 25% HFE, we assign the vibrational modes and examine their contributions to the relaxation energy related to the nonlocal electron-vibration interactions. The results show that the largest contribution (about 90%) is due to electron interactions with low-frequency vibrational modes. The relaxation energy in anthracene-PMDA is found to be about five times smaller than the electronic coupling.

Crystal structures of four δ-keto esters and a Cambridge Structural Database analysis of cyano-halogen interactions.

The revived interest in halogen bonding as a tool in pharmaceutical cocrystals and drug design has indicated that cyano-halogen interactions could play an important role. The crystal structures of four closely related δ-keto esters, which differ only in the substitution at a single C atom (by H, OMe, Cl and Br), are compared, namely ethyl 2-cyano-5-oxo-5-phenyl-3-(piperidin-1-yl)pent-2-enoate, C19H22N2O3, (1), ethyl 2-cyano-5-(4-methoxyphenyl)-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C20H24N2O4, (2), ethyl 5-(4-chlorophenyl)-2-cyano-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C19H21ClN2O3, (3), and the previously published ethyl 5-(4-bromophenyl)-2-cyano-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C19H21BrN2O3, (4) [Maurya, Vasudev & Gupta (2013). RSC Adv. 3, 12955-12962]. The molecular conformations are very similar, while there are differences in the molecular assemblies. Intermolecular C-H...O hydrogen bonds are found to be the primary interactions in the crystal packing and are present in all four structures. The halogenated derivatives have additional aromatic-aromatic interactions and cyano-halogen interactions, further stabilizing the molecular packing. A database analysis of cyano-halogen interactions using the Cambridge Structural Database [CSD; Groom & Allen (2014). Angew. Chem. Int. Ed. 53, 662-671] revealed that about 13% of the organic molecular crystals containing both cyano and halogen groups have cyano-halogen interactions in their packing. Three geometric parameters for the C-X...N[triple-bond]C interaction (X= F, Cl, Br or I), viz. the N...X distance and the C-X...N and C-N...X angles, were analysed. The results indicate that all the short cyano-halogen contacts in the CSD can be classified as halogen bonds, which are directional noncovalent interactions.

A first-principles study of the vibrational properties of crystalline tetracene under pressure

We present a comprehensive study of the hydrostatic pressure dependence of the vibrational properties of tetracene using periodic density-functional theory (DFT) within the local density approximation (LDA). Despite the lack of van der Waals dispersion forces in LDA we find good agreement with experiment and are able to assess the suitability of this approach for simulating conjugated organic molecular crystals. Starting from the reported x-ray structure at ambient pressure and low temperature, optimized structures at ambient pressure and under 280 MPa hydrostatic pressure were obtained and the vibrational properties calculated by the linear response method. We report the complete phonon dispersion relation for tetracene crystal and the Raman and infrared spectra at the centre of the Brillouin zone. The intermolecular modes with low frequencies exhibit high sensitivity to pressure and we report mode-specific Grüneisen parameters as well as an overall Grüneisen parameter . Our results suggest that the experimentally reported improvement of the photocurrent under pressure may be ascribed to an increase in intermolecular interactions as also the dielectric tensor.

A new approach to calculate charge carrier transport mobility in organic molecular crystals from imaginary time path integral simulations.

We present a new non-perturbative method to calculate the charge carrier mobility using the imaginary time path integral approach, which is based on the Kubo formula for the conductivity, and a saddle point approximation to perform the analytic continuation. The new method is first tested using a benchmark calculation from the numerical exact hierarchical equations of motion method. Imaginary time path integral Monte Carlo simulations are then performed to explore the temperature dependence of charge carrier delocalization and mobility in organic molecular crystals (OMCs) within the Holstein and Holstein-Peierls models. The effects of nonlocal electron-phonon interaction on mobility in different charge transport regimes are also investigated.