Review of Applications of Density Functional Theory (DFT) Quantum Mechanical Calculations to Study the High-Pressure Polymorphs of Organic Crystalline Materials

Since its inception, chemistry has been predominated by the use of temperature to generate or change materials, but applications of pressure of more than a few tens of atmospheres for such purposes have been rarely observed. However, pressure is a very effective thermodynamic variable that is increasingly used to generate new materials or alter the properties of existing ones. As computational approaches designed to simulate the solid state are normally tuned using structural data at ambient pressure, applying them to high-pressure issues is a highly challenging test of their validity from a computational standpoint. However, the use of quantum chemical calculations, typically at the level of density functional theory (DFT), has repeatedly been shown to be a great tool that can be used to both predict properties that can be later confirmed by experimenters and to explain, at the molecular level, the observations of high-pressure experiments. This article's main goal is to compile, analyze, and synthesize the findings of works addressing the use of DFT in the context of molecular crystals subjected to high-pressure conditions in order to give a general overview of the possibilities offered by these state-of-the-art calculations.

A first-order phase transition in Blatter's radical at high pressure

The crystal structure of Blatter's radical (1,3-diphenyl-1,4-dihydrobenzo[e][1,2,4]triazin-4-yl) has been investigated between ambient pressure and 6.07 GPa. The sample remains in a compressed form of the ambient-pressure phase up to 5.34 GPa, the largest direction of strain being parallel to the direction of π-stacking interactions. The bulk modulus is 7.4 (6) GPa, with a pressure derivative equal to 9.33 (11). As pressure increases, the phenyl groups attached to the N1 and C3 positions of the triazinyl moieties of neighbouring pairs of molecules approach each other, causing the former to begin to rotate between 3.42 to 5.34 GPa. The onset of this phenyl rotation may be interpreted as a second-order phase transition which introduces a new mode for accommodating pressure. It is premonitory to a first-order isosymmetric phase transition which occurs on increasing pressure from 5.34 to 5.54 GPa. Although the phase transition is driven by volume minimization, rather than relief of unfavourable contacts, it is accompanied by a sharp jump in the orientation of the rotation angle of the phenyl group. DFT calculations suggest that the adoption of a more planar conformation by the triazinyl moiety at the phase transition can be attributed to relief of intramolecular H...H contacts at the transition. Although no dimerization of the radicals occurs, the π-stacking interactions are compressed by 0.341 (3) Å between ambient pressure and 6.07 GPa.

Use of a miniature diamond-anvil cell in a joint X-ray and neutron high-pressure study on copper sulfate pentahydrate

Single-crystal X-ray and neutron diffraction data are usually collected using separate samples. This is a disadvantage when the sample is studied at high pressure because it is very difficult to achieve exactly the same pressure in two separate experiments, especially if the neutron data are collected using Laue methods where precise absolute values of the unit-cell dimensions cannot be measured to check how close the pressures are. In this study, diffraction data have been collected under the same conditions on the same sample of copper(II) sulfate pentahydrate, using a conventional laboratory diffractometer and source for the X-ray measurements and the Koala single-crystal Laue diffractometer at the ANSTO facility for the neutron measurements. The sample, of dimensions 0.40 × 0.22 × 0.20 mm3 and held at a pressure of 0.71 GPa, was contained in a miniature Merrill-Bassett diamond-anvil cell. The highly penetrating diffracted neutron beams passing through the metal body of the miniature cell as well as through the diamonds yielded data suitable for structure refinement, and compensated for the low completeness of the X-ray measurements, which was only 24% on account of the triclinic symmetry of the sample and the shading of reciprocal space by the cell. The two data-sets were combined in a single 'XN' structure refinement in which all atoms, including H atoms, were refined with anisotropic displacement parameters. The precision of the structural parameters was improved by a factor of up to 50% in the XN refinement compared with refinements using the X-ray or neutron data separately.

Low Temperature and High-Pressure Study of Bending L-Leucinium Hydrogen Maleate Crystals

The polymorphism of molecular crystals is a well-known phenomenon, resulting in modifications of physicochemical properties of solid phases. Low temperatures and high pressures are widely used to find phase transitions and quench new solid forms. In this study, L-Leucinium hydrogen maleate (LLHM), the first molecular crystal that preserves its anomalous plasticity at cryogenic temperatures, is studied at extreme conditions using Raman spectroscopy and optical microscopy. LLHM was cooled down to 11 K without any phase transition, while high pressure impact leads to perceptible changes in crystal structure in the interval of 0.0–1.35 GPa using pentane-isopentane media. Surprisingly, pressure transmitting media (PTM) play a significant role in the behavior of the LLHM system at extreme conditions—we did not find any phase change up to 3.05 GPa using paraffin as PTM. A phase transition of LLHM to amorphous form or solid–solid phase transition(s) that results in crystal fracture is reported at high pressures. LLHM stability at low temperatures suggests an alluring idea to prove LLHM preserves plasticity below 77 K.

Periodic DFT Calculations-Review of Applications in the Pharmaceutical Sciences

In the introduction to this review the complex chemistry of solid-state pharmaceutical compounds is summarized. It is also explained why the density functional theory (DFT) periodic calculations became recently so popular in studying the solid APIs (active pharmaceutical ingredients). Further, the most popular programs enabling DFT periodic calculations are presented and compared. Subsequently, on the large number of examples, the applications of such calculations in pharmaceutical sciences are discussed. The mentioned topics include, among others, validation of the experimentally obtained crystal structures and crystal structure prediction, insight into crystallization and solvation processes, development of new polymorph synthesis ways, and formulation techniques as well as application of the periodic DFT calculations in the drug analysis.

A Short Review of Current Computational Concepts for High-Pressure Phase Transition Studies in Molecular Crystals

High-pressure chemistry of organic compounds is a hot topic of modern chemistry. In this work, basic computational concepts for high-pressure phase transition studies in molecular crystals are described, showing their advantages and disadvantages. The interconnection of experimental and computational methods is highlighted, showing the importance of energy calculations in this field. Based on our deep understanding of methods’ limitations, we suggested the most convenient scheme for the computational study of high-pressure crystal structure changes. Finally, challenges and possible ways for progress in high-pressure phase transitions research of organic compounds are briefly discussed.

Intermolecular Interactions in Ionic Crystals of Nucleobase Chlorides—Combining Topological Analysis of Electron Densities with Energies of Electrostatic Interactions

Understanding intermolecular interactions in crystals of molecular ions continues to be difficult. On the one hand, the analysis of interactions from the point of view of formal charges of molecules, similarly as it is commonly done for inorganic ionic crystals, should be performed. On the other hand, when various functional groups are present in the crystal, it becomes natural to look at the interactions from the point of view of hydrogen bonding, π…π stacking and many other kinds of non-covalent atom–atom bonding. Often, these two approaches seem to lead to conflicting conclusions. On the basis of experimental charge densities of cytosinium chloride, adeninium chloride hemihydrate, and guanine dichloride crystals, with the help of theoretical simulations, we have deeply analysed intermolecular interactions among protonated nucleobases, chloride anions and water molecules. Here, in the second paper of the series of the two (Kumar et al., 2018, IUCrJ 5, 449–469), we focus on applying the above two approaches to the large set of dimers identified in analysed crystals. To understand electrostatic interactions, we analysed electrostatic interaction energies (Ees) computed directly from molecular charge densities and contrasted them with energies computed only from net molecular charges, or from a sum of electric multipolar moments, to find the charge penetration contribution to Ees. To characterize non-covalent interactions we performed topological analyses of crystal electron densities and estimated their interaction energies (EEML) from properties of intermolecular bond critical points. We show that the overall crystal architecture of the studied compounds is governed by the tight packing principle and strong electrostatic attractions and repulsions between ions. Many ions are oriented to each other in a way to strengthen attractive electrostatic interactions or weaken strong repulsion, but not all of them. Numerous bond critical points and bond paths were found between ions, including nucleobase cations despite their overall repulsive interactions. It is clear there is no correlation between EEML and Ees. However, strong relation between EEML and the charge penetration component of Ees is observed. The relation holds regardless of interaction types or whether or not interacting molecules bear the same or opposite charges. Thus, a charge density-based approach for computing intermolecular interaction energies and the atom–atom approach to analyse non-covalent interactions do complement each other, even in ionic systems.

The Effect of Pressure on Halogen Bonding in 4-Iodobenzonitrile

The crystal structure of 4-iodobenzonitrile, which is monoclinic (space group I2/a) under ambient conditions, contains chains of molecules linked through C≡N···I halogen-bonds. The chains interact through CH···I, CH···N and π-stacking contacts. The crystal structure remains in the same phase up to 5.0 GPa, the b axis compressing by 3.3%, and the a and c axes by 12.3 and 10.9 %. Since the chains are exactly aligned with the crystallographic b axis these data characterise the compressibility of the I···N interaction relative to the inter-chain interactions, and indicate that the halogen bond is the most robust intermolecular interaction in the structure, shortening from 3.168(4) at ambient pressure to 2.840(1) Å at 5.0 GPa. The π∙∙∙π contacts are most sensitive to pressure, and in one case the perpendicular stacking distance shortens from 3.6420(8) to 3.139(4) Å. Packing energy calculations (PIXEL) indicate that the π∙∙∙π interactions have been distorted into a destabilising region of their potentials at 5.0 GPa. The structure undergoes a transition to a triclinic ( P 1 ¯ ) phase at 5.5 GPa. Over the course of the transition, the initially colourless and transparent crystal darkens on account of formation of microscopic cracks. The resistance drops by 10% and the optical transmittance drops by almost two orders of magnitude. The I···N bond increases in length to 2.928(10) Å and become less linear [<C-I∙∙∙N = 166.2(5)°]; the energy stabilises by 2.5 kJ mol^-1 and the mixed C-I/I..N stretching frequency observed by Raman spectroscopy increases from 249 to 252 cm^-1. The driving force of the transition is shown to be relief of strain built-up in the π∙∙∙π interactions rather than minimisation of the molar volume. The triclinic phase persists up to 8.1 GPa.

The structural, electronic and optical properties of γ-glycine under pressure: a first principles study

The crystallized amino acid γ-glycine is a large band gap insulator that shows promise in the fields of photonics and non-linear optics.

High-pressure polymorphism in l-threonine between ambient pressure and 22 GPa

The amino acid l-threonine undergoes three phase transitions between ambient pressure and 22.3 GPa which modify both hydrogen bonding and the molecular conformation.

Efficient Synthesis and in Silico Studies of the Benzimidazole Hybrid Scaffold with the Quinolinyloxadiazole Skeleton with Potential α-Glucosidase Inhibitory, Anticoagulant, and Antiplatelet Activities for Type-II Diabetes Mellitus Management and Treating Thrombotic Disorders

The current study evaluates antidiabetic, anticoagulant, and antiplatelet activity of novel benzimidazole-containing quinolinyl oxadiazoles. These derivatives are synthesized and characterized using spectroscopy (FT-IR, ¹H NMR, and mass spectroscopy) and single-crystal X-ray diffraction methods. The inhibitory effects of these compounds were evaluated by the α-glucosidase inhibitory assay and shows the activity in the range of IC₅₀ = 0.66 ± 0.05 to 3.79 ± 0.46 μg/mL. In addition, molecular docking studies revealed that benzimidazole-containing quinolinyl oxadiazoles can correctly dock into the target receptor protein of the human intestinal α-glucosidase, while their bioavailability/drug-likeness was predicted to be acceptable but requires further optimization. On the other hand, compound 8a and 8d showed anticoagulant activity as they enhanced the clotting time from control 180-410 and 180-390 s, respectively, in platelet rich plasma and 230-460 and 230-545 s in platelet poor plasma. Furthermore, only 8a showed antiplatelet activity by inhibiting epinephrine-induced platelet aggregation, and the observed aggregation inhibition was found to be 93.4%. Compounds 8a-f show nontoxic properties because of the non-hydrolyzing properties in the RBC cells. In addition, 8a and 8d show anti-edema and anti-hemorrhagic properties in the experimental mice. These findings reveal that benzimidazole-containing quinolinyl oxadiazoles act as α-glucosidase inhibitors to develop novel therapeutics for treating type-II diabetes mellitus and can act as lead molecules in drug discovery as potential antidiabetic and antithrombotic agents.

Behavior of intermolecular interactions in α-glycine under high pressure

Pressure-response on the crystal structure of deuterated α-glycine was investigated at room temperature, using powder and single-crystal X-ray diffraction, and powder neutron diffraction measurements under high pressure. No phase change was observed up to 8.7 GPa, although anisotropy of the lattice compressibility was found. No significant changes in the compressibility and the intramolecular distance between non-deuterated α-glycine and deuterated α-glycine were observed. Neutron diffraction measurements indicated the distance of the intermolecular D⋯O bond along with the c-axis increased with compression up to 6.4 GPa. The distance of another D⋯O bond along with the a-axis decreased with increasing pressure and became the shortest intermolecular hydrogen bond above 3 GPa. In contrast, the lengths of the bifurcated N-D⋯O and C-D⋯O hydrogen bonds, which are formed between the layers of the α-glycine molecules along the b-axis, decreased significantly with increasing pressure. The decrease of the intermolecular distances resulted in the largest compressibility of the b-axis, compared to the other two axes. The Hirshfeld analysis suggested that the reduction of the void region size, rather than shrinkage of the strong N-D⋯O hydrogen bonds, occurred with compression.

Pressure-driven phase transition mechanisms revealed by quantum chemistry: l-serine polymorphs

The present study delivers a computational approach for the understanding of the mechanism of phase transitions between polymorphs of small organic molecules.

Advanced Input Files & Parametric Quantitative Analysis Using Topas

Topas is a powerful and flexible software suite for the analysis of powder diffraction (and other) data. In this paper we describe methods to interact with the software in efficient and customisable ways. We also provide brief details of a wiki site for sharing ideas and methods for this software (topas.dur.ac.uk). Finally we give an overview of the potential advantages of parametric refinement methods within Topas and exemplify them with a quantitative analysis study of the phase transitions in WO3.

Parametric Rietveld refinement for the evaluation of powder diffraction patterns collected as a function of pressure

Under the assumption that the structural parameters of a crystalline phase change `smoothly' with increasing pressure, the evolution of the parameters can be parameterized as a function of pressure using continuous monotonic functions. Four different approaches to determine the structural evolution of As2O5with increasing pressure from a set of powder diffraction patterns collected over the pressure range from 2.5 to 19.5 GPa have been investigated. Approach (A) was the common sequential refinement of atomic coordinates with restraints on the geometry and was compared with three parameterization approaches. Approach (B) used direct parameterization by low-order polynomials of each crystallographically distinct atomic coordinate, (C) described the atoms of the asymmetric unit as a rigid body and allowed the internal degrees of freedom of the rigid body to vary with the change in pressure using rigid unit modes, and (D) described the crystal structure as a distortion of the higher-symmetry structure of As2O5(which is here also a high-temperature phase) by using symmetry-adapted distortion modes. Approach (D) offers the possibility to directly introduce an order parameter into Rietveld refinement through an empirical power law derived from Landau theory and thus to obtain the value of the critical exponent. In contrast, the rigid-body approach did not fit the data as well. All parameterizations greatly reduce the number of required parameters.

In situ XAS and XRPD parametric rietveld refinement to understand dealumination of Y zeolite catalyst

Dealumination of NH(4)-Y zeolite during steaming to 873 K was investigated with in situ, time-dependent, synchrotron radiation XRPD and in situ Al K-edge XAS. Water desorption is complete at 450 K, and ammonium decomposition occurs between 500 and 550 K. Only a small fraction of Al(3+) species (5%) leaves the framework during heating from 710 to 873 K; these species occupy site I' inside the sodalite cage. This fraction increases up to 8% in the first 50 min at 873 K and remains constant for the following 70 min isotherm and during the high-temperature part of the cooling experiment. During cooling from 500 to 450 K, the electron density at site I' increases suddenly, corresponding to a fraction of 30-35% of the total Al, confirmed by ex situ (27)Al MAS solid-state NMR. At that temperature, in situ Al K-edge XAS indicates a change in Al coordination of a large fraction of Al, and thermogravimetric (TG) data show the first water molecules start to repopulate the pores. Such molecules drive the dislodgment of most of the Al from the zeolitic framework. Our data indicate that considerable structural collapse caused by steaming does not occur at the highest temperature; however, defects form, which lead to significant migration of framework Al(3+) to extraframework positions, which occurs only as water is able to enter the pores again, that is, at much lower temperature. Contrary to general opinion, these results demonstrate that zeolite dealumination is not primarily a high-temperature process. The standard Rietveld refinement approach failed to identify extraframework Al species. These new results were obtained by adopting the innovative parametric refinement [J. Appl. Crystallogr. 2007, 40, 87]. Treating all of the XRPD patterns collected during the evolution of temperature as one unique data set significantly reduces the overall number of optimized variables and, thus, their relative correlation, and finally results in a more reliable estimate of the optimized parameters. Our results contribute to a better understanding of the phenomena involved on the atomic scale in the preparation of ultrastable Y zeolites (USY). USY are employed in fluid catalytic cracking (FCC), which is the most important conversion process in petroleum refineries to convert the high-boiling hydrocarbon fractions of petroleum crude oils to more valuable products like gasoline and olefinic gases.