Crystal Structure Prediction Calculations Research Articles

Suppression of Disorder in Benzamide and Thiobenzamide Crystals by Fluorine Substitution.

Disorder is a common feature of molecular crystals that complicates determination of structures and can potentially affect electric and mechanical properties. Suppression of disorder is observed in otherwise severely disordered benzamide and thiobenzamide crystals by substituting hydrogen with fluorine in the ortho-position of the phenyl ring. Fluorine occupancies of 20-30% are sufficient to suppress disorder without changing the packing motif. Crystal structure prediction calculations reveal a much denser lattice energy landscape for benzamide compared to 2-fluorobenzamide, suggesting that fluorine substitution makes disorder less likely.

Zwitterionic or Not? Fast and Reliable Structure Determination by Combining Crystal Structure Prediction and Solid-State NMR.

When it comes to crystal structure determination, computational approaches such as Crystal Structure Prediction (CSP) have gained more and more attention since they offer some insight on how atoms and molecules are packed in the solid state, starting from only very basic information without diffraction data. Furthermore, it is well known that the coupling of CSP with solid-state NMR (SSNMR) greatly enhances the performance and the accuracy of the predictive method, leading to the so-called CSP-NMR crystallography (CSP-NMRX). In this paper, we present the successful application of CSP-NMRX to determine the crystal structure of three structural isomers of pyridine dicarboxylic acid, namely quinolinic, dipicolinic and dinicotinic acids, which can be in a zwitterionic form, or not, in the solid state. In a first step, mono- and bidimensional SSNMR spectra, i.e., 1H Magic-Angle Spinning (MAS), 13C and 15N Cross Polarisation Magic-Angle Spinning (CPMAS), 1H Double Quantum (DQ) MAS, 1H-13C HETeronuclear CORrelation (HETCOR), were used to determine the correct molecular structure (i.e., zwitterionic or not) and the local molecular arrangement; at the end, the RMSEs between experimental and computed 1H and 13C chemical shifts allowed the selection of the correct predicted structure for each system. Interestingly, while quinolinic and dipicolinic acids are zwitterionic and non-zwitterionic, respectively, in the solid state, dinicotinic acid exhibits in its crystal structure a "zwitterionic-non-zwitterionic continuum state" in which the proton is shared between the carboxylic moiety and the pyridinic nitrogen. Very refined SSNMR experiments were carried out, i.e., 14N-1H Phase-Modulated (PM) pulse and Rotational-Echo Saturation-Pulse Double-Resonance (RESPDOR), to provide an accurate N-H distance value confirming the hybrid nature of the molecule. The CSP-NMRX method showed a remarkable match between the selected structures and the experimental ones. The correct molecular input provided by SSNMR reduced the number of CSP calculations to be performed, leading to different predicted structures, while RMSEs provided an independent parameter with respect to the computed energy for the selection of the best candidate.

An unexpectedly stable Y2B5 compound with the fractional stoichiometry under ambient pressure

Boron-rich yttrium borides are an exceptional group of compounds not only with excellent mechanical properties, but also with particular superconducting and thermoelectric properties. Although the Y–B compounds with integral components have been extensively investigated experimentally and theoretically, the yttrium borides with the fractional stoichiometries are rarely observed. Herein, utilizing a combination of the CALYPSO method for crystal structure prediction and first-principles calculations, we made an investigation on a broad range of stoichiometries of yttrium borides. An extraordinary stable Y2B5 compound possessing the fractional stoichiometry with the monoclinic P121/c1 phase is firstly uncovered. Structurally, the P121/c1-Y2B5 crystalline consists of the distorted B6 octahedrons and seven-member B rings. Remarkably, the B–B covalent network following the increment of the boron content in six concerned yttrium borides undergoes an increasing dimension, quasi one-dimensional chain → two-dimensional B ring → a combination of two-dimensional B ring and three-dimensional B6 octahedron → three-dimensional B24 cage. According to a microscopic hardness model, P121/c1–Y2B5 is considered as an incompressible and hard material with the hardness of 18.83 GPa. More importantly, Fm-3 m-YB12 can be classified into an ultra-incompressible material with the appreciable Vickers hardness of 33.16 GPa. The present consequences can provide important insights for understanding the complex crystal structures of boron-rich yttrium borides and stimulate further experimental synthesis of novel multifunctional materials with the fractional compositions.

Superconductivity of graphenelike hydrogen in H2He at high pressure

The structural diversity of hydrogen under high pressure is crucial for understanding its physical properties, especially for the superconductivity. Here, a combination of crystal structure prediction and first-principle calculations has predicted a metastable ${\mathrm{H}}_{2}\mathrm{He}$ at ultrahigh pressure of 800 GPa, where H atoms are arranged in graphenelike structure. ${\mathrm{H}}_{2}\mathrm{He}$ shows weak superconductivity with critical temperature of 4 K, which significantly increases to 155 and 201 K at electron doping of 0.6 and 1.2 $e$, respectively. Analysis suggests that the enhanced superconductivity is closely associated with the graphenelike H sublattice. The doped electrons almost transfer to H sublattice, inducing the increased H-derived density of states at the Fermi level, as well as their coupling with the phonon modes of graphenelike H layers. The current results could stimulate the experiment to search for more diverse hydrogen species at high pressure and provide a feasible way to design high-${T}_{\text{c}}$ superconductors as well.

Phase evolution for oxidizing bismuth selenide

The novel Bi2O2Se, produced by the oxidation of the layered Bi2Se3, has been considered as one of the most promising candidates for the next-generation electronics owing to its high carrier mobility and air-stability. In this work, by using crystal structure prediction and first-principles calculations, we report the phase transformations from the hexagonal Bi2Se3 to the monoclinic Bi2OSe2, and then to the tetragonal Bi2O2Se with the gradual oxidization. Owing to the difference in electronegativity between selenium (Se) and oxygen (O), the oxidation process is accompanied by an increase in bond ionicity. Our results shed light on the phenomena occurring in the interaction between the precursors Bi2Se3 and O2 and have a potential contribution to the application of optoelectronic devices. The intermediate Bi2OSe2 with calculated band gap of 1.01 eV, may be a candidate for photovoltaic application in future.

Exploring high pressure structural transformations, electronic properties and superconducting properties of MH2 (M = Nb, Ta)

The high-pressure structures and properties of MH2 (M = Nb, Ta) are explored through an ab initio evolutionary algorithm for crystal structure prediction and first-principles calculations. It is found that NbH2 undergoes a phase transition from a cubic Fm3¯m structure with regular NbH8 cubes to an orthorhombic Pnma structure with fascinating distorted NbH9 tetrakaidecahedrons at 48.8 GPa, while the phase transition pressure of TaH2 from a hexagonal P63mc phase with slightly distorted TaH7 decahedron to an orthorhombic Pnma phase with attractive distorted TaH9 tetrakaidecahedrons is about 90.0 GPa. Besides, the calculated electronic band structure and density of states demonstrate that all of these structures are metallic. The Poisson’s ratio, electron localization function, and Bader charge analysis suggest that these phases possess dominant ionic bonding character with the effective charges transferring from the metal atom to H. From our electron–phonon calculations, the calculated superconducting critical temperature Tc of the Pnma-NbH2 is 6.903 K at 50 GPa. Finally, via the quasi-harmonic approximation method, the phase diagrams at pressure up to 300 GPa and temperature up to 1000 K of MH2 (M = Nb, Ta) are established, where the transition pressure of Fm3¯m-NbH2 → Pnma-NbH2 and P63mc-TaH2 → Pnma-TaH2 were found to decrease with increasing temperature.

"Crystal memory" Affects the Properties of Peptide Hydrogels - The Case of the Cyclic Tyr-Tyr dipeptide.

In this work a relationship between the crystal form and morphology and rheological properties of peptide-based hydrogels is examined. We show, that under favorable circumstances a correlation between a starting solid material and a self-assembly processes in solution can exist, leading to different properties of a resulting soft matter. This observation, together with an in-depth analysis of the influence of stereochemistry of self-assembled (ll) and (dl) Tyr-Tyr cyclic dipeptides (cYY) on the observed relationship between gelation and crystallization allowed us to gain a deeper understanding of the peptide hydrogelation processes at a molecular level, using liquid state NMR, rheological studies and scanning electron microscopy. In the course of our studies, several crystal forms of (ll)-cYY has been discovered and described in details using single crystal X-ray diffraction, as well as advanced solid state NMR, X-ray diffraction of powders, thermal analysis, FTIR, circular dichroism and crystal structure prediction (CSP) calculations. Subsequently, we found that while (ll)-cYY easily assembles into hydrogels with different properties depending on the starting solid form, (dl)-cYY always precipitated as one crystal form in the tested conditions. Molecular-level justification for this observation is given.

Narrowing down the conformational space with solid-state NMR in crystal structure prediction of linezolid cocrystals

Many solids crystallize as microcrystalline powders, thus precluding the application of single crystal X-Ray diffraction in structural elucidation. In such cases, a joint use of high-resolution solid-state NMR and crystal structure prediction (CSP) calculations can be successful. However, for molecules showing significant conformational freedom, the CSP-NMR protocol can meet serious obstacles, including ambiguities in NMR signal assignment and too wide conformational search space to be covered by computational methods in reasonable time. Here, we demonstrate a possible way of avoiding these obstacles and making as much use of the two methods as possible in difficult circumstances. In a simple case, our experiments led to crystal structure elucidation of a cocrystal of linezolid (LIN), a wide-range antibiotic, with 2,3-dihydroxybenzoic acid, while a significantly more challenging case of a cocrystal of LIN with 2,4-dihydroxybenzoic acid led to the identification of the most probable conformations of LIN inside the crystal. Having four rotatable bonds, some of which can assume many discreet values, LIN molecule poses a challenge in establishing its conformation in a solid phase. In our work, a set of 27 conformations were used in CSP calculations to yield model crystal structures to be examined against experimental solid-state NMR data, leading to a reliable identification of the most probable molecular arrangements.

Orthocarbonates of Ca, Sr, and Ba—The Appearance of sp3-Hybridized Carbon at a Low Pressure of 5 GPa and Dynamic Stability at Ambient Pressure

Orthocarbonates are a newly discovered class of compounds that are stable at high pressures. The presence of sp3-hybridized carbon, having structural similarity to orthosilicates, and their potential participation in the global planetary carbon cycle have triggered intensive theoretical and experimental investigations into these compounds. Here, based on the density functional theory and crystal structure prediction calculations, we predict new stable crystal structures of the orthocarbonates Sr3CO5-Cmcm, Sr3CO5-I4/mcm, Ba2CO4-Pnma, and Ba3CO5-I4/mcm. Summarizing the obtained data, we show that orthocarbonates of alkaline-earth metals are isotypic to ambient-pressure orthosilicates with only rare exceptions. The lower-pressure stability limit for Ba-orthocarbonates is around 5 GPa. However, the stability limit increases with decreasing cation radius and reaches 13 GPa for Ca-orthocarbonates. Based on the calculations of Gibbs free energies with the quasi-harmonic approximation, the reaction 2M2CO4 = M3CO5 + MCO3 (M = Sr and Ba) is established. At 20 GPa, this reaction is realized at temperatures above 1080 K for Sr2CO4 and above 740 K for Ba2CO4, and the Clapeyron slope is positive in both cases. The obtained P–T diagrams for SrCO3 and BaCO3 show that equilibrium between the structures of aragonite and postaragonite is observed at 15–17 GPa for SrCO3 and 5–7 GPa for BaCO3. The transition pressure is almost independent of temperature. No other more favorable structures than postaragonite have been found for these compounds in the considered pressure range, up to 200 GPa. Thus, in contrast to CaCO3 and MgCO3, the transition from sp2 to sp3 hybridization is not realized for these compounds. Two of the found structures, Sr2CO4-Pnma and Sr3CO5-Cmcm, are dynamically stable at ambient pressure. This indicates the possibility of recovering the crystals from a high-pressure environment and conducting further laboratory investigation.

Structural, Vibrational, and Electronic Properties of 1D-TlInTe2 under High Pressure: A Combined Experimental and Theoretical Study

Analogous to 2D layered transition-metal dichalcogenides, the TlSe family of quasi-one dimensional chain materials with the Zintl-type structure exhibits novel phenomena under high pressure. In the present work, we have systematically investigated the high-pressure behavior of TlInTe2 using Raman spectroscopy, synchrotron X-ray diffraction (XRD), and transport measurements, in combination with first principles crystal structure prediction (CSP) based on evolutionary approach. We found that TlInTe2 undergoes a pressure-induced semiconductor-to-semimetal transition at 4 GPa, followed by a superconducting transition at 5.7 GPa (with Tc = 3.8 K). An unusual giant phonon mode (Ag) softening appears at ∼10-12 GPa as a result of the interaction of optical phonons with the conduction electrons. The high-pressure XRD and Raman spectroscopy studies reveal that there is no structural phase transitions observed up to the maximum pressure achieved (33.5 GPa), which is in agreement with our CSP calculations. In addition, our calculations predict two high-pressure phases above 35 GPa following the phase transition sequence as I4/mcm (B37) → Pbcm → Pm3̅m (B2). Electronic structure calculations suggest Lifshitz (L1 & L2-type) transitions near the superconducting transition pressure. Our findings on TlInTe2 open up a new avenue to study unexplored high-pressure novel phenomena in TlSe family induced by Lifshitz transition (electronic driven), giant phonon softening, and electron-phonon coupling.

No observation of lead hydride in the Pb–H system under pressure up to 140 GPa

The possibility of high pressure formation of lead hydrides has been investigated through the direct reaction of lead with hydrogen in a laser-heated diamond anvil cell. Synchrotron x-ray diffraction was used to detect any structural changes and volume expansion due to hydrogen absorption in the Pb metal. The compression curve of lead embedded in helium, measured under the same experimental conditions, was used as a reference. No volume expansion of the Pb lattice was measured, hence indicating no formation of an interstitial hydride. The observed structural changes match those of pure lead with the sequence of compact structures fcc, hcp, and bcc. The PbH6 and PbH4 compounds, found by various crystal structure prediction calculations to be stable below 140 GPa, were not observed. Lead seems very reluctant to absorbing hydrogen, which could be used for plating materials to resist hydrogen embrittlement under extreme conditions.

Ammonium fluoride's analogy to ice: Possibilities and limitations.

Ammonium fluoride, NH4F, is often seen as an analog to ice, with several of its solid phases closely resembling known ice phases. While its ionic and hydrogen-ordered nature puts topological constraints on the ice-like network structures it can form, it is not clear what consequences these constraints have for NH4F compound formation and evolution. Here, we explore computationally the reach and eventual limits of the ice analogy for ammonium fluoride. By combining data mining of known and hypothetical ice networks with crystal structure prediction and density functional calculations, we explore the high-pressure phase diagram of NH4F and host-guest compounds of its hydrides. Pure NH4F departs from ice-like behavior above 80GPa with the emergence of close-packed ionic structures. The predicted stability of NH4F hydrides shows that NH4F can act as a host to small guest species, albeit in a topologically severely constraint configuration space. Finally, we explore the binary NH3-HF chemical space, where we find candidate structures for several unsolved polyfluoride phases; among them is the chemical analog to H2O2 dihydrate.

Prediction of the Relative Free Energies of Drug Polymorphs above Zero Kelvin

Crystal structure prediction (CSP) calculations can reduce risk and improve efficiency during drug development. Traditionally CSP calculations use lattice energies computed through density function...

Structural, mechanical and electronic properties and hardness of ionic vanadium dihydrides under pressure from first-principles computations

Based on a combination of the CALYPSO method for crystal structure prediction and first-principles calculations, we explore the crystal structures of VH2 under the pressure range of 0−300 GPa. The cubic Fm-3m phase with regular VH8 cubes is predicted to transform into orthorhombic Pnma structure with fascinating distorted VH9 tetrakaidecahedrons at 47.36 GPa. Both the Fm-3m phase at 0 GPa and the Pnma phase at 100 GPa are mechanically and dynamically stable, as verified with the calculations of elastic constants and phonon dispersions, respectively. Moreover, the calculated electronic band structure and density of states indicate both stable phases are metallic. Remarkably, the analyses of the Poisson’s ratio, electron localization function (ELF) and Bader charge substantiate that both stable phases are ionic crystals on account of effective charges transferring from V atom to H. On the basis of the microscopic hardness model, the Fm-3m and Pnma crystals of VH2 are potentially incompressible and hard materials with the hardness values of 17.83 and 17.68 GPa, respectively.

Crystal structures of two furazidin polymorphs revealed by a joint effort of crystal structure prediction and NMR crystallography.

This work presents the crystal structure determination of two elusive polymorphs of furazidin, an antibacterial agent, employing a combination of crystal structure prediction (CSP) calculations and an NMR crystallography approach. Two previously uncharacterized neat crystal forms, one of which has two symmetry-independent molecules (form I), whereas the other one is a Z' = 1 polymorph (form II), crystallize in P21/c and P1 space groups, respectively, and both are built by different conformers, displaying different intermolecular interactions. It is demonstrated that the usage of either CSP or NMR crystallography alone is insufficient to successfully elucidate the above-mentioned crystal structures, especially in the case of the Z' = 2 polymorph. In addition, cases of serendipitous agreement in terms of 1H or 13C NMR data obtained for the CSP-generated crystal structures different from the ones observed in the laboratory (false-positive matches) are analyzed and described. While for the majority of analyzed crystal structures the obtained agreement with the NMR experiment is indicative of some structural features in common with the experimental structure, the mentioned serendipity observed in exceptional cases points to the necessity of caution when using an NMR crystallography approach in crystal structure determination.

Efficient Screening for Ternary Molecular Ionic Cocrystals Using a Complementary Mechanosynthesis and Computational Structure Prediction Approach.

The discovery of molecular ionic cocrystals (ICCs) of active pharmaceutical ingredients (APIs) widens the opportunities for optimizing the physicochemical properties of APIs whilst facilitating the delivery of multiple therapeutic agents. However, ICCs are often observed serendipitously in crystallization screens and the factors dictating their crystallization are poorly understood. We demonstrate here that mechanochemical ball milling is a versatile technique for the reproducible synthesis of ternary molecular ICCs in less than 30 min of grinding with or without solvent. Computational crystal structure prediction (CSP) calculations have been performed on ternary molecular ICCs for the first time and the observed crystal structures of all the ICCs were correctly predicted. Periodic dispersion‐corrected DFT calculations revealed that all the ICCs are thermodynamically stable (mean stabilization energy=−2 kJ mol−1) relative to the crystallization of a physical mixture of the binary salt and acid. The results suggest that a combined mechanosynthesis and CSP approach could be used to target the synthesis of higher‐order molecular ICCs with functional properties.

High dielectric ternary oxides from crystal structure prediction and high-throughput screening

The development of new high dielectric materials is essential for advancement in modern electronics. Oxides are generally regarded as the most promising class of high dielectric materials for industrial applications as they possess both high dielectric constants and large band gaps. Most previous researches on high dielectrics were limited to already known materials. In this study, we conducted an extensive search for high dielectrics over a set of ternary oxides by combining crystal structure prediction and density functional perturbation theory calculations. From this search, we adopted multiple stage screening to identify 441 new low-energy high dielectric materials. Among these materials, 33 were identified as potential high dielectrics favorable for modern device applications. Our research has opened an avenue to explore novel high dielectric materials by combining crystal structure prediction and high throughput screening.

Crystal structure determination of an elusive methanol solvate – hydrate of catechin using crystal structure prediction and NMR crystallography

A useful short-cut was developed to limit the number of molecular conformations that need to be regarded in crystal structure prediction calculations, which led to the crystal structure determination of new methanol solvate – hydrate of catechin.

Pressure induced superconductive 10-fold coordinated TaS2: a first-principles study

By crystal structure prediction and first-principles calculations, we researched the structure transformation and electronic states for a typical transition metal dichalcogenides (TMDs): 1T-TaS2 under hydrostatic pressure. The layered 1T-TaS2 will first transform to an 8-fold monoclinic C2/m phase and then to a 10-fold coordinated tetragonal I4/mmm phase which has 3D covalent bond network linked in space. Our calculations suggest that the lone pair electrons of S in 1T-TaS2, which keep the stablity of the layered structure, will be activated by pressure and participate the chemical bonding with Ta, to form the high-pressure C2/m and I4/mmm phases. Additionally, collective electronic states of superconductivity also retains in the I4/mmm phase and the critical transition temperature of superconductivity is 9 K at 100 GPa.

The role of CALYPSO in the discovery of high-Tc hydrogen-rich superconductors**Project supported by the National Natural Science Foundation of China (Grant Nos. 11804128 and 11722433), the Qing Lan Project of Jiangsu Province, China, and the Six Talent Peaks Project of Jiangsu Province, China.

Hydrogen-rich compounds are promising candidates for high-Tc or even room-temperature superconductors. The search for high-Tc hydrides poses a major experimental challenge because there are many known hydrides and even more unknown hydrides with unusual stoichiometries under high pressure. The combination of crystal structure prediction and first-principles calculations has played an important role in the search for high-Tc hydrides, especially in guiding experimental synthesis. Crystal structure AnaLYsis by Particle Swarm Optimization (CALYPSO) is one of the most efficient methods for predicting stable or metastable structures from the chemical composition alone. This review summarizes the superconducting hydrides predicted using CALYPSO. We focus on two breakthroughs toward room-temperature superconductors initiated by CALYPSO: the prediction of high-Tc superconductivity in compressed hydrogen sulfide and lanthanum hydrides, both of which have been confirmed experimentally and have set new record Tc values. We also address the challenges and outlook in this field.