Isomorphism: 'molecular similarity to crystal structure similarity' in multicomponent forms of analgesic drugs tolfenamic and mefenamic acid

Quantifying the non-isomorphism of global urban road networks using GNNs and graph kernels

A novel concept of quantifying graph non-isomorphism is introduced to measure structural differences between graphs, and thus overcoming the strict limitations of traditional graph isomorphism tests. This paper trains Graph Neural Networks (GNNs) and graph kernels to classify urban road networks and proposes using graph classification accuracy as a metric to quantify graph non-isomorphism. Experimental results demonstrate that Edge Convolutional Neural Network (EdgeCNN) not only leverages node attributes effectively but also fully utilizes edge features, achieving an 85% classification accuracy, which surpasses that of the Weisfeiler-Lehman (WL) kernel algorithm (80%). This finding challenges the claim that "GNNs are at most as powerful as the WL test in distinguishing graph structures." Furthermore, the paper explores the non-isomorphism of 10,361 road networks from 30 cities worldwide, providing valuable insights for future urban development.

Integrated study of Quercetin as a potent SARS-CoV-2 RdRp inhibitor: Binding interactions, MD simulations, and In vitro assays

To find an effective inhibitor for SARS-CoV-2, Quercetin's chemical structure was compared to nine ligands associated with nine key SARS-CoV-2 proteins. It was found that Quercetin closely resembles Remdesivir, the co-crystallized ligand of RNA-dependent RNA polymerase (RdRp). This similarity was confirmed through flexible alignment experiments and molecular docking studies, which showed that both Quercetin and Remdesivir bind similarly to the active site of RdRp. Molecular dynamics (MD) simulations over a 200 ns trajectory, analyzing various factors like RMSD, RG, RMSF, SASA, and hydrogen bonding were conducted. These simulations gave detailed insights into the binding interactions of Quercetin with RdRp compared to Remdesivir. Further analyses, including MM-GBSA, Protein-Ligand Interaction Fingerprints (ProLIF) and Profile PLIP studies, confirmed the stability of Quercetin's binding. Principal component analysis of trajectories (PCAT) provided insights into the coordinated movements within the systems studied. In vitro assays showed that Quercetin is highly effective in inhibiting RdRp, with an IC50 of 122.1 ±5.46 nM, which is better than Remdesivir's IC50 of 21.62 ±2.81 μM. Moreover, Quercetin showed greater efficacy against SARS-CoV-2 In vitro, with an IC50 of 1.149 μg/ml compared to Remdesivir's 9.54 μg/ml. The selectivity index (SI) values highlighted Quercetin's safety margin (SI: 791) over Remdesivir (SI: 6). In conclusion, our comprehensive study suggests that Quercetin is a promising candidate for further research as an inhibitor of SARS-CoV-2 RdRp, providing valuable insights for developing an effective anti-COVID-19 treatment.

Repurposing FDA-approved drugs for COVID-19: targeting the main protease through multi-phase in silico approach

BACKGROUND

The COVID-19 pandemic has created an urgent need for effective therapeutic agents. The SARS-CoV-2 Main Protease (Mpro) plays a crucial role in viral replication and immune evasion, making it a key target for drug development. While several studies have explored Mpro inhibition, identifying FDA-approved drugs with potential efficacy remains a critical research focus.

PURPOSE

This study aims to identify FDA-approved drugs that could inhibit SARS-CoV-2 Mpro. Using computational screening, we seek compounds that share structural similarities with a known co-crystallized ligand (PRD_002214) and exhibit strong binding affinity to the enzyme, providing viable candidates for COVID-19 treatment.

RESEARCH DESIGN

A systematic in silico approach was used, screening 3009 FDA-approved drugs. The initial screening focused on structural similarity to PRD_002214 (PDB ID: 6LU7), followed by molecular docking studies to predict binding affinity. Promising compounds were further analyzed through molecular dynamics (MD) simulations to evaluate their stability and interactions with Mpro over 100 ns.

STUDY SAMPLE

Of the 3009 FDA-approved drugs screened, 74 were selected for initial evaluation. After refinement, 28 compounds underwent docking analysis, with eight showing strong binding potential to Mpro.

ANALYSIS

Molecular docking assessed the binding affinity and interaction of the selected compounds with Mpro. MD simulations were conducted on the top compound, Atazanavir, to study its dynamic interactions. MM-GBSA, PLIP, and PCAT analyses were used to validate binding affinity and interactions.

RESULTS

Eight compounds, including Carfilzomib, Atazanavir, Darunavir, and others, exhibited promising binding affinities. Among them, Atazanavir showed the highest binding strength and was selected for further MD simulation studies. These simulations revealed that Atazanavir forms stable interactions with Mpro, demonstrating favorable binding and dynamic stability. The binding affinity was further confirmed through MM-GBSA, PLIP, and PCAT analyses, supporting Atazanavir's potential as an effective Mpro inhibitor.

CONCLUSIONS

In silico results suggest that Atazanavir is a promising candidate for targeting SARS-CoV-2 Mpro, with strong binding affinity and dynamic stability. These findings support its potential as a lead compound for further preclinical and clinical testing, though in vitro and in vivo validation are needed to confirm its therapeutic efficacy against COVID-19.

Supramolecular motifs formed by CH3/Cl-substituted arene groups: evidence for structural differences in thiophosphoramides and similarities in their complexes

Differences/similarities of supramolecular motifs are discussed in two new thiophosphoramide structures and their Ni molecular complexes: (C2H5O)2P(S)(NHC(S)NHCH2C6H4X) and [{(C2H5O)2P(S)(NC(S)NHCH2C6H4X)}2Ni] (X = Cl/CH3I/II and III/IV). The structures have equal numbers of donor/acceptor sites contributing to classical hydrogen bonds (PS/CS and 2 × NH in ligands and 2 × PS and 2 × NH in the complexes). However, these donor and acceptor sites contribute to inter/intramolecular hydrogen bonding in ligands and intramolecular hydrogen bonding in complexes. In the supramolecular assemblies of the ligands, the classic hydrogen bonds (N-H⋯S[double bond, length as m-dash]C) are restricted in dimer synthons, and the weaker interactions (formed by Cl/CH3 substituents) compete against each other. In the complexes, despite the lack of classic intermolecular hydrogen bond, numerous weak interactions, e.g., C-H⋯Y (Y = S, O, Ni, N, and π), contribute to the molecular assemblies, which do not include the participation of Cl/CH3. Thus, different packing features of ligands, but similar in complexes are observed. Each ligand and the associated complex show nearly equal supramolecular motifs in the slice of the substituted benzyl groups, related to the formation of C-H⋯Cl/π⋯π for the 4-Cl-C6H4CH2 groups in I/III and C-H⋯π for the 4-CH3-C6H4CH2 groups in II/IV. The repeatabilities of the motifs made by 4-Cl-C6H4CH2/4-CH3-C6H4CH2 were checked by surveying 142/844 structures with 178/1482 segments in the CSD, which show that 17% and 12% of the structures exhibited similarities with the title structures. The methods X-ray crystallography, 2D fingerprint plots, electrostatic potential surfaces, QTAIM, and energy framework calculations were applied to present the discussion.

Tale of Two Polymorphs: Investigating the Structural Differences and Dynamic Relationship between Nirmatrelvir Solid Forms (Paxlovid)

Two anhydrous polymorphs of the novel antiviral medicine nirmatrelvir were discovered during the development of Paxlovid, Pfizer's oral Covid-19 treatment. A comprehensive experimental and computational approach was necessary to distinguish the two closely related polymorphs, herein identified as Forms 1 and 4. This approach paired experimental methods, including powder X-ray diffraction and single-crystal X-ray diffraction, solid-state experimental methods, thermal analysis, solid-state nuclear magnetic resonance and Raman spectroscopy with computational investigations comprising crystal structure prediction, Gibbs free energy calculations, and molecular dynamics simulations of the polymorphic transition. Forms 1 and 4 were ultimately determined to be enantiotropically related polymorphs with Form 1 being the stable form above the transition temperature of ∼17 °C and designated as the nominated form for drug development. The work described in this paper shows the importance of using highly specialized orthogonal approaches to elucidate the subtle differences in structure and properties of similar solid-state forms. This synergistic approach allowed for unprecedented speed in bringing Paxlovid to patients in record time amidst the pandemic.

Solvatomorphism in a series of copper(II) complexes with the 5-phenylimidazole/perchlorate system as ligands

In the course of an investigation of the supramolecular behaviour of copper(II) complexes with the 5-phenylimidazole/perchlorate ligand system (`blend') remarkable solvatomorphism has been observed. By employing a variety of crystallization solvents (polar protic, polar/non-polar aprotic), a series of 12 crystalline solvatomorphs with the general formula [Cu(ClO4)2(LH)4]·x(solvent) have been obtained [LH = 5-phenylimidazole, x(solvent) = 3.3(H2O) (1), 2(methanol) (2), 2(ethanol) (3), 2(1-propanol) (4), 2(2-propanol) (5), 2(2-butanol) (6), 2(dimethylformamide) (7), 2(acetone) (8), 2(tetrahydrofurane) (9), 2(1,4-dioxane) (10), 2(ethyl acetate) (11) and 1(diethyl ether) (12)]. The structures have been solved using single-crystal X-ray diffraction and the complexes were characterized by thermal analysis and infrared spectroscopy. The solvatomorphs are isostructural (triclinic, P1), with the exception of compound 9 (monoclinic, P21/n). The supramolecular structures and the role of the various solvents is discussed. All potential hydrogen-bond functionalities, both of the [Cu(ClO4)2(LH)4] units and of the solvents, are utilized in the course of the crystallization process. The supramolecular assembly in all structures is directed by strong recurring Nimidazole-H...Operchlorate motifs leading to robust scaffolds composed of the [Cu(ClO4)2(LH)4] host complexes. The solvents are located in channels and, with the exception of the disordered waters in 1 and the diethyl ether in 12, participate in hydrogen-bonding formation with the [Cu(ClO4)2(LH)4] complexes, serving as both hydrogen-bond acceptors and donors (for the polar protic solvents in 2-6), or solely as hydrogen-bond acceptors (for the polar/non-polar aprotic solvents in 7-11), linking the complexes and contributing to the stability of the crystalline compounds.

Crystal property engineering using molecular-supramolecular equivalence: mechanical property alteration in hydrogen bonded systems

Most crystal engineering strategies exercised until now mainly rely on the alteration of weak non-covalent interactions to design structures and thus properties. Examples of mechanical property alteration for a given structure type are rare with only a few halogen bonded cases. The modular nature of halogen bonds with interaction strength tunability makes the task straightforward to obtain property differentiated crystals. However, the design of such crystals using hydrogen bond interactions has proven to be non-trivial, because of its relatively higher difference in bonding energies, and more importantly, disparate geometries of the functional groups. In the present crystal property engineering exercise, with the support of CSD analysis, we replaced a supramolecular precursor that leads to plastically bendable crystals, with a molecular equivalent, and obtained an equivalent crystal structure. As a result, the new structure, with comparable hydrogen bonding chains, produces elastically bendable single crystals (as opposed to plastically bendable crystals). In addition, the crystals show multidirectional (here two) elastic bending as well as rare elastic twisting. The occurrence of multiple isostructural examples, including a solid solution, with identical properties further demonstrates the general applicability of the proposed model. Crystals cannot display the concerned mechanical property in the absence of the desired structure type and fracture in a brittle manner on application of an external stress. Nanomechanical experiments and energy framework calculations also complement our results. To the best of our knowledge, this is the first example of a rational crystal engineering exercise using solely hydrogen bond interactions to obtain property differentiated crystals. This strategy namely molecular-supramolecular equivalence has been unexplored till now to tune mechanical properties, and hence is useful for crystal property engineering.

What is isostructurality? Questions on the definition

Investigation of isostructurality leads to a deeper understanding of close-packing principles and contributes to the ability of crystal engineering. A given packing motif may tolerate small molecular changes within a limit. Slight alterations of a crystal packing arrangement are carried out in order to fine-tune the structural and macroscopic properties, keeping the balance of the spatial requirements and electrostatic effects of the altered molecules in the crystals, preserving their isostructurality. Even so, the definition of isostructurality is not explicit about several issues. Are the corresponding structures required to have the same stoichiometry, Z', symmetry elements and the same space group? Because it is not obvious in the definition, studies on structure analysis and software calculating various numerical descriptors developed for the quantitative comparison of the degree of similarity of isostructural crystals self-define their criteria. The extent of the difference between corresponding crystal structures referred to as isostructural is not limited. Should it be determined numerically? There is nothing in the definition about a demand for similar supramolecular arrangements in isostructural crystals. Should the similarity of supramolecular interactions be a criterion of isostructurality? The definition of isostructurality deserves reconsideration regarding symmetry, measure of similarity and formation of supramolecular interactions.

Development of a scalar-based geometric parameterization approach for the crystal structure landscape of dithienylethene-based crystalline solids

Dithienylethenes (DTEs) are a promising class of organic photoswitches that can be used to create crystalline solids with properties controlled by light. However, the ability of DTEs to adopt multiple conformations, only one of which is photoactive, complicates the rational design of these materials. Herein, the synthesis and structural characterization of 19 crystalline solids containing a single DTE molecule are described. A novel D-D analysis of the molecular geometries obtained from rotational potential energy surface calculations and the ensemble of experimental structures were used to construct a crystal landscape for DTE. Of the 19 crystal structures, 17 contained photoinactive DTE rotamers and only 2 were photoactive. These results highlight the challenges associated with the design of these materials. Overall, the D-D analysis described herein provides rapid, effective and intuitive means of linking the molecular structure to photoactivity that could be applied more broadly to afford a general strategy for producing photoactive diarylethene-based crystalline solids.

Computer-assisted drug discovery of potential natural inhibitors of the SARS-CoV-2 RNA-dependent RNA polymerase through a multi-phase in silico approach

BACKGROUND

The COVID-19 pandemic has led to significant loss of life and economic disruption worldwide. Currently, there are limited effective treatments available for this disease. SARS-CoV-2 RNA-dependent RNA polymerase (SARS-CoV-2 RdRp) has been identified as a potential target for drug development against COVID-19. Natural products have been shown to possess antiviral properties, making them a promising source for developing drugs against SARS-CoV-2.

OBJECTIVES

The objective of this study is to identify the most effective natural inhibitors of SARS-CoV-2 RdRp among a set of 4924 African natural products using a multi-phase in silico approach.

METHODS

The study utilized remdesivir (RTP), the co-crystallized ligand of RdRp, as a starting point to select compounds that have the most similar chemical structures among the examined set of compounds. Molecular fingerprints and structure similarity studies were carried out in the first part of the study. The second part of the study included molecular docking against SARS-CoV-2 RdRp (PDB ID: 7BV2) and Molecular Dynamics (MD) simulations including the calculation of RMSD, RMSF, Rg, SASA, hydrogen bonding, and PLIP. Moreover, the calculations of Molecular mechanics with generalised Born and surface area solvation (MM-GBSA) Lennard-Jones and Columbic electrostatic interaction energies have been conducted. Additionally, in silico ADMET and toxicity studies were performed to examine the drug likeness degrees of the selected compounds.

RESULTS

Eight compounds were identified as the most effective natural inhibitors of SARS-CoV-2 RdRp. These compounds are kaempferol 3-galactoside, kaempferol 3-O-β-D-glucopyranoside, mangiferin methyl ether, luteolin 7-O-β-D-glucopyranoside, quercetin-O-β-D-3-glucopyranoside, 1-methoxy-3-indolylmethyl glucosinolate, naringenin, and asphodelin A 4'-O-β-D-glucopyranoside.

CONCLUSION

The results of this study provide valuable information for the development of natural product-based drugs against COVID-19. However, the elected compounds should be further studied in vitro and in vivo to confirm their efficacy in treating COVID-19.

Supramolecular assemblies in the molecular complexes of 4-cyanophenylboronic acid with different N-donor ligands

Molecular complexes of 4-cyanophenylboronic acid (CB) with various N-donor compounds having different conformational features, for example, rigid (1,10-phenanthroline (110phen), 4,7-phenanthroline (47phen), 1,7-phenanthroline (17phen) and acridine (acr)) and linear (1,2-bis(4-pyridyl)ethane (bpyea), 1,2-bis(4-pyridyl)ethene (bpyee) and 4,4'-azopyridine (azopy)), have been reported. In all complexes, the -B(OH)2 moiety is found to be in a syn-anti confirmation, with the exception of structures containing 110phen, bpyee, and azopy, wherein, syn-syn conformation is observed. Further, CB molecules remain intact in all structures except in the complexes with some linear N-donor ligands, wherein -B(OH)2 transforms to monoester (-B(OH)(OCH3)) prior to the formation of corresponding molecular complexes. In such boronic monoester complexes, the conformation of -B(OH)(OCH3) is syn-anti with respect to the -OH and -OCH3 groups. Also, complexes mediated by azopy and bpyee exist in both hydrated and anhydrous forms. In these anhydrous structures, the recognition pattern is through homomeric (juxtaposed -CN and -B(OH)2) as well as heteromeric (between hetero N-atom and -B(OH)2) O-H⋯N hydrogen bonds, while only heteromeric O-H⋯N hydrogen bonds hold co-formers in all other structures. Depending upon the conformational features of both co-formers, molecules are packed in crystal lattices in the form of stacked layers, helical chains, and crossed ribbons. All structures are fully characterized by single-crystal X-ray diffraction and phase purity is established by powder X-ray diffraction. Additionally, correlation among structures is explained by calculating a similarity index and performing a Hirshfeld surface analysis to quantify the strength and effectiveness of different types of intermolecular bonds that stabilize these structures along with the presentation of energy frameworks, representing the strength of the interactions in the form gradient cylinders. Also, the morphology of each complex was computed by BFDH methodology to correlate with the actual crystal morphology and packing arrangement.

Conformational State of Fenamates at the Membrane Interface: A MAS NOESY Study

The present work analyzes the ¹H NOESY MAS NMR spectra of three fenamates (mefenamic, tolfenamic, and flufenamic acids) localized in the lipid-water interface of phosphatidyloleoylphosphatidylcholine (POPC) membranes. The observed cross-peaks in the two-dimensional NMR spectra characterized intramolecular proximities between the hydrogen atoms of the fenamates as well as intermolecular interactions between the fenamates and POPC molecules. The peak amplitude normalization for an improved cross-relaxation (PANIC) approach, the isolated spin-pair approximation (ISPA) model, and the two-position exchange model were used to calculate the interproton distances indicative of specific conformations of the fenamates. The results showed that the proportions of the A+C and B+D conformer groups of mefenamic and tolfenamic acids in the presence of POPC were comparable within the experimental error and amounted to 47.8%/52.2% and 47.7%/52.3%, respectively. In contrast, these proportions for the flufenamic acid conformers differed and amounted to 56.6%/43.4%. This allowed us to conclude that when they bind to the POPC model lipid membrane, fenamate molecules change their conformational equilibria.

Rucaparib cocrystal: Improved solubility and bioavailability over camsylate

Rucaparib (Ruc) is a drug used to treat advanced ovarian cancer associated with deleterious BRCA mutations. Its commercial form, the camsylate salt (Ruc-Cam), suffers from poor aqueous solubility and thus causes low and erratic oral bioavailability. In this work, we aimed to improve the oral exposure of Ruc through cocrystallization. Liquid-assisted grinding, slurry, and solvent evaporation methods were employed to prepare new solid forms of Ruc. Cocrystals of rucaparib-theophylline monohydrate (Ruc-Thp MH), rucaparib-maltol (Ruc-Mal), and rucaparib-ethyl maltol (Ruc-Emal) were obtained. Powder X-ray diffraction, Fourier transform infrared spectroscopy, thermogravimetric analysis, differential scanning calorimetry, and dynamic vapor sorption were utilized to characterize these multi-component systems. All cocrystals dissolve faster than Ruc-Cam at pH 2.0 and 4.5, and Ruc-Thp MH displays the highest apparent solubility in pH 4.5 and 6.8 buffers. Pharmacokinetic studies in rats show that Ruc-Thp MH exhibits 2.4 times the C_max and 1.4 times the AUC_0-24h at a single dose compared with Ruc-Cam. The enhanced solubility and bioavailability of Ruc-Thp MH showcase the power of cocrystallization in addressing absorption issues in drug development.

Lidocaine Pharmaceutical Multicomponent Forms: A Story about the Role of Chloride Ions on Their Stability

In this investigation, three new crystal forms of lidocaine, and another three of lidocaine hydrochloride with hydroquinone, resorcinol, and pyrogallol were synthetised. All the new forms were characterised using multiple techniques, PXRD, SC-XRD, DSC, and FTIR. The stability of the forms was studied, and, for the more stable forms, i.e., (lidhcl) forms, the solubility was determined through FTIR analysis. The new crystalline forms obtained with (lidhcl) and the three conformers showed an interesting steric stabilisation mechanism of the oxidation of hydroxybenzenes and showed good physicochemical properties with respect to (lidhcl), constituting a mechanism of modulation of the physicochemical properties.

Investigation of crystal structures, energetics and isostructurality in halogen-substituted phosphoramidates

A total of 14 compounds, one unsubstituted and 13 halogen-substituted phosphoramidates, have been synthesized from unsubstituted and halogenated (fluoro-, difluoro-, chloro-, bromo-, iodo-substituted) aniline and diphenyl phosphoryl chloride to investigate their molecular assembly in solid-state structures. Amongst them, six groups were formed based on similarities in unit-cell dimensions, space group and molecular assembly of the crystal. The analysis reveals that all the crystal structures contain robust N-H...O hydrogen bonds which are the primary building blocks with ancillary interactions such as C-H...O, C-H...π, C-H...F/Cl/Br/I, F...F, F...π, I...π, Br...π, I...O and Br...O. The role of short and directional C-H...O and C-H...π interactions providing significant stabilization to the densely packed crystalline arrangement is discussed. The contribution of these interactions in stabilizing the crystalline assembly was deduced via computing total interaction energy between dimers and the overall lattice energies using the computer programs Crystal Explorer 17.5 and PIXELC, respectively. Additionally, the occurrence of 3D isostructurality in phosphoradimates and their halogenated analogs was investigated using the XPac program. A comparison of the magnitudes of the torsion angles in the compounds substantiates the role of conformational flexibility in the solid state.

Ligand and Structure-Based In Silico Determination of the Most Promising SARS-CoV-2 nsp16-nsp10 2'-o-Methyltransferase Complex Inhibitors among 3009 FDA Approved Drugs

As a continuation of our earlier work against SARS-CoV-2, seven FDA-approved drugs were designated as the best SARS-CoV-2 nsp16-nsp10 2'-o-methyltransferase (2'OMTase) inhibitors through 3009 compounds. The in silico inhibitory potential of the examined compounds against SARS-CoV-2 nsp16-nsp10 2'-o-methyltransferase (PDB ID: (6W4H) was conducted through a multi-step screening approach. At the beginning, molecular fingerprints experiment with SAM (S-Adenosylmethionine), the co-crystallized ligand of the targeted enzyme, unveiled the resemblance of 147 drugs. Then, a structural similarity experiment recommended 26 compounds. Therefore, the 26 compounds were docked against 2'OMTase to reveal the potential inhibitory effect of seven promising compounds (Protirelin, (1187), Calcium folinate (1913), Raltegravir (1995), Regadenoson (2176), Ertapenem (2396), Methylergometrine (2532), and Thiamine pyrophosphate hydrochloride (2612)). Out of the docked ligands, Ertapenem (2396) showed an ideal binding mode like that of the co-crystallized ligand (SAM). It occupied all sub-pockets of the active site and bound the crucial amino acids. Accordingly, some MD simulation experiments (RMSD, RMSF, Rg, SASA, and H-bonding) have been conducted for the 2'OMTase-Ertapenem complex over 100 ns. The performed MD experiments verified the correct binding mode of Ertapenem against 2'OMTase exhibiting low energy and optimal dynamics. Finally, MM-PBSA studies indicated that Ertapenem bonded advantageously to the targeted protein with a free energy value of -43 KJ/mol. Furthermore, the binding free energy analysis revealed the essential amino acids of 2'OMTase that served positively to the binding. The achieved results bring hope to find a treatment for COVID-19 via in vitro and in vivo studies for the pointed compounds.

Insights Into the Properties of Amygdalin Solvatomorphs: X-ray Structures, Intermolecular Interactions, and Transformations

Amygdalin is an effective component of the traditional Chinese medicine bitter almond, peach kernel, and plum kernel. It has pharmacological effects, such as relieving cough and asthma. In a study of the crystallization process, we found a series of solvatomorphs of amygdalin (including hydrate). Interestingly, in the structures of these solvatomorphs, the same characteristic structural fragment is present, that is, amygdalin dihydrate. Multiple analytical techniques were used to characterize the solvatomorphs, such as X-ray diffraction and thermogravimetry-mass spectrometry. Void calculations of water and solvent were used to analyze the occupied volume in the unit cell of the corresponding solvatomorphs to explain the formation mechanism of the solvatomorphs from the perspective of space. To elucidate the formation mechanism of the solvatomorphs with this kind of characteristic structure from the perspective of energy, theoretical calculations based on density functional theory were applied, such as energy decomposition and molecular electrostatic potential surfaces. In addition, the transformation phenomenon between these solvatomorphs and amygdalin was identified, and the transformation pathways are described in detail.

The features of the crystal structure of the layered series hydrates of uridine-5'-monophosphate salts (UMPNa x ·yH2O)

Almost all reported salts of nucleotides crystallized from solutions are in the form of hydrate. Layered hydrates often occur in crystals with more than five water molecules per host molecule. In the present report, five single-crystal structures of uridine-5'-monophosphate (UMP) series hydrates of acid or salts (UMPNa _x ·yH₂O, x = 0-2) were determined and analysed. It was found that all crystal hydrates were orthorhombic with a C222₁ space group but with mere variation in the plane angle of adjacent bases and the distance between phosphate arms. The packing arrangements of UMPNa _x ·yH₂O hydrates present typical layered sandwich structures and show that the UMP molecular layers alternate with water molecular layers parallel to the ac plane, linked by hydrogen bonds or coupled with coordinate bonds besides ionic electrostatic interaction. Metal ions were located in water molecular layers as a form of hydration. In addition, we tried to deduce and give insights into the formation of UMPNa _x ·yH₂O hydrates. The effect of water molecules and metal ions on the crystal structure and stability was investigated. It was found that the coexistence of relatively rigid architectures constructed by host molecules and flexible interlayer regions was a key factor to the formation of these hydrates. Excessive loss of lattice water would give rise to the irreversible collapse of the host structure and loss of ability to recover to the initial state under humidity. Approximately seven crystal-water molecules were the balance point of sodium salt hydrates at room temperature under 43-76% RH conditions. The number of sodium ions in the crystal lattice is positively correlated with their thermal stability.

Structural systematics in the isomorphous binary co-crystal solvates comprising 2,2'-dithiodibenzoic acid, 4-halobenzoic acid and dimethylformamide (1:1:1), for halide = chloride, bromide and iodide

The 1:1:1 binary co-crystal solvates formulated as 2,2'-dithiodibenzoic acid (DTBA), 4-halobenzoic acid (4-XBA) and dimethylformamide (DMF) for X = Cl (1), Br (2) and I (3) are isomorphous and the...

Polymorphism and cocrystal salt formation of 2-((2,6-dichlorophenyl)amino)benzoic acid, harvest of a second form of 2-((2,6-dimethylphenyl)amino)benzoic acid, and isomorphism between the two systems

Isomorphism and isostructurality were observed between form I of 2-((2,6-dimethylphenyl)amino)benzoic acid and its analog 2-((2,6-dichlorophenyl)amino)benzoic acid, which suggests double Cl–CH3 exchange also leads to structural similarity.

Isostructurality in amino molecular salts of two dicarboxylic acids driven by noncovalent synthons

Isostructurality was investigated for the molecular salts of two carboxylates. The luminescence properties of the solid solutions of 4apy salts of these carboxylates indicate that this property can be used to fine tune the physical properties.

Isostructural cocrystals of metaxalone with improved dissolution characteristics

Muscle relaxant and pain reliever metaxalone (MET) is a biopharmaceutical classification systems (BCS) class II drug with poor aqueous solubility and high permeability. The presence of an aromatic skeleton and cyclic carboxamate moiety are the probable reasons for the decreased aqueous solubility, which impacts on its low bioavailability. A high dose (800 mg) of the drug often creates adverse side effects on the central nervous system that needs urgent remedy. Cocrystallization of MET with nicotinamide (NAM), salicylamide (SAM), and 4-hydroxybenzoic acid (HBA) resulted in multicomponent solids that were characterized by PXRD, DSC and single crystal X-ray diffraction. Cocrystals with SAM and NAM form 2D isostructural cocrystals, whereas with HBA the result is a differently packed cocrystal hydrate (or anisole hemisolvate) depending upon the crystallization medium. Similar to the reported MET cocrystals, these cocrystals also confirm the preference for an imide⋯imide homosynthon in the drug. The dominance of the drug–drug homodimer over drug-coformer heterodimers was demonstrated based on binding energy calculations. Further, powder dissolution experiments in pH 6.8 phosphate buffer indicate that the cocrystals improved the apparent solubility compared to the native drug by 3–9 fold. The absence of stronger heterosynthons between MET and the coformers, their lower melting points and the high solubility of the coformers are the probable reasons for the enhanced solubility of the bioactive component. The MET–NAM cocrystal exhibited the highest solubility/dissolution rate among the three binary solid forms, which may offer improved bioavailability and a lower dose with minimal side effects.

Metaxalone forms isostructural cocrystals with nicotinamide and salicylamide that offer a solubility advantage compared to the native drug. A drug–drug homosynthon is retained in all the cocrystal structures.

Reply to the 'Comment on "Trimorphs of 4-bromophenyl 4-bromobenzoate. Elastic, brittle, plastic"' by J. J. Whittaker, A. J. Brock, A. Grosjean, M. C. Pfrunder, J. C. McMurtrie and J. K. Clegg, Chem. Commun., 2021, , DOI: 10.1039/D0CC07668F

Crystals that differ in their molecular constitution may yet share the same mechanical property, such as plastic deformation, because they are equivalent in a supramolecular sense.

Varying degrees of homostructurality in a series of cocrystals of antimalarial drug 11-azaartemisinin with salicylic acids

The X-ray structures of three new 1:1 pharmaceutical cocrystals of 11-azaartemisinin (11-Aza; systematic name: 1,5,9-trimethyl-14,15,16-trioxa-11-azatetracyclo[10.3.1.0^4,13.0^8,13]hexadecan-10-one, C₁₅H₂₃NO₄) with bromo-substituted salicylic acids [namely, 5-bromo- (5-BrSalA, C₇H₅BrO₃), 4-bromo- (4-BrSalA, C₇H₅BrO₃) and 3,5-dibromosalicylic acid (3,5-Br₂SalA, C₇H₄Br₂O₃)] are reported. All the structures are related to the parent 11-Aza:SalA cocrystal (monoclinic P2₁) reported previously. The 5-BrSalA analogue is isostructural with the parent, with lattice expansion along the c axis. The 4-BrSalA and 3,5-Br₂SalA cocrystals retain the highly preserved 2₁ stacks of the molecular pairs, but these pack with a varying degree of slippage with respect to neighbouring stacks, altering the close contacts between them, and represent two potential alternative homostructural arrangements for the parent compound. Structure redeterminations of the bromosalicylic acids 5-BrSalA, 4-BrSalA and 3,5-Br₂SalA at 100 K show that the packing efficiency of the cocrystals need not be higher than the parent coformers, based on specific-volume calculations, attributable to the strong O-H...O=C hydrogen bonds of 2.54 Å in the cocrystals.

Crystal engineering in IUCrJ: from 'the' crystal structure to 'a' crystal structure

What is 'structure' in the context of a molecular solid?

The unexpected discovery of the ninth polymorph of tolfenamic acid

A new polymorph of tolfenamic acid, form IX, has been crystallised from a simple cooling crystallisation experiment raising the question as to why this polymorph had never been reported before.

Quasi-Isostructural Co(II) and Ni(II) Complexes with Mefenamato Ligand: Synthesis, Characterization, and Biological Activity

Three metal complexes of mefenamato ligand 1 were synthesized: [Co2(mef)4(EtOH)2(H2O)4]: 2; [Co(mef)2(MeOH)4]∙2MeOH: 3; and [Ni(mef)2(MeOH)4]∙2MeOH: 4. Their compositions and properties were investigated by elemental analysis (EA), flame atomic absorption spectrometry (FAAS), Fourier-transform infrared spectroscopy (FTIR), and thermogravimetric analysis (TGA). Crystal structures were determined by the single crystal X-ray diffraction technique. Additionally, their antioxidant and antimicrobial activity were established, thus proving good/moderate bioactivity against Gram-positive bacteria and yeasts. In the crystal structure of 2, an apical water molecule is shared between two adjacent cobalt(II) ions, resulting in the formation of a polymeric chain extending along the [100] direction. Meanwhile, structures 3 and 4 have strong intermolecular hydrogen bonds with diverse topologies that yield unique quasi-isostructural arrangements. The packing topology is reflected by the Hirshfeld surface analysis of intermolecular contacts.

Crystal engineering in all its hues in

The articles in crystal engineering and structural chemistry in IUCrJ published from 2019 onwards reflect the breadth and outreach of this new and important subject.

Methods for easy recognition of isostructurality – lab jack-like crystal structures of halogenated 2-phenylbenzimidazoles

Easy recognition and numerical description of isostructurality; how different the similar structures can be; supramolecular aspects of isostructurality.