Intermolecular Interactions in Functional Crystalline Materials: From Data to Knowledge

Is there a Covalent Au(I)-Au(I) Bond in the trans-(AuX)2 (X = F, Cl, Br, I) Structure? A Post-Hartree-Fock and Density Functional Theory Study

We present an exhaustive exploration of the driving forces dominating the interaction between gold atoms in the trans-(AuX)2, where X is a halogen ligand. This work provides insights into the nature of the gold-gold contact in the trans-(AuX)2. The geometries and energies were calculated at the MP2, CCSD(T), and DFT-D3(BJ) (B3LYP, PBE, and TPSS) levels of theory. The results show a short Au-Au distance, typical of a covalent bond, but with a weak interaction energy associated with noncovalent interactions. It is established that the physical contributions from polarization and the electronic correlation forces are the most relevant at the post-Hartree-Fock level of theory. Also, the electrostatic term is attractive but with low contribution. Finally, the Wiberg indices and NBO analysis exposed a small covalent character between the gold atoms, revealing that this contribution is insufficient to explain the stability of the dimers. It is concluded that a sum of contributions makes it possible to establish an attraction between the gold atoms in the dimers studied beyond a classical aurophilic interaction.

Formation of Eigen or Zundel Features at Protonated Water Cluster-Aromatic Interfaces

Interfacial interactions of protonated water clusters adsorbed at aromatic surfaces play an important role in biology, and in atmospheric, chemical and materials sciences. Here, we investigate the interaction of protonated water clusters ((H+ H2 O)n (where n=1-3)) with benzene (Bz), coronene (Cor) and dodecabenzocoronene (Dbc)). To study the structure, stability and spectral features of these complexes, computations are done using DFT-PBE0(+D3) and SAPT0 methods. These interactions are probed by AIM electron density topography and non-covalent interactions index (NCI) analyses. We suggest that the excess proton plays a crucial role in the stability of these model interfaces through strong inductive effects and the formation of Eigen or Zundel features. Also, computations reveal that the extension of the π-aromatic system and the increase of the number of water molecules in the H-bounded water network led to a strengthening of the interactions between the corresponding aromatic compound and protonated water molecules, except when a Zundel ion is formed. The present findings may serve to understand in-depth the role of proton localized at aqueous medium interacting with large aromatic surfaces such as graphene interacting with acidic liquid water. Besides, we give the IR and UV-Vis spectra of these complexes, which may help for their identification in laboratory.

N-N(+) Bond-Forming Intramolecular Cyclization of O-Tosyloxy β-Aminopropioamidoximes and Ion Exchange Reaction for the Synthesis of 2-Aminospiropyrazolilammonium Chlorides and Hexafluorophosphates

Our research area is related to the spiropyrazolinium-containingcompounds, which are insufficiently studied compared with pyrazoline-containing compounds. Nitrogen-containing azoniaspiromolecules have also been well studied. In drug design and other areas, they are a priori important structures, since rigid spirocyclic scaffolds with the reduced conformational entropy are able to organize a closely spaced area. Azoniaspirostructures are currently of wide practical interest as ionic liquids, current sources (membranes), structure-directing agents in organocatalysis, and in the synthesis of ordered ceramics. Our goal was the synthesis of 2-aminospiropyrazolilammonium chlorides and hexafluorophosphates. Our methodology is based on the tosylation of β-aminopropioamidoximes with six-membered N-heterocycles (piperidine, morpholine, thiomorpholine, and phenylpiperazine) at the β-position. 2-Aminospiropyrazolilammonium chlorides and hexafluorophosphates were obtained by the reaction of double ion substitution in the reaction of toluenesulfonates of 2-aminospiropyrazolinium compounds with an ethereal solution of HCl in ethanol and with ammonium hexafluorophosphate in ethanol in quantitative yields of 55-97%. The physicochemical characteristics of the synthesized compounds and their IR and NMR spectra are presented. The obtained salts were additionally characterized by the single-crystal XRD analysis. The presence of both axial and equatorial conformations of spirocations in solids was confirmed. 2-Aminospiropyrazolilammonium chlorides and hexafluorophosphates have weak in vitro antimicrobial activity on Gram-positive and Gram-negative bacterial lines.

Polymorphism of Carbamazepine Pharmaceutical Cocrystal: Structural Analysis and Solubility Performance

Polymorphism is a common phenomenon among single- and multicomponent molecular crystals that has a significant impact on the contemporary drug development process. A new polymorphic form of the drug carbamazepine (CBZ) cocrystal with methylparaben (MePRB) in a 1:1 molar ratio as well as the drug's channel-like cocrystal containing highly disordered coformer molecules have been obtained and characterized in this work using various analytical methods, including thermal analysis, Raman spectroscopy, and single-crystal and high-resolution synchrotron powder X-ray diffraction. Structural analysis of the solid forms revealed a close resemblance between novel form II and previously reported form I of the [CBZ + MePRB] (1:1) cocrystal in terms of hydrogen bond networks and overall packing arrangements. The channel-like cocrystal was found to belong to a distinct family of isostructural CBZ cocrystals with coformers of similar size and shape. Form I and form II of the 1:1 cocrystal appeared to be related by a monotropic relationship, with form II being proven to be the thermodynamically more stable phase. The dissolution performance of both polymorphs in aqueous media was significantly enhanced when compared with parent CBZ. However, considering the superior thermodynamic stability and consistent dissolution profile, the discovered form II of the [CBZ + MePRB] (1:1) cocrystal seems a more promising and reliable solid form for further pharmaceutical development.

Supramolecular Organization in Salts of Riluzole with Dihydroxybenzoic Acids—The Key Role of the Mutual Arrangement of OH Groups

Intermolecular interactions, in particular hydrogen bonds, play a key role in crystal engineering. The ability to form hydrogen bonds of various types and strengths causes competition between supramolecular synthons in pharmaceutical multicomponent crystals. In this work, we investigate the influence of positional isomerism on the packing arrangements and the network of hydrogen bonds in multicomponent crystals of the drug riluzole with hydroxyl derivatives of salicylic acid. The supramolecular organization of the riluzole salt containing 2,6-dihydroxybenzoic acid differs from that of the solid forms with 2,4- and 2,5-dihydroxybenzoic acids. Because the second OH group is not at position 6 in the latter crystals, intermolecular charge-assisted hydrogen bonds are formed. According to periodic DFT calculations, the enthalpy of these H-bonds exceeds 30 kJ·mol−1. The positional isomerism appears to have little effect on the enthalpy of the primary supramolecular synthon (65–70 kJ·mol−1), but it does result in the formation of a two-dimensional network of hydrogen bonds and an increase in the overall lattice energy. According to the results of the present study, 2,6-dihydroxybenzoic acid can be treated as a promising counterion for the design of pharmaceutical multicomponent crystals.

Ligand-Receptor Interactions of Lamivudine: A View from Charge Density Study and QM/MM Calculations

The nature and strength of interactions for an anti-HIV drug, Lamivudine, were studied in a pure crystal form of the drug and the ligand–receptor complexes. High-resolution single-crystal X-ray diffraction studies of the tetragonal polymorph allowed the drug’s experimental charge density distribution in the solid state to be obtained. The QM/MM calculations were performed for a simplified model of the Lamivudine complex with deoxycytidine kinase (two complexes with different binding modes) to reconstruct the theoretical charge density distribution. The peculiarities of intramolecular interactions were compared with previously reported data for an isolated molecule. Intermolecular interactions were revealed within the quantum theory of ‘Atoms in Molecules’, and their contributions to the total crystal energy or ligand–receptor binding energy were evaluated. It was demonstrated that the crystal field effect weakened the intramolecular interactions. Overall, the energies of intermolecular interactions in ligand–receptor complexes (320.1–394.8 kJ/mol) were higher than the energies of interactions in the crystal (276.9 kJ/mol) due to the larger number of hydrophilic interactions. In contrast, the sum of the energies of hydrophobic interactions was found to be unchanged. It was demonstrated by means of the Voronoi tessellation that molecular volume remained constant for different molecular conformations (250(13) Å3) and increased up to 399 Å3 and 521(30) Å3 for the Lamivudine phosphate and triphosphate.

The Cambridge structural database (CSD): important resources for teaching concepts in structural chemistry and intermolecular interactions

The Cambridge Structural Database (CSD) is a repository of all published organic and metal-organic crystal structures of small molecules. These compounds have been crystallized under different conditions and have variable bond parameters and molecular landscapes. Entries in the database therefore serve as real models that can be used to illustrate structural properties such as bond angles, bond distances, torsion angles and other intra- and intermolecular interactions. This paper illustrates how the CSD programs ConQuest and Mercury can be used to search the database for 3D molecular structures to teach concepts such as molecular geometry, symmetry and group theory, organometallic chemistry and intermolecular interactions involving hydrogen bonding and Full Interaction Maps (FIMs) to explore molecular landscapes for halogen bond interactions. Results obtained from these studies are beneficial to understand and predict crystal properties as well as the structural properties of molecules and ions in crystal environments.

N-(4-Methyl-3-((4-(pyridin-3-yl)pyrimidin-2-yl)amino)phenyl)-4-((4-methylpiperazin-1-yl)methyl)benzamide

Imatinib is one of the most used therapeutic agents to treat leukemia, which specifically inhibits the activity of tyrosine kinases. This polytopic molecule has been structurally characterized only in the form of its piperazin-1-ium salt (mesylate, picrate, citrate, fumarate or malonate). Herein we present the crystal structure of the freebase Imatinib which precipitated from a 1:10 mixture with arginine. The molecule realizes an extended conformation and forms infinite H-bonded chains through its amide, amine and pyrimidine groups.

Crystal structure and antidiabetic activity of 2-aminospiropyrazolinium tosylates and the product of O-tosylation of β-(benzimidazol-1-yl)propioamidoxime

2-Amino-1,5-diazaspiro[4.5]dec-1-en-5-ium salts possess bioactivity tuned by the nature of the heteroatoms in the six-membered ring and the counter-ion. The molecular environment of these cations in solids provides an opportunity to establish the conformations and hydrogen-bonding patterns typical for this family. β-Aminopropioamidoxime tosylation products [2-amino-1,5-diazaspiro[4.5]dec-1-en-5-ium tosylates and the product of the O-tosylation of β-(benzimidazol-1-yl)propioamidoxime, namely, 2-amino-1,5-diazaspiro[4.5]dec-1-en-5-ium tosylate, C₈H₁₆N₃⁺·C₇H₇O₃S^- (6), 2-amino-8-oxa-1,5-diazaspiro[4.5]dec-1-en-5-ium tosylate, C₇H₁₄N₃O⁺·C₇H₇O₃S^- (7), the monohydrate of 7, C₇H₁₄N₃O⁺·C₇H₇O₃S^-·H₂O (7a), 2-amino-8-thia-1,5-diazaspiro[4.5]dec-1-en-5-ium tosylate, C₇H₁₄N₃S⁺·C₇H₇O₃S^- (8), 2-amino-8-phenyl-1,5,8-triazaspiro[4.5]dec-1-en-5-ium tosylate, C₁₃H₁₉N₄⁺·C₇H₇O₃S^- (9), and 3-(1H-benzimidazol-1-yl)-N'-(tosyloxy)propanimidamide, C₁₇H₁₈N₄O₃S (10)] were investigated using X-ray diffraction to study peculiarities of their molecular geometry and intermolecular interactions. In vitro antitubercular and antidiabetic screening of the β-aminopropioamidoxime tosylation products was also carried out. It was revealed that this series of compounds does not have activity against drug-sensitive and multidrug-resistant M. tuberculosis strains, and exhibits high and moderate antidiabetic α-amylase and α-glucosidase activity. Using the hydrogen-bond propensity tool, we found that the inclination of counter-ions and atoms to act as acceptors of hydrogen bonds for the amino group decreases passing from tosylate O atoms to water molecules and the N atoms of five-membered rings. This fact is probably the reason for the formation in the solids of hydrogen-bonded tetramers consisting of two anions and two cations, and the rare occurrence of 2-aminospiropyrazolinium salt hydrates.

Hybrid iron(II) phthalocyaninatoclathrochelates with a terminal reactive vinyl group and their organo-inorganic polymeric derivatives: synthetic approaches, X-ray structures and copolymerization with styrene

Hybrid metallo(IV)phthalocyaninate-capped tris-dioximate iron(II) complexes (termed as "phthalocyaninatoclathrochelates") with non-equivalent apical fragments and functionalized with one terminal reactive vinyl group were prepared for the first time using three different synthetic approaches: (i) transmetallation (capping group exchange) of the appropriate labile boron,antimony-capped cage precursors, (ii) capping of the initially isolated reactive semiclathrochelate intermediate, and (iii) direct one-pot template condensation of their ligand synthons on the iron(II) ion as a matrix. The obtained polytopic cage complexes were characterized using elemental analysis, ¹H NMR, MALDI-TOF MS and UV-vis spectra, and the single-crystal X-ray diffraction experiments. One of the obtained vinyl-terminated iron(II) phthalocyaninatoclathrochelates and its semiclathrochelate precursor were tested as monomers in a copolymerization reaction with styrene as the main component. These vinyl-terminated (semi)clathrochelate iron(II) complexes were found to be successfully copolymerized with this industrially important monomer, affording the intensely colored copolymer products. Because of a low solubility of the tested zirconium(IV) phthalocyaninate-capped tris-nioximate monomer in styrene as a solvent, a molar ratio of 1 : 500 was used. The obtained copolymer products and the kinetics of their formation were studied using GPC, FTIR, UV-vis, TGA and DSC methods. Even at such a low concentration of the Fe,Zr-binuclear metallocomplex component, an increase in the rate of the UV-light degradation of the organo-inorganic products, as well as in their thermal stability, was observed.

How do electron donating substituents affect the electronic structure, molecular topology, vibrational properties and intra- and intermolecular interactions of polyhalogenated pyridines?

Seven polyhalogenated pyridine derivatives bearing an amino or a hydroxyl group, either at the ortho or para position, were studied using a combined experimental and computational approach. The presence of an electron donating substituent strongly impacted on the geometry, electronic structure, electrostatic properties, molecular topology and vibrational characteristics of these compounds compared to the corresponding polyhalogenated pyridines. In particular the attention was focused on changes in wavenumbers, force constants and intensity of the seven in-plane Ring Normal Modes (RNMs). Due to the nature and position of the substituents, intra- and intermolecular interactions also underwent dramatic modifications, as revealed using Natural Bond Orbital (NBO) analysis, Non-Covalent Interaction (NCI) analysis and Atom-In-Molecule (AIM) theory. Raman and FT-IR spectra of these seven compounds were also collected in solid phase and rationalised by the simulated spectra for hydrogen bonding and/or π-π stacking based homodimers. The present study provides a strategy not only for the vibrational characterisation for the individual compounds, but also for shedding light on the ways of molecular packing in the molecular crystals or cocrystals involving these compounds.

Redetermination of the structure of 2-amino-8-thia-1,5-diazaspiro[4.5]dec-1-en-5-ium chloride monohydrate

The crystal structure of the title compound was redetermined at two temperatures [120.0 (2) and 295.0 (2) K]. The previously reported P2₁2₁2₁ chiral space group is corrected to centrosymmetric Pbca.

The reaction of β-(thio­morpholin-1-yl)propio­amidoxime with tosyl chloride in CHCl₃ in the presence of DIPEA when heated at 343 K for 8 h afforded the title hydrated salt, C₇H₁₄N₃S⁺·Cl⁻·H₂O, in 84% yield. This course of the tosyl­ation reaction differs from the result of tosyl­ation obtained for this substrate at room temperature, when only 2-amino-8-thia-1,5-di­aza­spiro­[4.5]dec-1-ene-5-ammonium tosyl­ate was isolated in 56% yield. The structure of the reaction product was established by physicochemical methods, spectroscopy, and X-ray diffraction. The single-crystal data demonstrated that the previously reported crystal structure of this compound [Kayukova et al. (2021). Chem. J. Kaz, 74, 21–31] had been refined in a wrong space group. In the extended structure, the chloride anions, water mol­ecules and amine groups of the cations form two-periodic hydrogen-bonded networks with the fes topology.

meso-Tetra-(4-pyridyl)porphyrin/palladium(II) complexes as anticancer agents

This study reports the synthesis, structural characterization and cytotoxic activity of four new palladium/pyridylporphyrin complexes, with the general formula {TPyP[PdCl(P-P)]₄}(PF₆)₄, where P-P is 1,2-bis(diphenylphosphino)ethane (dppe), 1,3-bis(diphenylphosphino)propane (dppp), 1,2-bis(diphenylphosphino)butane (dppb) or 1,1'-bis(diphenylphosphino)ferrocene (dppf). The complexes were characterized by elemental analysis, and by FT-IR, UV/Vis, ¹H and ³¹P{¹H} NMR (1D/2D) spectroscopy. The slow evaporation of a methanolic solution of {TPyP[PdCl(dppb)]₄}(PF₆)₄ (in an excess of NaBF₄ salt) resulted in single crystals suitable for X ray diffraction, allowing the determination of the tridimensional structure of this complex, which crystallized in the P2₁/a space group. The cytotoxicity of the complexes against MDA-MB-231 (breast cancer cells) and MCF-10A (non-tumor breast cancer cells), was determined by the colorimetric MTT method, which revealed that all four complexes show selective indexes close to 1.2, lower than that of cisplatin for the same cells (12.12). The interaction of the complexes with CT-DNA was evaluated by UV-visible and viscosity measurements and it was determined that the complexes interact moderately with CT-DNA, probably by H-bonding/π-π stacking and electrostatic interactions.

Influence of Fluorine Substitution on Nonbonding Interactions in Selected Para-Halogeno Anilines

A series of 4-halogeno aniline derivatives was studied employing combined theoretical and experimental methods (i. e. crystal structure analysis and vibrational spectroscopies). This simplified model system was selected to shed light on the impact of fluorine substitution on the formation of noncovalent interactions such as halogen bonds (XBs) and hydrogen bonds (HBs), which are key interactions in fluorinated/halogenated drug-protein complex formation. Comparative analysis of three previously reported and five newly determined crystal structures indicated that, in most cases, 2-fluoro and 2,6-difluoro substitution of 4-X anilines increases the ability of adjacent amine to form strong N-H⋅⋅⋅N HBs. Additionally, fluorine substituents in the difluorinated derivatives are competitive and attractive HB and XB acceptors and increase the probability of halogen-halogen contacts. A peculiar observation was made for 4-iodoaniline and 2,6-difluoro-4-iodoaniline, which form distinct interaction patterns compared to the corresponding 4-Cl and 4-Br analogs. The observed intramolecular N-H⋅⋅⋅F interactions lead to additional NH bands in the FT-IR spectra.

Boulton-Katritzky Rearrangement of 5-Substituted Phenyl-3-[2-(morpholin-1-yl)ethyl]-1,2,4-oxadiazoles as a Synthetic Path to Spiropyrazoline Benzoates and Chloride with Antitubercular Properties

The analysis of stability of biologically active compounds requires an accurate determination of their structure. We have found that 5-aryl-3-(2-aminoethyl)-1,2,4-oxadiazoles are generally unstable in the presence of acids and bases and are rearranged into the salts of spiropyrazolinium compounds. Hence, there is a significant probability that it is the rearranged products that should be attributed to biological activity and not the primarily screened 5-aryl-3-(2-aminoethyl)-1,2,4-oxadiazoles. A series of the 2-amino-8-oxa-1,5-diazaspiro[4.5]dec-1-en-5-ium (spiropyrazoline) benzoates and chloride was synthesized by Boulton–Katritzky rearrangement of 5-substituted phenyl-3-[2-(morpholin-1-yl)ethyl]-1,2,4-oxadiazoles and characterized using FT-IR and NMR spectroscopy and X-ray diffraction. Spiropyrazolylammonium chloride demonstrates in vitro antitubercular activity on DS (drug-sensitive) and MDR (multidrug-resistant) of MTB (M. tuberculosis) strains (1 and 2 µg/mL, accordingly) equal to the activity of the basic antitubercular drug rifampicin; spiropyrazoline benzoates exhibit an average antitubercular activity of 10–100 μg/mL on MTB strains. Molecular docking studies revealed a series of M. tuberculosis receptors with the energies of ligand–receptor complexes (−35.8–−42.8 kcal/mol) close to the value of intermolecular pairwise interactions of the same cation in the crystal of spiropyrazolylammonium chloride (−35.3 kcal/mol). However, only in complex with transcriptional repressor EthR2, both stereoisomers of the cation realize similar intermolecular interactions.

Novel Polymorph of Favipiravir-An Antiviral Medication

Various solid forms of pharmaceutically important compounds exhibit different physical properties and bioactivity; thus, knowledge of the structural landscape and prediction of spontaneous polymorph transformations for an active pharmaceutical ingredient is of practical value for the pharmaceutical industry. By recrystallization from ethyl acetate, a novel polymorph of 6-fluoro-3-hydroxypyrazine-2-carboxamide (trademark favipiravir, RNA polymerase inhibitor) was obtained and characterized using differential scanning calorimetry (DSC), infra-red spectroscopy and powder X-ray diffraction (XRD) analysis. The favipiravir molecule in two polymorphs realizes similar H-bonding motifs, but the overall H-bonded networks differ. Based on periodic density functional theory calculations, the novel tetragonal polymorph with two interpenetrated H-bonded networks is slightly less stable than the orthorhombic one with the zst topology of the underlying H-bonded net that is in accord with experimentally observed powder XRD patterns of slow conversion of the tetragonal phase to the orthorhombic one. However, topological analysis of net relations revealed that no transformations can be applied to convert H-bonded networks in the experimental unit cells, and DSC data indicate no solid-state reactions at heating.

Heteroleptic Cu(ii) saccharin complexes: intriguing coordination modes and properties

A new Cu(ii) O,S-coordinated saccharinate complex is reported, showing crystallochromism and NIR emission in the solid state, in silico ligand exchange reactions with N/S-donor ligands in the presence of model molecules mimicking biological targets.

Self-organization of 1,6-dialkyl-3a,6a-diphenylglycolurils in the crystalline state

Glycolurils with hydrophobic substituents readily form solids with low-energy surfaces and hydrophobic properties.

Intermolecular Interactions in Crystal Structures of Imatinib-Containing Compounds

Imatinib, one of the most used therapeutic agents to treat leukemia, is an inhibitor that specifically blocks the activity of tyrosine kinases. The molecule of imatinib is flexible and contains several functional groups able to take part in H-bonding and hydrophobic interactions. Analysis of molecular conformations for this drug was carried out using density functional theory calculations of rotation potentials along single bonds and by analyzing crystal structures of imatinib-containing compounds taken from the Cambridge Structural Database and the Protein Data Bank. Rotation along the N-C bond in the region of the amide group was found to be the reason for two relatively stable molecular conformations, an extended and a folded one. The role of various types of intermolecular interactions in stabilization of the particular molecular conformation was studied in terms of (i) the likelihood of H-bond formation, and (ii) their contribution to the Voronoi molecular surface. It is shown that experimentally observed hydrogen bonds are in accord with the likelihood of their formation. The number of H-bonds in ligand-receptor complexes surpasses that in imatinib salts due to the large number of donors and acceptors of H-bonding within the binding pocket of tyrosine kinases. Contribution of hydrophilic intermolecular interactions to the Voronoi molecular surface is similar for both conformations, while π...π stacking is more typical for the folded conformation of imatinib.

The Cambridge Structural Database in chemical education: analysis of hydrogen-bonded networks in salts of hexaaqua metal ions with organic counter-ions

This paper describes a laboratory course that introduces basic crystallographic data analysis to chemistry students encountering for the first time the world of crystals and crystal structures. The aim of the course is to provide students with direct contact with crystal structures and hands-on experience in structure analysis. To this end, a set of appropriately simple inorganic molecular structures was selected, consisting of salts of hexaaqua metal ions with organic counter-ions. By exploiting the crystallographic tools available in the Cambridge Structural Database program Mercury, students learn how to visualize and analyse a set of atomic coordinates. In this way they learn how to extract bonding and structural information concerning intramolecular interactions in both salt components. Intermolecular interactions are next analysed by looking closely at supramolecular motifs and packing patterns generated by hydrogen bonds. This pragmatic approach turned out to be effective and extremely useful for summarizing many chemical concepts learned by students during a bachelor degree course in chemistry. The experience provides at the same time some basic capabilities for properly managing crystal structure analysis.

Synthesis, crystal structure and docking studies of tetracyclic 10-iodo-1,2-dihydroisoquinolino[2,1-b][1,2,4]benzothiadiazine 12,12-dioxide and its precursors

The title compound, 10-iodo-1,2-dihydroisoquinolino[2,1-b][1,2,4]benzothiadiazine 12,12-dioxide, C₁₅H₁₁IN₂O₂S (8), was synthesized via the metal-free intramolecular N-iodosuccinimide (NIS)-mediated radical oxidative sp³-C-H aminative cyclization of 2-(2'-aminobenzenesulfonyl)-1,3,4-trihydroisoquinoline, C₁₅H₁₆N₂O₂S (7). The amino adduct 7 was prepared via a two-step reaction, starting from the condensation of 2-nitrobenzenesulfonyl chloride (4) with 1,2,3,4-tetrahydroisoquinoline (5), to afford 2-(2'-nitrobenzenesulfonyl)-1,3,4-trihydroisoquinoline, C₁₅H₁₄N₂O₄S (6), in 82% yield. The catalytic hydrogenation of 6 with hydrogen gas, in the presence of 10% palladium-on-charcoal catalyst, furnished 7. Products 6-8 were characterized by their melting points, IR and NMR (¹H and ¹³C) spectroscopy, and single-crystal X-ray diffraction. The three compounds crystallized in the monoclinic space group, with 7 exhibiting classical intramolecular hydrogen bonds of 2.16 and 2.26 Å. All three crystal structures exhibit centrosymmetric pairs of intermolecular C-H...π(ring) and/or π-π stacking interactions. The docking studies of molecules 6, 7 and 8 with deoxyribonucleic acid (PDB id: 1ZEW) revealed minor-groove binding behaviours without intercalation, with 7 presenting the most favourable global energy of the three molecules. Nonetheless, molecule 8 interacted strongly with the DNA macromolecule, with an attractive van der Waals energy of -15.53 kcal mol^-1.

A Supramolecular Approach to Structure-Based Design with A Focus on Synthons Hierarchy in Ornithine-Derived Ligands: Review, Synthesis, Experimental and in Silico Studies

The success of innovative drugs depends on an interdisciplinary and holistic approach to their design and development. The supramolecular architecture of living systems is controlled by non-covalent interactions to a very large extent. The latter are prone to extensive cooperation and like a virtuoso play a symphony of life. Thus, the design of effective ligands should be based on thorough knowledge on the interactions at either a molecular or high topological level. In this work, we emphasize the importance of supramolecular structure and ligand-based design keeping the potential of supramolecular H-bonding synthons in focus. In this respect, the relevance of supramolecular chemistry for advanced therapies is appreciated and undisputable. It has developed tools, such as Hirshfeld surface analysis, using a huge data on supramolecular interactions in over one million structures which are deposited in the Cambridge Structure Database (CSD). In particular, molecular interaction surfaces are useful for identification of macromolecular active sites followed by in silico docking experiments. Ornithine-derived compounds are a new, promising class of multi-targeting ligands for innovative therapeutics and cosmeceuticals. In this work, we present the synthesis together with the molecular and supramolecular structure of a novel ornithine derivative, namely N-α,N-δ)-dibenzoyl-(α)-hydroxymethylornithine, 1. It was investigated by modern experimental and in silico methods in detail. The incorporation of an aromatic system into the ornithine core induces stacking interactions, which are vital in biological processes. In particular, rare C=O…π intercontacts have been identified in 1. Supramolecular interactions were analyzed in all structures of ornithine derivatives deposited in the CSD. The influence of substituent was assessed by the Hirshfeld surface analysis. It revealed that the crystal packing is stabilized mainly by H…O, O…H, C…H, Cl (Br, F)…H and O…O interactions. Additionally, π…π, C-H…π and N-O…π interactions were also observed. All relevant H-bond energies were calculated using the Lippincott and Schroeder H-bond model. A library of synthons is provided. In addition, the large synthons (Long-Range Synthon Aufbau Module) were considered. The DFT optimization either in vacuo or in solutio yields very similar molecular species. The major difference with the relevant crystal structure was related to the conformation of terminal benzoyl C15-C20 ring. Furthermore, in silico prediction of the extensive physicochemical ADME profile (absorption, distribution, metabolism and excretion) related to the drug-likeness and medicinal chemistry friendliness revealed that a novel ornithine derivative 1 has the potential to be a new drug candidate. It has shown good in silico absorption and very low toxicity.

Solid-State Photoinitiated Cycloaddition Reaction of 4,4′-(Ethene-1,2-diyl)bis(pyridinium) Dinitrate: Charge-Density Perspective on Initial Stage of the Reaction

Solid-state photoinitiated [2 + 2] cycloaddition reaction 2(H2bpe)(NO3)2 → (H4tpcb)(NO3)4 (bpe = 1,2-bis(pyrid-4-yl)ethylene; tpcb = 1,2,3,4-tetrakis(pyrid-4-yl)cyclobutane) was carried out in a single-crystal-to-single-crystal manner. The reaction product was characterized by means of X-ray diffraction and 1H NMR spectroscopy. Only the rctt-isomer of tpcb was found as the reaction product. Intermolecular interactions in a single crystal of (H2bpe)(NO3)2 were studied within the QTAIM approach. Although sum energy of strong and weak hydrogen bonds dominates in total packing energy, contribution of π…π stacking interactions to the packing energy is also prominent. At solid (H2bpe)(NO3)2, stacking of photoreactive H2bpe2+ cations is realized via N…C, C…C and C–H…C bonding, although no four-membered cycles formed by these bond paths was found in molecular graph representation. Reduced density gradient (RDG) surfaces and molecular Voronoi surfaces clearly demonstrate accumulation of charge density between olefin groups prone to take part in photoinitiated cycloaddition reactions. Good correlation between description of hydrogen bonding in terms of QTAIM and Voronoi approaches was demonstrated. The Voronoi approach confirmed that during the photoreaction the system of hydrogen bonds remained almost unchanged.