Hydrogen Bond, π-π, and CH-π Interactions Governing the Supramolecular Assembly of Some Hydrazone Ligands and Their MnIIComplexes - Structural and Theoretical Interpretation

H(N3)dap (Hdap = 2,6-Diaminopurine) Recognition by Cu2(EGTA): Structure, Physical Properties, and Density Functional Theory Calculations of [Cu4(μ-EGTA)2(μ-H(N3)dap)2(H2O)2]·7H2O

Reactions in water between the Cu2(µ-EGTA) chelate (EGTA = ethylene-bis(oxyethyleneimino)tetraacetate(4-) ion) and Hdap in molar ratios 1:1 and 1:2 yield only blue crystals of the ternary compound [Cu4(μ-EGTA)2(μ-H(N3)dap)2(H2O)2]·7H2O (1), which has been studied via single-crystal X-ray diffraction and various physical methods (thermal stability, spectral and magnetic properties), as well as DFT theoretical calculations. In the crystal, uncoordinated water is disordered. The tetranuclear complex molecule also has some irrelevant disorder in an EGTA-ethylene moiety. In the complex molecule, both bridging organic molecules act as binucleating ligands. There are two distorted five- and two six-coordinated Cu(II) centers. Each half of EGTA acts as a tripodal tetradentate Cu(II) chelator, with a mer-NO2 + O(ether, distal) conformation. Hdap exhibits the tautomer H(N3)dap, with the dissociable H-atom on its less basic N-heterocyclic atom. These features favor the efficient cooperation between Cu-N7 or Cu-N9 bonds with appropriate O-EGTA atoms, as N6-H···O or N3-H···O interligand interactions, respectively. The bridging role of both organics determines the tetranuclear dimensionality of the complex. In this crystal, such molecules associate in zig-zag chains built by alternating π-π interactions between the five- or six-atom rings of Hdap ligands of adjacent molecules. DFT theoretical calculations (using two different theoretical models and characterized by the quantum theory of "atoms in molecules") reveal the importance of these π-π interactions between Hdap ligands, as well as those corresponding to the referred hydrogen bonds in the contributed tetranuclear molecule.

Hydrogen-bond-driven supramolecular helical assembly of a coumarin-substituted phthalonitrile derivative: synthesis and in vitro anticancer activity against colorectal adenocarcinoma

Phthalonitrile derivatives are generally reported to crystallize in space groups P21/c and P 1 in the literature. In this study, 7-hydroxy-4,8-dimethyl-3-pentylcoumarin (2) and its phthalonitrile derivative (2d) were crystallized; 2d crystallized in the rare trigonal space group R 3. In the phthalonitrile derivative (2d), weak C—H...O hydrogen-bonding interactions promoted the formation of supramolecular double helices, and these supramolecular P and M double helices came together to form a honeycomb-like architectural motif involving one-dimensional tubular channels. In silico molecular-docking studies were performed to support the experimental processes and the results agree with each other. In vitro studies of compounds 2 and 2d were performed in LoVo colorectal adenocarcinoma and CCD18Co healthy human cell lines using flow cytometry. For compounds 2 and 2d, there was a statistically significant increase (p < 0.001) in both early and late apoptosis with respect to the control in a dose-dependent manner.

Soft 3D hybrid network for delivery and controlled release of poorly soluble dihydropyrimidinone compound: An insight into the novel system for potential application in leukemia treatment

Researchers are faced with everyday demands for safer and more efficient therapy for many diseases, especially serious one such as various types of cancer. Numerous anticancer drugs are poorly-water soluble and therefore their encapsulation and controlled release remain quite challenge. In present study, we deepened our research of hydrophilic carrier based on poly(methacrylic acid) and casein (PMAC) by investigating its potential for encapsulation and controlled release of novel poorly water-soluble dihydropyrimidion-azo-pyridon compound (DHPMP). DHPMP is a dye that has been proven to show cytotoxic activity against chronic myeloid leukemia K562 cells. By encapsulating DHPMP into the carrier and delivering it into the intestines, DHPMP absorption could be the fastest and the number of therapeutic doses and side effects can be reduced. Carriers based on PMAC and DHPMP (PMAC-DHPMP) were synthetized and characterized by FTIR, SEM and single compression tests. The swelling behavior of PMAC-DHPMP carriers and cumulative DHPMP release were investigated depending on the amount of crosslinker and encapsulated DHPMP in two media which were simulating pH environments in human stomach and intestines. The prolonged and controlled release of DHPMP was achieved. In vitro cytotoxic activity of PMAC-DHPMP carriers against K562 cells and the cell cycle analysis showed great potential of the carriers for application in leukemia treatment.

Experimental and computational evidence for stabilising parallel, offset π[C(O)N(H)NC]⋯π(phenyl) interactions in acetohydrazide derivatives

Stabilising π[C(O)N(H)NC]⋯π(phenyl) interactions are described.

Theoretical insights on the encapsulated hydronium ion mediated supramolecular assembly of nickel(ii) Schiff base complexes: strong hydrogen bonding interaction due to charge transfer from the lone pair of oxygen to the antibonding orbital of the O–H bond

Strong hydrogen bonding interactions are observed in a hydronium ion trapped nickel(ii) Schiff base complex. The energetics regarding these interactions which provide the stability to the supramolecular structure are analysed by DFT calculations.

Effective methods for the synthesis of hydrazones, quinazolines, and Schiff bases: reaction monitoring using a chemometric approach

Synthesis of hydrazones (1a–4a and 1b–4b), quinazolines (3c·MeOH and 3d·MeOH), and hydrazone-Schiff bases (4c and 4d) is achieved by combining suitable aldehydes (2,3- or 2,4-dihydroxybenzaldehyde) with four hydrazides (isonicotinic, nicotinic, and 2- or 4-aminobenzoic acid hydrazide). A suite of approaches for their preparation is described: solution-based synthesis, mechanosynthesis, and solid-state melt reactions. The mechanochemical approach is generally a better choice for the quinazolines, while the solid-state melt reaction is more efficient for derivatives of (iso)nicotinic based hydrazones. Crystalline amine-functionalised hydrazones 4a and 4b undergo post-synthetic modifications in reactions with 3- or 4-pyridinecarbaldehyde vapours to form hydrazone-Schiff bases 4a-3py, 4b-3py, 4a-4py, and 4b-4py. Mechanochemical and vapour-mediated reactions are followed by ex situ powder X-ray diffraction and IR-ATR methods, respectively. The chemometric analysis of these data using principal component analysis provided an insight into the reaction profiles and reaction times. Azines (5a and 5b), achieved from aldehydes and hydrazine, reversibly change colour in response to temperature changes. The structures of all products are ascertained by a combined use of spectroscopic and X-ray diffraction methods. The cytotoxic and antimicrobial activities of all compounds against selected human cancer cell lines and bacterial strains are evaluated.

We compare different routes to prepare hydrazones, quinazolines, and hydrazone-Schiff bases: solution-based, vapor-mediated, mechanochemical, and solid-state melt synthesis.

Rapid and accurate molecular deprotonation energies from quantum alchemy

We assess the applicability of alchemical perturbation density functional theory (APDFT) for quickly and accurately estimating deprotonation energies. We have considered all possible single and double deprotonations in one hundred small organic molecules drawn at random from QM9 [Ramakrishnan et al., JCTC, 2015]. Numerical evidence is presented for 5160 deprotonated species at both HF/def2-TZVP and CCSD/6-31G* levels of theory. We show that the perturbation expansion formalism of APDFT quickly converges to reliable results: using CCSD electron densities and derivatives, regular Hartree-Fock calculations are outperformed at the second or third order for ranking all possible doubly or singly deprotonated molecules, respectively. CCSD single deprotonation energies are reproduced within 1.4 kcal mol^-1 on average within third order APDFT. We introduce a hybrid approach where the computational cost of APDFT is reduced even further by mixing first order terms at a higher level of theory (CCSD) with higher order terms at a lower level of theory only (HF). We find that this approach reaches 2 kcal mol^-1 accuracy in absolute deprotonation energies compared to CCSD at 2% of the computational cost of third order APDFT.

On the supramolecular properties of neutral, anionic and cationic cadmium complexes harvested from dithiolate–polyamine binary ligand systems

Three Cd(ii) complexes [Cd(i-mnt)(DMSO)₂]_n (1), {[Cd(i-mnt)pn]·2H₂O} (2), and [Cd(i-mnt)₃][Cd(tren)₂]₂ (3) harvested from 1,1-dicyanoethylene-2,2-dithiolate (i-mnt²⁻) and polyamine ligand systems have been designed, synthesized and structurally characterized.

New rhenium-tricarbonyl complexes bearing halogen-substituted bidentate ligands: structural, computational and Hirshfeld surfaces studies

The intermolecular interactions in a series of new complexes Re(CO)₃(N,N)X (N,N is a halogen substituted bidentate N–N donor and X is Cl or Br) have been studied crystallographically and computationally. Metal-bound halogens are more effective than carbon-bound halogens in forming significant intermolecular interactions.

Effects of N-oxidation on the molecular and crystal structures and properties of isocinchomeronic acid, its metal complexes and their supramolecular architectures: experimental, CSD survey, solution and theoretical approaches

A series of new coordination complexes bearing H₂pydco, an O-donor ligand, were synthesized and compared to corresponding complexes with H₂pydc. The molecular and supramolecular structures were investigated using crystallography, solution phase and high level DFT studies.

A series of 3D lanthanide coordination polymers decorated with a rigid 3,5-pyridinedicarboxylic acid linker: syntheses, structural diversity, DFT study, Hirshfeld surface analysis, luminescence and magnetic properties

Single crystal X-ray diffraction studies reveal the formation of six new coordination polymers (CPs) with the general formulas [Dy(3,5-pdc)(3,5-pdcH)(H2O)2]n·nH2O (1), [Pr2(3,5-pdc)3(H2O)2]n·2n(H2O) (2), [Sm2(3,5-pdc)3(H2O)3]n·nH2O (3), {[Eu2(3,5-pdc)3(H2O)3(CH3CHO)]n·n[2(H2O)(DMF)]} (4), {[Gd2(3,5-pdc)3 (H2O)2]n·2nH2O} (5) and [Er(3,5-pdc)(adip)0.5(H2O)]n (6) (where 3,5-pdc2- = fully deprotonated; 3,5-pdcH- = partially deprotonated 3,5-pyridinedicarboxylic acid; adip2- = fully deprotonated adipic acid; and DMF = dimethylformamide) by solvothermal self-assembly of lanthanide ions with rigid 3,5-pyridinedicarboxylic acid as a linker and adipic acid as an auxiliary flexible spacer (only coordinated in CP 6). CPs 1 and 2 crystallize in the triclinic P1[combining macron] space group, whereas CPs 3, 4 and 6 crystallize in the monoclinic P21/n, P21/c and C2/c space groups, respectively. CP 5 exhibits the trigonal R3 space group. The 3,5-pdc ligand exhibits eight diverse coordination modes in CPs 1-6, whereas the adipic acid spacer in CP 6 shows only one coordination mode (μ4-κO:κO,O:κO:κO,O). The organic ligands interconnect with metal ions to generate 3D metal-organic frameworks with a variety of intriguing topologies. Theoretical studies, DFT calculations and Hirshfeld surface analysis support the structures adopted by the various CPs. CPs 3 (Sm) and 4 (Eu) emit strong ligand-sensitized characteristic f-f luminescence. Weak ferromagnetic interactions have been studied at low temperatures for CP 1 and CP 5.

Estimation of conventional C-Hπ (arene), unconventional C-Hπ (chelate) and C-Hπ (thiocyanate) interactions in hetero-nuclear nickel(ii)-cadmium(ii) complexes with a compartmental Schiff base

Three new heteronuclear nickel(ii)/cadmium(ii) complexes, [(SCN)(Cl)Cd(L)Ni(DMF)₂] (1), [(SCN)(CH₃CO₂)Cd(L)Ni(CH₃OH)₂] (2) and [(SCN)(Cl)Cd(L)Ni(NH₂CH₂CH₂CH₂NH₂)]_n (3) {where H₂L = N,N'-bis(3-ethoxy-salicylidene)propane-1,3-diamine is a N₂O₄ compartmental Schiff base}, have been synthesized and characterized. The structures of the complexes have been confirmed by single crystal X-ray diffraction studies. In each complex, nickel(ii) is placed in the inner N₂O₂ environment and cadmium(ii) is placed in the outer O₄ compartment of the compartmental Schiff base. Furthermore, the importance of unconventional C-Hπ (chelate) interactions in the solid state of both complexes and C-Hπ (thiocyanate) interaction in complex 2 has been described by means of DFT and MEP calculations and characterized using NCI plots. All complexes show photoluminescence at room temperature upon irradiation by ultraviolet light. The lifetimes of excited states are in the range of 2-6 ns.

A combined experimental and computational study on supramolecular assemblies in hetero-tetranuclear nickel(ii)-cadmium(ii) complexes with N2O4-donor compartmental Schiff bases

Two new hetero-tetranuclear nickel(ii)/cadmium(ii) complexes, a cubane [(CH₃CO₂)₂Ni₂(L¹)₂Cd₂(NCS)₂] (1) and a linear tetramer [(DMSO)₂NiL²Cd(NCS)(μ_1,3-SCN)Ni(DMSO)L²Cd(NCS)₂] (2) {where H₂L¹ = N,N'-bis(3-methoxysalicylidene)propane-1,3-diamine and H₂L² = N,N'-bis(3-ethoxysalicylidene)propane-1,3-diamine are potential octadentate compartmental Schiff bases}, were synthesized and characterized. The structures of both complexes were confirmed by single crystal X-ray diffraction studies. Complex 1 contained a Ni₂Cd₂O₄ cubane core, whereas complex 2 featured an end-to-end thiocyanate-bridged tetranuclear moiety. Furthermore, complex 1 showed C-HH-C interactions, whereas a unique Sπ interaction was observed in complex 2. Theoretical studies were performed using several computational tools such as NBO and AIM analyses. Both complexes showed photoluminescence in DMSO medium at room temperature upon irradiation with ultraviolet light. The lifetimes of the excited states were ∼27 ns.

Structure guided or structure guiding? Mixed carbon/hydrogen bonding in a bis-Schiff base of N-allyl isatin

A supramolecular motif listed as ‘carbon bonded’ or ‘hydrogen bonded’ may have the character of both. We highlight the hybrid character of the non-covalent interaction in a bis-Schiff base of N-allyl isatin by combining theory and experiment.

σ-Hole halogen bonding interactions in a mixed valence cobalt(iii/ii) complex and anti-electrostatic hydrogen bonding interaction in a cobalt(iii) complex: a theoretical insight

Supramolecular interactions in the solid state structures of a mixed valence cobalt(ii/iii) complex and a cobalt(iii) complex have been studied using DFT calculations.

One pot synthesis of two cobalt(iii) Schiff base complexes with chelating pyridyltetrazolate and exploration of their bio-relevant catalytic activities

Two new cobalt(iii) tetrazolato complexes [Co(L¹)(PTZ)(N₃)] (1) and [Co(L²)(PTZ)(N₃)] (2) {where H₂L¹ = 2((3-(methylamino)propylimino)methyl)-6-methoxyphenol, H₂L² = 2((3-(dimethylamino)propylimino)methyl)-6-ethoxyphenol and HPTZ = 5-(2-pyridyl)tetrazole}, have been synthesized via in situ 1,3-dipolar cycloaddition reaction of 2-cyanopyridine and sodium azide in the presence of cobalt(ii) nitrate hexahydrate and respective Schiff bases in the open atmosphere. The structures of both complexes have been confirmed by single crystal X-ray diffraction studies. Features of noncovalent interactions in the solid state of both complexes have been studied by means of DFT and MEP calculations and characterized using Bader's theory of “atoms in molecules” (AIM). These complexes act as biomimetic catalysts promoting the aerobic oxidation of 3,5-di-tert-butylcatechol (3,5-DTBC) to the corresponding o-benzoquinone at room temperature. The reaction follows Michaelis–Menten enzymatic reaction kinetics with turnover numbers of ∼0.030 s⁻¹ in an acetonitrile–methanol (2 : 1) mixture. Both complexes are also reactive towards aerobic oxidation of o-aminophenol in acetonitrile–methanol (2 : 1) with turnover numbers ∼0.095 s⁻¹.

Two cobalt(iii) tetrazolato complexes have been synthesized and characterized. Noncovalent interactions have been analysed by DFT and MEP calculations and characterized using Bader's theory of AIM. Both complexes catalyze the aerial oxidation of 3,5-DTBC and OAPH.

Effect of temperature and ligand protonation on the electronic ground state in Cu(ii) polymers having unusual secondary interactions: a magnetic and catechol oxidase study

Two new polymeric Cu(ii) compounds with significant catecholase activity are described.

Formation of a water-mediated assembly of two neutral copper(ii) Schiff base fragments with a Cu2(NCS)4moiety: exploration of non-covalent C–H⋯π(bimetallo ring) interactions

The energetic features of dimer formation and water encapsulation in an interesting copper(ii) Schiff base complex, [(CuL)₂⊂(H₂O)][Cu₂(μ_1,3-NCS)₂(NCS)₂], have been studied using DFT calculations.

Influence of ancillary ligands on preferential geometry and biomimetic catalytic activity in manganese(III)-catecholate systems: A combined experimental and theoretical study

The present report describes the synthesis and structural characterizations of six new manganese(III) complexes with redox-active tetrachlorocatecholate ligand in the presence of different ancillary ligands (pyridines and imidazole). X-ray crystal structure analysis reveals that the geometry of manganese(III) centres in 1 and 2 is essentially square pyramidal, while it is discrete octahedron in compounds 3-6. These preferential structural diversities in these systems have been critically analysed by theoretical calculations. Remarkably, the characterization of both π⋯π stacking interactions and MnMn bonds in the supramolecular dimeric aggregates in the solid state in 1 and 2 by means of the Bader's theory of "atoms in molecules" (AIM) is quite interesting as that nicely corroborates the experimental fact. All the complexes are active toward the phenoxazinone synthase like activity and the detailed kinetic analysis was performed to get better insight into their catalytic efficiency. Electrochemical property of these complexes as well as different donor property of the ancillary ligands clearly establish that the ease of reduction of the metal centre i.e., the catalytic ability is favoured when the metal centre is bonded to the electron deficient pyridyl systems. EPR spectroscopy and theoretical study are further helpful to get insight into origin of the catalytic activity in these compounds. The present report overall highlights that tuning of the geometry and catalytic activity of manganese(III) complexes with tetrachlorocatecholate ligand can be attained by the introduction of different substitutions in ancillary pyridine ligands.