Inclusion complexes of β-cyclodextrin with pyrazinamide and piperazine: Crystallographic and theoretical studies

The inclusion complexes of β-cyclodextrin (β-CD) with pyrazinamide (PYA) and piperazine (PIZ) have been investigated both in the solid phase by single-crystal X-ray diffraction analysis and in the gas phase by semi-empirical PM3 calculation. In the crystalline phase, the disordered PYA and PIZ molecules are entirely embedded in the β-CD cavity. The PYA pyrazine-centre displaces upwards by 1.15(1) Å from the β-CD plane, whereas the PIZ centre shifts downwards by 0.76(1) Å from the β-CD plane. The inclusion scenario changed in the gas phase. Two inclusion geometries of the PYA molecule are comparatively stable with binding energies of ? 22.28 and ? 25.29 kJ mol^? 1: the pyrazine centre shifts upwards by 0.5 Å and downwards by 2.0 Å from the β-CD plane. The PIZ molecule positioning at 2.0 Å below the β-CD plane gives a more stable inclusion complex than does the PYA molecule by 22–25 kJ mol^? 1.

Structural distinction of the β-CD–PYA and β-CD–PIZ inclusion complexes in the solid phase (by X-ray crystallography) and gas phase (by PM3 calculation) is a paradigm of the CD conformational flexibility, the induced-fit mechanism and the dynamics of the inclusion process.     

Crystallographic and theoretical studies of 4,4′-dimethyl-7,7′-bi([1,2,5]thiadiazolo[3,4-b]pyridylidene)–chloranilic acid (1/1) with intermolecular O–H···N hydrogen bonds and S···O heteroatom interactions

Abstract  The molecular and crystal structure of a 1:1 co-crystal of 4,4′-dimethyl-7,7′-bi([1,2,5]thiadiazolo[3,4-b]pyridylidene)–chloranilic acid, (1), has been determined by X-ray diffraction at the monoclinic space group P2₁/c with cell parameters of a = 8.422(6), b = 7.343(4), c = 16.112(7) ?, β = 104.988(8)°, V = 962.5(10) ?³ and Z = 2. In the crystal structure, two components connect via the intermolecular O–H···N hydrogen bonds [2.804(4) ?] and S···O heteroatom interaction [2.945(3) ?] with R ₂ ²(7) couplings to form a unique and infinite one-dimensional supramolecular tape structure. The calculations of (1) at the HF/6-31G(d), MP2/6-31G(d), and B3LYP/6-31G(d) levels can almost reproduce X-ray geometry. In addition, the distances of the intermolecular O–H···N and S···O interactions by MP2/6-31G(d) and B3LYP/6-31G(d) levels agree well with those in the crystal. The calculated binding energies corrected BSSE and ZPE are −4.487 (HF), −7.473 (MP2), and −5.640 (B3LYP) kcal/mol. The results suggest that the complex (1) is very stable and the dispersion interaction is significantly important for the attractive intermolecular interaction in (1). The NBO analysis has revealed that the n(N) → σ*(O–H) interaction gives the strongest stabilization to the system and the major interaction for the intermolecular S···O contact is n(O) → σ*(S–N). Index Abstract  In the crystal structure of the title compound, the molecules are linked by intermolecular O–H···N hydrogen bonds and short S···O heteroatom interactions with R ₂ ²(7) couplings to construct a unique and infinite one-dimensional supramolecular tape structure.      

1-benzoyl-2-(2-naphthyl)-selenourea

During our synthesis of N-benzoyl-N'-aryl selenourea derivatives, we isolated the title compound. One of them was selected optically for the diffraction study. The crystal belongs to the Monoclinic space group P21/n, Mr = 353.27, a = 11.073(1)? , b = 5.745(1) ?, c = 24.356(5) ?, β = 92.10 (1) , V = 1548.3 (4) ?3, Z = 4, Dx=1.515 Mg/m3,λ(Mo Kα)=0.71073 ?,θ = 1.67-25,μ o = 2.428 mm-1 , T = 296 (2) K. View of the molecule showing the labeling of the non-H atoms are described as: The se…     

Time-resolved fluorescence of α-(9-anthryl)-ω-(1-naphthyl)-oligosilanes: intramolecular electronic energy and charge transfer through π-π and σ-π interactions

The photophysical properties of a series of α,ω-diaryloligosilanes: (9-anthryl)-(SiMe₂)_n-(1-naphthyl) (1-4, and 6), n=1, 2, 3, 4, and 6, were investigated. For n?2, the intramolecular exciplex emission was observed in cyclohexane. For the stationary and the time-resolved fluorescence (TR-FL) measurements, the excitation of the naphthyl moiety showed a very efficient intramolecular energy transfer to the anthryl moiety, thus only fluorescence from the anthryl moiety was observed. In the case of 4 and 6, a charge-transfer (CT) emission was observed in acetonitrile. Then TR-FL of 6 revealed that the intramolecular-energy transfer from the naphthyl to anthryl moieties is faster than the CT.     

A Practical Synthesis of (S)-(+)-2-(6-methoxyl-2-naphthyl) propionic Acid

a-Arylpropionic acids are an important class of non-steroidal anti-inflammatory agents1,2. The therapeutic efficacy of this class of drugs is well demonstrated by the introduction and extensive use of more than a dozen compounds exemplified by ibuprofen, naproxen, ketoprofen and flurbiprofen etc. However, in recent years the use of enantiomerical pure drugs in chemotherapy is becoming almost mandatory for enhancing specificity of drug action and reducing the toxicity. This awareness led to …     

A structural analysis of the complexes of (S,S)-dimethylpyridino-18-crown-6 with (R) and (S)-[α-(1-naphthyl)ethyl]ammonium perchlorate by NMR techniques and molecular modeling

Significant - interaction is found in the complexes of (S, S)-dimethylpyridino-18-crown-6 with (R)- and (S)-[-(1-naphthyl)ethyl]ammonium perchlorate. This finding is supported by the¹H NOESY NMR spectral technique, greater chemical shift changes of aromatic protons in both host and guest molecules upon complexation, and by molecular mechanics calculations. Because of the flexibility of the ligand, the tripod hydrogen bonding causes¹³C relaxation times of all periphery carbons to decrease without significant selectivity. Rotational energy barrier calculations of the methyl groups of the complexed ligand also show that the (S, S)-host-(R)-guest is the more stable complex.     

Spectroscopic (fluorescence, 1D-ROESY) and theoretical studies of the thiabendazole and β-cyclodextrin inclusion complex

The inclusion complex between the anti-helminthic drug thiabendazole (TBZ) and the β-cyclodextrin (βCD) was characterized in solution using fluorescence and ¹H-Nuclear Magnetic Resonance spectroscopy and studied theoretically by semi empirical PM3 and density functional theory (DFT) quantum mechanical calculations. Thermodynamic stability associated with the formation of the TBZ:βCD inclusion complex in aqueous solution was determined treating the drug’s fluorescence enhancement in the presence of cyclodextrin by a non-linear model, which indicated a moderate host–guest affinity at equilibrium (K 150 ± 31 at 25 °C). Its supramolecular structure in solution was studied through the 1D-ROESY NMR experiment, which produced evidence that the guest molecular encapsulation occurs preferably via the drug’s benzimidazole group. Theoretical study employing molecular optimization with the semi empirical PM3 method provided two energetic-equivalent complex structures that are in accordance with the NMR experimental evidences. Single point energy calculations with DFT at the B3LYP/6-31G (d,p) level suggest the most stable structure of the inclusion complex and further comprehension on the interactions and conformational strains involved in its formation.     

Experimental and theoretical studies of Palladium-hydrazide complexes’ interaction with DNA and BSA,in vitro cytotoxicity activity and plasmid cleavage ability

New palladium complexes with general formula trans-[Pd(L)₂(OAc)₂] (1,2), (L = Benzhydrazide and 2-Furoic hydrazide) have been synthesized and characterized with various methods including elemental analysis, FT-IR, ¹HNMR and mass spectroscopy. Afterward their interactions with bovine serum albumin and calf thymus deoxyribonucleic acid have been investigated by UV–vis absorption, fluorescence emission and circular dichroism spectroscopy. Also, site‐selective replacement experiments with site probes have been carried out. Analysis of fluorescence spectrum indicated static quenching mechanism. Spectroscopic measurements for DNA binding showed the groove binding to DNA for both complexes. Furthermore, cytotoxicity studies of complexes and cis-platin have been done against colon carcinoma (CT26) and breast cancer (4T1) cell lines. Evaluation of complexes (1) and (2) on induction of apoptosis in CT26 cells has been done. Finally, plasmid cleavage ability of (1) and (2) was investigated by gel electrophoresis that indicate the more activity of (1) than (2).     

The use of (S)-(−)-1-(1-naphthyl)ethylamine as a resolving agent for α-methoxy fatty acids

A general method was developed for the diastereoselective resolution of α-methoxy fatty acids utilizing (S)-(−)-1-(1-naphthyl)ethylamine as resolving agent. The diastereomeric amides can be easily separated by silica gel column chromatography and/or capillary gas chromatography, thus allowing for a preparative and analytical method for determining the enantiomeric purity of naturally occurring and/or synthetic α-methoxy fatty acids. The first synthesis of the naturally occurring (R)-2-methoxyhexadecanoic acid was also accomplished in four steps starting from commercially available (±)-2-hydroxyhexadecanoic acid.     

Para-selective nitration of bromobenzene catalyzed by Hβ zeolite with NO2 and its theoretical studies

Research on Chemical Intermediates - A novel heterogeneous catalytic system was developed for the preparation of para-nitrobromobenzene (p-NBr) with nitrogen dioxide (NO2) as nitrating agent in the...     

Synthesis, spectroscopic studies of new water-soluble Co(II) and Cu(II) macrocyclic complexes of 4,15-bis(2-hydroxyethyl)-2,4,6,13,15,17-hexaazatricyclodocosane: their interaction studies with calf thymus DNA and guanosine 5′ monophosphate

New water soluble Co(II) 1, Ni(II) 2 and Cu(II) 3 complexes of 4,15-bis(2-hydroxyethyl)-2,4,6,13,15,17-hexaazatricyclodocosane Co(II) were synthesized and characterized by various techniques, viz. elemental analysis, conductivity measurements, infrared, electronic, ESI-MS, ¹H and ¹³C NMR spectroscopy. Molar conductance measurements in aqueous solution showed that complexes 1, 2 and 3 are ionic in nature. On the basis of spectroscopic data, a square planar geometry was assigned to the complexes involving four N-atoms of the two cyclohexane moieties. Interaction studies of 1 and 3 with CT-DNA were carried using UV/Visible absorption spectroscopy, fluorescence spectrophotometry, cyclic voltammetry and viscosity measurements. Absorption spectral traces reveal 27.7 and 23.3% hyperchromism for complexes 1 and 3, respectively indicative of strong binding to CT-DNA. These results were authenticated by fluorescence quenching experiments and viscosity measurements. The intrinsic binding constants K _b of 1 and 3 are 2.94 × 10⁴ and 2.71 × 10⁴ M^?1, respectively. Early transition metals show preference for O6 position while later ones copper and cobalt prefer N7 position of DNA base guanine. To validate this hypothesis, interaction studies of copper (II) and cobalt (II) complexes were carried out with 5′GMP, which revealed electrostatic interactions are more favored along with hydrogen bonding than coordinate covalent interaction to N7 position of guanine.     

(R)- and (S)-α-Methoxy-(1-naphthyl) acetic acids: resolution by fractional crystallization and use for the NMR stereochemical analysis of alkylsulfoxides

Both enantiomers of α-methoxy-(1-naphthyl) acetic acid (1-NMA) were conveniently obtained via fractional crystallization using the enantiomers of 1-(1-naphthyl) ethylamine. 1-NMA was shown to be very powerful for differentiating the enantiomeric signals of quasi-symmetrical aliphatic sulfoxides.     

Dispersion interactions of carbohydrates with condensate aromatic moieties: theoretical study on the CH-π interaction additive properties

In this article we present the first systematic study of the additive properties (i.e. degree of additivity) of the carbohydrate-aromatic moiety CH-π dispersion interaction. The additive properties were studied on the β-D-glucopyranose, β-D-mannopyranose and α-L-fucopyranose complexes with the naphthalene molecule by comparing the monodentate (single CH-π) and bidentate (two CH-π) complexes. All model complexes were optimized using the DFT-D approach, at the BP/def2-TZVPP level of theory. The interaction energies were refined using single point calculations at highly correlated ab initio methods at the CCSD(T)/CBS level, calculated as E + (E(CCSD(T))-E(MP2))(Small Basis). Bidentate complexes show very strong interactions in the range from -10.79 up to -7.15 and -8.20 up to -6.14 kcal mol(-1) for the DFT-D and CCSD(T)/CBS level, respectively. These values were compared with the sum of interaction energies of the appropriate monodentate carbohydrate-naphthalene complexes. The comparison reveals that the bidentate complex interaction energy is higher (interaction is weaker) than the sum of monodentate complex interaction energies. Bidentate complex interaction energy corresponds to 2/3 of the sum of the appropriate monodentate complex interaction energies (averaging over all modeled carbohydrate complexes). The observed interaction energies were also compared with the sum of interaction energies of the corresponding previously published carbohydrate-benzene complexes. Also in this case the interaction energy of the bidentate complex was higher (i.e. weaker interaction) than the sum of interaction energies of the corresponding benzene complexes. However, the obtained difference is lower than before, while the bidentate complex interaction energy corresponds to 4/5 of the sum of interaction energy of the benzene complexes, averaged over all structures. The mentioned comparison might aid protein engineering efforts where amino acid residues phenylalanine or tyrosine are to be replaced by a tryptophan and can help to predict the changes in the interactions. The observed results also show that DFT-D correctly describes the CH-π interaction energy and their additive properties in comparison to CCSD(T)/CBS calculated interaction energies. Thus, the DFT-D approach might be used for calculation of larger complexes of biological interest, where dispersion interaction plays an important role.     

Comeplexes of 1-(2′-hydroxybenzyl)-2-(2′-hydroxyphenyl)-benzimidazole with U(VI) and Ce(IV)

Some new U(VI) and Ce(IV) complexes of 1-(2′-hydroxybenzyl)-2-(2′-hydroxyphenyl)-benzimidazole have been prepared and characterized by spectrg magnetic and conductance studies. IR spectral data suggests that the ligand in all the complexes is monodenate through the tertiary nitrogen and that the phenolic oxygen is free from coordination. Conductivity measurements indicate that the nitrate and acetate complexes of U(VI) are non-electrolytes, whereas the nitrate complex of Ce(IV) is a 1:1 electrolyte.     

Reactive quenching of OH A (2)Σ(+) by O(2) and CO: Experimental and nonadiabatic theoretical studies of H- and O-atom product channels

The outcomes following collisional quenching of electronically excited OH A (2)Σ(+) by O(2) and CO are examined in a combined experimental and theoretical study. The atomic products from reactive quenching are probed using two-photon laser-induced fluorescence to obtain H-atom Doppler profiles, O ((3)P(J)) atom fine structure distributions, and the relative yields of these products with H(2), O(2), and CO collision partners. The corresponding H-atom translational energy distributions are extracted for the H + O(3) and H + CO(2) product channels, in the latter case revealing that most of the available energy is funneled into internal excitation of CO(2). The experimental product branching ratios show that the O-atom producing pathways are the dominant outcomes of quenching: the OH A (2)Σ(+) + O(2) → O + HO(2) channel accounts for 48(3)% of products and the OH A (2)Σ(+) + CO → O + HCO channel yields 76(5)% of products. In addition, quenching of OH A (2)Σ(+) by O(2) generates H + O(3) products [12(3)%] and returns OH to its ground X (2)Π electronic state [40(1)%; L. P. Dempsey, T. D. Sechler, C. Murray, and M. I. Lester, J. Phys. Chem. A 113, 6851 (2009)]. Quenching of OH A (2)Σ(+) by CO also yields H + CO(2) reaction products [26(5)%]; however, OH X (2)Π (v(") = 0,1) products from nonreactive quenching are not observed. Theoretical studies characterize the properties of energy minimized conical intersections in four regions of strong nonadiabatic coupling accessible from the OH A (2)Σ(+) + CO asymptote. Three of these regions have the O-side of OH pointing toward CO, which lead to atomic H and vibrationally excited CO(2) products and∕or nonreactive quenching. In the fourth region, energy minimized points are located on a seam of conical intersection from the OH A (2)Σ(+) + CO asymptote to an energy minimized crossing with an extended OH bond length and the H-side of OH pointing toward CO in a bent configuration. This region, exoergic with respect to the reaction asymptote, is likely to be the origin of the dominant O + HCO product channel.     

Studies on the crystal structure and characterization of N-(4-acetylphenyl)-N’-(2-nitrobenzoyl)-thiourea

N-(4-acetylphenyl)-N′-(2-nitrobenzoyl)-thiourea has been synthesized in high yield under PEG-400 as the phase-transfer catalyst and its the compound structure was determined by single crystal X-ray diffraction. The compound is also a considerable plant-growth regulator. In addition, the compound L exhibited selective recognition for Hg²⁺ over other metals ions such as Ag⁺, Ca²⁺, Co²⁺, Ni²⁺, Cd²⁺, Pb²⁺, Zn²⁺, Cr³⁺, and Mg²⁺ in DMSO solutions.     

Cation···π interactions: QTAIM and NBO studies on the interaction of alkali metal cations with heteroaromatic rings

The cation···π interactions of alkali metal cations (Li⁺, Na⁺, and K⁺) with five-membered heteroaromatic rings [furan(C₄H₄O), thiophene(C₄H₄S), pyrrole(C₄H₅N)] were examined by high level ab initio calculations, to investigate the different roles of C₄H₄O, C₄H₄S, and C₄H₅N as the electron donor, the influential factors that affect these interactions, the nature of this kind of cation···π interaction, and to determine topological and energetical properties to characterize these interactions. The sulfur atom in C₄H₄S plays a certain role in the cation···π interactions except the C–C π bond, which is different from C₄H₄O and C₄H₅N. The size of cation and the character of heteroaromatic ring are two influential factors that affect the cation···π interactions. The studied cation···π interactions can be classified as “closed-shell” and noncovalent interactions. The electron density and its Laplacian at the bond critical points and ring critical points generated upon complexation are useful measurements for the strength of cation···π interactions.