Host-guest complexes of calix[4]tubes--prediction of ion selectivity by quantum chemical calculations VI

Understanding Ring Puckering in Small Molecules and Cyclic Peptides

The geometry of a molecule plays a significant role in determining its physical and chemical properties. Despite its importance, there are relatively few studies on ring puckering and conformations, often focused on small cycloalkanes, 5- and 6-membered carbohydrate rings, and specific macrocycle families. We lack a general understanding of the puckering preferences of medium-sized rings and macrocycles. To address this, we provide an extensive conformational analysis of a diverse set of rings. We used Cremer-Pople puckering coordinates to study the trends of the ring conformation across a set of 140 000 diverse small molecules, including small rings, macrocycles, and cyclic peptides. By standardizing using key atoms, we show that the ring conformations can be classified into relatively few conformational clusters, based on their canonical forms. The number of such canonical clusters increases slowly with ring size. Ring puckering motions, especially pseudo-rotations, are generally restricted and differ between clusters. More importantly, we propose models to map puckering preferences to torsion space, which allows us to understand the inter-related changes in torsion angles during pseudo-rotation and other puckering motions. Beyond ring puckers, our models also explain the change in substituent orientation upon puckering. We also present a novel knowledge-based sampling method using the puckering preferences and coupled substituent motion to generate ring conformations efficiently. In summary, this work provides an improved understanding of general ring puckering preferences, which will in turn accelerate the identification of low-energy ring conformations for applications from polymeric materials to drug binding.

Theoretical assessment of calix[4]arene-N-β-ketoimine (n=1-4) derivatives: Conformational studies, optoelectronic, and sensing of Cu2+cation

Herein, we have investigated the key functions of the calix[4]arene, abbreviated as CX [1], and designed its several derivatives by substitution of the functional groups. Molecular geometry provides an intuitive understanding of the effect of functional groups on various physical properties. The addition of the N-β-ketoimine (n = 1-4) ligands has a direct effect on the stretching vibration of the H-bonding interaction. The results showed that all molecules possess absorption bands at 190 nm and in the range between 200 and 300 nm assigned to π-π* and n-π* transitions. HOMO-LUMO energy gap of the CX[4]-N-β-ketoimine, one with chemical hardness of 1.62 eV, has been found to be 3.24 eV calculated at B3LYP/6-31 + G(d) level of theory. This finding explains the good kinetic stability of this compound. The large values of electrophilicity make the current molecules as a good electrophilic species. The atom in molecule (AIM) and the reduced density gradient (RDG) analyses showed the type and the strength of the interactions taking place between Cu²⁺ and the β-ketoimine ligands.

Assembling triazolated calix[4]semitubes by means of copper(i)-catalyzed azide–alkyne cycloaddition

Calix[4]arene-based bis(alkynes) and bis(azides) react with each other under thoroughly tuned CuAAC conditions and produce diverse biscalixarene semitube assemblies linked by two triazole units, which are capable of binding transition metal cations.

Wirt-Gast-Komplexe von [bfu.bfu.bfu]: Vorhersage von Ionenselektivitäten mittels quantenchemischer Rechnungen XIII

The CH2–O–C2H4–O–CH2 moieties in Lehn’s cryptand [2.2.2] have been substituted by 2,2′-bifurane groups to get the cryptand [bfu.bfu.bfu]. The ion selectivity of this new cryptand was investigated by DFT calculations (RB3LYP/LANL2DZp, RB3LYP/LACVP*, RBP86/LANL2DZp and RBP86/LACVP*) based on model equations and analysis of the [M ⊂ bfu.bfu.bfu] n+ cryptate structures. The cryptand [bfu.bfu.bfu] is best suited for the alkali cations Na+ and K+, and the alkaline earth cation Sr2+ followed by Ca2+. The cavity of [bfu.bfu.bfu] is thus similar to that in [phen.phen.phen] or [bpy.bpy.bpy]. The selectivity of [bfu.bfu.bfu] is due to the flexibility of the OCCO und CN···NC dihedral angles. The results are independent of the selected DFT methods.

Inorganic reaction mechanisms. A personal journey

This review covers highlights of the work performed in the van Eldik group on inorganic reaction mechanisms over the past two decades in the form of a personal journey. Topics that are covered include, from NO to HNO chemistry, peroxide activation in model porphyrin and enzymatic systems, the wonder-world of Ru^III(edta) chemistry, redox chemistry of Ru(iii) complexes, Ru(ii) polypyridyl complexes and their application, relevant physicochemical properties and reaction mechanisms in ionic liquids, and mechanistic insight from computational chemistry. In each of these sections, typical examples of mechanistic studies are presented in reference to related work reported in the literature.

Experimental and quantum chemical study оn the DNA/protein binding and the biological activity of a rhodium(iii) complex with 1,2,4-triazole as an inert ligand

A rhodium(iii) complex with 1,2,4-triazole and a pincer type nitrogen-donor ligand was synthesized, and its interaction with biomolecules was examined.

Synthesis of Camphor-Derived Bis(pyrazolylpyridine) Rhodium(III) Complexes: Structure-Reactivity Relationships and Biological Activity

Two novel rhodium(III) complexes, namely, [Rh^III(X)Cl₃] (X = 2 2,6-bis((4 S,7 R)-7,8,8-trimethyl-4,5,6,7-tetrahydro-1 H-4,7-methanoindazol-3-yl)pyridine or 2,6-bis((4 S,7 R)-1,7,8,8-tetramethyl-4,5,6,7-tetrahydro-1 H-4,7-methanoindazol-3-yl)pyridine), were synthesized from camphor derivatives of a bis(pyrazolylpyridine), tridentate nitrogen-donor chelate system, giving [Rh^III(H₂L*)Cl₃] (1a) and [Rh^III(Me₂L*)Cl₃] (1b). A rhodium(III) terpyridine (terpy) ligand complex, [Rh^III(terpy)Cl₃] (1c), was also synthesized. By single-crystal X-ray analysis, 1b crystallizes in an orthorhombic P2₁2₁2₁ system, with two molecules in the asymmetric unit. Tridentate coordination by the N,N,N-donor localizes the central nitrogen atom close to the rhodium(III) center. Compounds 1a and 1b were reactive toward l-methionine (l-Met), guanosine-5'-monophosphate (5'-GMP), and glutathione (GSH), with an order of reactivity of 5'-GMP > GSH > l-Met. The order of reactivity of the Rh^III complexes was: 1b> 1a > 1c. The Rh^III complexes showed affinity for calf thymus DNA and bovine serum albumin by UV-vis and emission spectral studies. Furthermore, 1b showed significant in vitro cytotoxicity against human epithelial colorectal carcinoma cells. Since the Rh^III complexes have similar coordination modes, stability differences were evaluated by density functional theory (DFT) calculations (B3LYP(CPCM)/LANL2DZp). With (H₂L*) and (terpy) as model ligands, DFT calculations suggest that both tridentate ligand systems have similar stability. In addition, molecular docking suggests that all test compounds have affinity for the minor groove of DNA, while 1b and 1c have potential for DNA intercalation.

New monofunctional platinum(II) and palladium(II) complexes: Studies of the nucleophilic substitution reactions, DNA/BSA interaction, and cytotoxic activity

Four new complexes [Pd(H₂L^tBu)Cl]Cl (Pd1), [Pt(H₂L^tBu)Cl]Cl (Pt1), [Pd(Me₂L^tBu)Cl]Cl (Pd2) and [Pt(Me₂L^tBu)Cl]Cl (Pt2) (where H₂L^tBu = 2,6-bis(5-(tert-butyl)-1H-pyrazol-3-yl)pyridine and Me₂L^tBu = 2,6-bis(5-(tert-butyl)-1-methyl-1H-pyrazol-3-yl)pyridine) were synthesized and characterized by elemental microanalysis, IR, ¹H NMR and ESI-MS methods. The reactivity of complexes towards thiourea (Tu), l-methionine (l-Met), l-cysteine (l-Cys) and guanosine-5'-monophosphate (5'-GMP) was investigated. The obtained order was established as follows: Tu > l-Cys > l-Met > 5'-GMP. Complexes Pd1 and Pt1, that contain H₂L^tBu as chelator, showed higher reactivity towards biomolecules than those with Me₂L^tBu. The interaction of complexes with calf thymus DNA (CT-DNA) and bovine serum albumin (BSA) was studied by UV-Vis and fluorescence spectroscopy. The results have shown that complexes can bind to DNA exhibiting high binding constants (K_b = 10⁴ M^-1). Obtained results during the examination of competitive reaction with ethidium bromide (EB) showed that complexes can replace EB-bound DNA. High values of binding constants indicate good binding affinity of complexes towards BSA. We evaluated the stability differences between complexes based on terpy as well as H₂L^tBu/Me₂L^tBu by DFT calculations (B3LYP(CPCM)/LANL2DZp), showing that both tridentate ligand systems lead to complexes of similar stability. The results of biological testing showed that all complexes exert moderate to high selective cytotoxicity, inducing apoptosis and autophagy in HeLa and PANC-1 tumor cell lines. Pd1 exhibited the strongest cytotoxic effect. Finally, cell cycle analysis showed that in HeLa cells Pd1, Pd2 and Pt1 induced accumulation of cells in S phase, whereas in PANC-1 cells Pd2 and Pt1 induced G2/M cycle arrest and Pd1 induced G0/G1 arrest.

Complexation of some alkali and alkaline earth metal cations by macrocyclic compounds containing four pyridine subunits – a DFT study

Tetradentate pyridine-based macrocyclic compounds offer useful ligands capable of efficient and selective complexation of M = Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺and Ca²⁺.