Host–guest interactions between octa acid and cations/nucleobases

The nature of host–guest interaction in between octa acid cavitand (OA) and some representative cationic guests (Li⁺, Na⁺, K⁺, Be⁺², Mg⁺², Ca⁺², Li₃O⁺, Na₃O⁺, K₃O⁺) as well as heterocyclic moieties like [adenine (A), guanine (G), cytosine (C), thymine (T), uracil (U), and tetrathiafulvalene (TTF)] has been examined with the aid of density functional theory (DFT)‐based computations. Thermochemical results indicate that all the guests bind with OA in a thermodynamically favorable fashion at 298.15 K temperature and one atmospheric pressure. OA exhibits high selectivity in binding the lighter cations/metal cluster cations as compared to the heavier congeners along each given series. Moreover, OA exhibits enhanced affinity as well as selectivity in binding A/G/TTF molecules as compared to C/T/U. Noncovalent interaction and energy decomposition analyses reveal that in addition to the van der Waals interaction, significant contribution from electrostatic as well as orbital interactions dictate the outcome in all the host–guest complexes. Time dependent DFT calculations have been carried out to assess the role of the guests in tuning the electronic properties as well as absorption spectrum of OA. © 2017 Wiley Periodicals, Inc.     

Performance of DFT hybrid functionals in the theoretical treatment of H‐bonds: Analysis term‐by‐term

The performance of DFT to reproduce noncovalent interactions like H‐bonds was assessed. Three DFT hybrid functionals (B3LYP, BHandHLYP from Jaguar5.5, and BHandHLYP from G03) were used to calculate the interaction energies and H‐bond distances of several host–guest complexes theoretically designed. Two reference systems (whose experimental data were available) were also calculated at the same levels of theory. In all the cases B3LYP and BHandHLYP from G03 gave rather the same results of interaction energy and distances, whereas the functional BHandHLYP from Jaguar5.5 overestimated the interaction energies and underestimated the H‐bond distances. Considering the construction of each functional, the terms responsible for such differences are the gradient correction to the exchange functional (Becke88) and the correlation functional (VWN, LYP) and not the Hartree–Fock contribution. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Selective complexation of alkali metal ions and nanotubular cyclopeptides: a DFT study

A density functional theory based on interaction of alkali metal cations (Li⁺, Na⁺, K⁺, Rb⁺ and Cs⁺) with cyclic peptides constructed from 3 or 4 alanine molecule (CyAla3 and CyAla4), has been investigated using mixed basis set (C, H, O, Li⁺, Na⁺ and K⁺ using 6-31+G(d), and the heavier cations: Rb⁺ and Cs⁺ using LANL2DZ). The minimum energy structures, binding energies, and various thermodynamic parameters of free ligands and their metal cations complexes have been determined with B3LYP and CAM-B3LYP functionals. The order of interaction energies were found to be Li⁺ > K⁺ > Na⁺ > Rb⁺ > Cs⁺ and Li⁺ > Na⁺ > K⁺ ? Rb⁺ > Cs⁺, calculated at CAM-B3LYP level for the M/CyAla3 and M/CyAla4 complexes, respectively. Their selectivity trend shows that the highest cation selectivity for Li⁺ over other alkali metal ions has been achieved on the basis of thermodynamic analysis. The main types of driving force host–guest interactions are investigated, the electron-donating O offers lone pair electrons to the contacting LP* of alkali metal cations.     

DFT study of the cryptand and benzocryptand and their complexes with alkali metal cations: Li+, Na+, K+

In the present work, a theoretical study of the cryptand 4, 7, 13, 16, 21, 24-hexaoxa-1, 10- diazabicyclo [8,8,8] hexacosan (the named [222]) and the cryptand 5, 6-benzo-4, 7, 13, 16, 21, 24-hexaoxa-1, 10-diazabicyclo [8, 8, 8] hexacosan (the nemed [222B]) had been done using density functional theory (DFT) with B3LYP/6-31G* method in order to obtain the electronic and geometrical structure of the cryptands and their complexes with alkali metal ions: Li(+), Na(+), and K(+). The nucleophilicity of cryptands had been investigated by the Fukui function. For complexes, the match between cation and cavity size, the status of interaction between alkali metal ions and donor atoms in the cryptands and the rigidity of the cryptands had been analyzed through the other calculated parameters. In addition, the enthalpies of complexation reaction and cation exchange reaction had been studied by the calculated thermodynamic data. The calculated results are in a good agreement with the experimental data for the complexes.     

Impact of divalent metal cations on the catalysis of peptide bonds: a DFT study

Within the ATP-grasp family of enzymes, divalent alkaline earth metals are proposed to chelate terminal ATP phosphates and facilitate the formation of peptide bonds. Density functional theory methods are used to explore the impact of metal ions on peptide bond formation, providing an insight into experimental metal substitution studies. Calculations show that alkaline earth and transition metal cations coordinate with an acylphosphate reactant and aid in the separation of the phosphate leaving group. The critical biochemical reaction is proposed to proceed through the formation of a six-membered transition state in the relatively nonpolar active site of human glutathione synthetase, an ATP-grasp enzyme. While the identity of the metal ion has a moderate impact on the thermodynamics of peptide bond formation, kinetic differences are much sharper. Simulations indicate that several transition metal ions, most notably Cu²⁺, may be particularly advantageous for catalysis. The detailed mechanistic study serves to elucidate the vital role of coordination chemistry in the formation of peptide bonds.     

A theoretical study of the sulfenate–sulfoxide rearrangement. Effect of the hydrogen bond complexation

A DFT study of the thermal and radical sulfenate–sulfoxide rearrangement of derivatives of 3‐propenyl sulfoxide has been carried out. The effect of the substitution and hydrogen bond complexation has been analyzed. The results show that without external factors the radical breakdown path is the one preferred by the alkyl and aromatic derivatives while the unsubstituted system proceeds preferentially through a two‐step series of [1,3]‐ and [2,3]‐sigmatropic shifts. The inclusion of a hydrogen bond donor interacting with the oxygen atom increases the stability of all the species except the radical and the final products. Thus, in the dimethyl derivative the radical and two‐step processes present similar limiting steps. The analysis of the electron density of the systems provides some relationships between the properties at the bond critical point and the interatomic distances for the S···C and H···O cases. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2391–2397, 2010     

The effect of donor atoms on the complexation of alkali cations with spherands: A density functional investigation

Spherands are highly preorganized hosts composed of methoxy 1, fluoro 2, and cyano 3 benzene units attached to one another at their 2,6‐positions. Density functional theory calculations were used to investigate the complexation between these spherands and alkali metal ions (Li⁺, Na⁺, and K⁺) to understand the intrinsic factors affecting cation complexation. A comparison of binding energies for these spherands shows that, this order O? Me ? F ? CN. Although anisyl units are basically poor ligands for metal ions, the rigid placements of their oxygen during synthesis rather than during complexation are undoubtedly responsible for the enhanced binding and selectivity of the spherand. The ion–dipolar moiety interactions are found to be the main factors affecting the preference of external binding in the CN‐spherands. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

DFT study on the selective complexation of B12N12 nanocage with alkali metal ions

Density functional theory (DFT) calculations were applied at the M05-2X/6-311++G(d,p) level of the theory to investigate the interaction of the B₁₂N₁₂ nanocage (BN) and alkali metal ions (Li⁺, Na⁺, K⁺, Rb⁺ and Cs⁺) in the gas phase and in water. On the basis of the results, BN nanocage is able to form a selective complex with Li⁺. Water, as a solvent, reduces the stability of the metal ion-BN complexes in comparison with the gas phase. Natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) analyses, reveal that the electrostatic interaction between the BN and metal ions can be considered as the driving force for complex formation in which the role of water is of significance. Density of states (DOSs) analysis of the BN nanocage structure in the presence of different metal ions showed a noticeable change in the frontier orbitals, especially in the gas phase, and Fermi level shifting toward the lower values.     

Theoretical analyses of the host–guest interaction within chlorine hydrate

The host–guest interaction is necessary for the stabilization of hydrates. Using Density Function Theory methods, the host–guest interaction within an unconventional chlorine hydrate was investigated, in combination with typical noncovalent analyses. The host–guest interaction energy was predicted to be as high as 17.51 kcal/mol, which was stronger than the typical van der Waals (vdW) interaction, due to an involvement of up to 20 Cl…O interactions. Polarization and dispersion energies made up the main contribution to the total interaction energy. Further visualization of the host–guest interaction validated, together with the general Cl…O interaction, another vdW interaction between the guest‐Cl atom and the five‐membered H₂O cluster. Isosurfaces associated with two patterns of vdW interactions yielded a better “fit” in shape, suggesting their cooperativity in stabilizing the steric configuration. The σ‐region on the guest‐Cl atom was verified to regulate the electron redistribution over the molecular space. These results are useful for understanding specific halogen behavior, and the origin and nature of host–guest interaction in hydrates. © 2013 Wiley Periodicals, Inc.     

A Halogen‐Bonding Bis‐triazolium Rotaxane for Halide‐Selective Anion Recognition

A systematic study on the anion‐binding properties of acyclic halogen‐ and hydrogen‐bonding bis‐triazolium carbazole receptors is described. The halide‐binding potency of halogen‐bonding bis‐iodotriazolium carbazole receptors was found to be far superior to their hydrogen‐bonding bis‐triazolium‐based analogues. This led to the synthesis of a mixed halogen‐ and hydrogen‐bonding rotaxane host containing a bis‐iodotriazolium carbazole axle component. The rotaxane’s anion recognition properties, determined by ¹H NMR titration experiments in a competitive aqueous solvent mixture, demonstrated the preorganised halogen‐bonding interlocked host cavity to be halide‐selective, with a strong binding affinity for bromide.     

Synthesis and DFT study of the spectral behavior of new 4‐hydroxycoumarins

4‐Hydroxycoumarins are compounds with a lot of applications as drugs and herbicides. They have very interesting spectral and chemical properties, which are investigated theoretically and experimentally. Some new 4‐hydroxycoumarins with arylydene‐β‐ketoester or arylydene‐2,4‐pentanedione side chain were synthesized by two step synthetic scheme. Their structure was characterized by UV–vis, IR, and ¹H NMR methods. The spectral behavior of the optimized structures of these compounds was reproduced by the hybrid DFT methods B3LYP and B3P86 with 6‐31G** and aug‐cc‐pVDZ basis sets. Electronic excited states and vibrational frequencies were calculated. HF method was also used for comparison, because of the lack of electronic correlation. The theoretical spectra were compared with the experimental ones. A lot of compounds show good agreement between experimental and some of the theoretical data, especially obtained by aug‐cc‐pVDZ basis set. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Pillar[n]MaxQ: A New High Affinity Host Family for Sequestration in Water

We report the synthesis, X‐ray crystal structure, and molecular recognition properties of pillar[n]arene derivative P[6]AS , which we refer to as Pillar[6]MaxQ along with analogues P[5]AS and P[7]AS toward guests 1 – 18 . The ultratight binding affinity of P[5]AS and P[6]AS toward quaternary (di)ammonium ions renders them prime candidates for in vitro and in vivo non‐covalent bioconjugation, for imaging and delivery applications, and as in vivo sequestration agents.     

Host–Guest Chemistry of a Bis‐Calix[4]pyrrole Derivative Containing a trans/cis‐Switchable Azobenzene Unit with Several Aliphatic Bis‐Carboxylates

The azobenzene unit used as a photochemically and thermally switchable linker in the assembly of a bis‐calix[4]pyrrole receptor provides a means to modulate the binding of bis‐carboxylates of significant biological importance in cancer research. Conversely, the complexation of different bis‐anionic guests has significant kinetic effects on both the photochemical and thermal trans/cis isomerization of the azobenzene unit.     

Supramolecular complexation of alkali cations through mechanochemical reactions between crystalline solids

The organometallic zwitterion [Co(III)(eta(5)-C(5)H(4)COOH)(eta(5)-C(5)H(4)COO)] reacts quantitatively as a solid polycrystalline phase with a number of crystalline alkali salts MX (M = K(+), Rb(+), Cs(+), NH(4) (+); X = Cl(-), Br(-), I(-), PF(6)(-), although not in all cation/anion permutations) to afford supramolecular complexes of the formula [Co(III)(eta(5)-C(5)H(4)COOH)(eta(5)-C(5)H(4)COO)](2).M(+)X(-). In some cases, the mechanochemical complexation requires kneading of the two solids with a catalytic amount of water. The characterization of the solid-state products has been achieved by a combination of X-ray single-crystal and powder-diffraction experiments. The hydrogen-bonding interactions have been investigated by solid-state NMR spectroscopy. The mechanochemical reactions imply a profound solid-state rearrangement accompanied by breaking and forming of O-H...O hydrogen-bonding interactions between the organometallic molecules. All compounds could also be obtained by solution crystallization of the inorganic salts in the presence of the organometallic unit. The solid-state complexation of alkali cations by the organometallic zwitterion has been described as a special kind of solvation process taking place in the solid state.     

A Metal–Organic Framework with a Pore Size/Shape Suitable for Strong Binding and Close Packing of Methane

Much effort has been devoted to develop new porous structures for methane storage. We report a new porous coordination framework showing exceptional methane uptakes (e.g. 263 v/v at 298 K and 65 bar) and adsorption enthalpies (21.6 kJ mol^?1) as high as current record holders functionalized by open metal sites. Computational simulations demonstrated that the hierarchical pore structure consisting of single‐wall nanocages has suitable sizes/shapes and organic binding sites to enforce not only strong host–methane and methane–methane interactions but also dense packing of methane molecules.     

The Structure of the Pyridine Complex of p-tetrakis(phenylazo)-tetra-hydroxythiacalix[4]arene

p-Tetrakis(phenylazo)-tetra-hydroxythiacalix[4]arene shows complexing properties with neutral molecules. A complex with pyridine was crystallized and the crystal structure determined. The crystals are monoclinic, space group C2/c, a = 49.953(10), b = 21.566(4), c = 23.448(5) Å, = 105.12(3)°, V = 24386(8) Å ³, Z = 16. Two macrocycles are positioned in such a way that they form a cavity where two pyridine molecules are encapsulated giving a 2:2 endocomplex. 5.5 other pyridine molecules are trapped between the macrocycles, two of them giving H-bonds with the calixarenes.