Novel Amphi-Ionophores

Anion recognition by cyclic peptides

Cyclic peptides provide excellent scaffolds for anion recognition and improved binding affinity and selectivity has been achieved through peptide backbone rigidification and the introduction of side chains bearing anion recognition groups.

Characterization of fluoride-tolerant halophilic Bacillus flexus NM25 (HQ875778) isolated from fluoride-affected soil in Birbhum District, West Bengal, India

A new Gram-positive, nonpigmented, rod-shaped fluoride-tolerant bacterial strain, NM25, was isolated from waterlogged muddy field soil collected from the fluoride endemic area of Rampurhat II block (average fluoride in water, 4.7 mg/l, and in soil, 1.5 mg/kg) in Birbhum District, West Bengal, India. The study was undertaken to characterize the fluoride-tolerant bacterial isolate, to determine its role in bioaccumulation of fluoride, and to analyze the water and soil quality of the bacterial environment. The isolate was positive for catalase, lipase, urease, protease, oxidase, and H2S production, but negative for indole production, nitrate reduction, and Vogues-Proskauer test. The organisms were sensitive to recommended doses of ofloxacin, kanamycin, rifampicin, levofloxacin, vancomycin, gatifloxacin, gentamicin, doxycycline, streptomycin, and nalidixic acid but resistant to ampicillin. Based on the phenotypic characteristics, 16S rRNA gene sequence, and phylogenetic analysis, the bacterial isolate NM25 was identified as Bacillus flexus. The G+C content of the 16S rDNA was 53.14 mol%. This strain tolerated up to 20% (w/v) NaCl in nutrient agar medium and was grown at the pH range 4-12. It reduced fluoride concentration up to 67.45% and tolerated more than 1,500 ppm of fluoride in brain-heart infusion agar medium.

Multifunctional Macrocyclic Receptors as Templates for Aromatic Amino Acids: A Rare Example of a Highly Selective Multi-Input Multi-Output Chemo-"Logic Gate"

Proton-bound [M⋅H⋅G]⁺ diastereomeric complexes between some chiral aromatic amino acids or dipeptides (G) and a chiral multifunctional macrocyclic receptor (M=Chirabite-A) undergo, in the gas phase, highly selective substitution and addition reactions by amines, such as 2-aminobutane and piperidine. All the [M⋅H⋅G]⁺ complexes follow time-dependent monoexponential decays. In some cases, the kinetic curves exhibit a plateau revealing the presence of unreactive [M⋅H⋅G]⁺ structures. In them, the amino acid is accommodated in the macrocycle cavity in the zwitterionic form by sharing its acidic hydrogen atoms with the pyridine nitrogen atoms of the host. The same interactions are structurally inaccessible to G=dipeptides or monofunctional amines, which then can be readily released from [M⋅H⋅G]⁺ . When the amino acid interacts with the amidocarbonyl oxygen atoms pointing outside the macrocycle cavity, it saves the canonical structure and can be readily displaced by the amine. The Chirabite-A may act as an efficient template for aromatic amino acids by releasing them or not depending upon the amino acid configuration and the basicity of the amine. These unique properties confer to the gas-phase diastereomeric [M⋅H⋅G]⁺ complexes the features of multi-input multi-output chemo-"logic gates".

Studies on synthesis and anion recognition properties of (3′-nitrobenzo)[2,3-d]-(3″-nitrobenzo)[9,10-d]-1,4,8,11-tetraazacyclotetradecane-5,7,12,14-tetraone

A novel artificial receptor, (3'-nitrobenzo)[2,3-d]-(3''-nitrobenzo)[9,10-d]-1,4,8,11-tetraazacyclotetradecane-5,7,12,14-tetraone, was designed and synthesized. The interactions of this receptor with different anions were determined by UV-vis and (1)H NMR titration experiments, and their affinity constants to different anions were compared with those of other similar/different systems. The results indicated that this receptor showed a high selective and recognitive ability for F(-) among F(-), Cl(-), Br(-), I(-), AcO(-), OH(-), and H(2)PO(4)(-). Moreover, the low energy configuration of this receptor was further determined by means of theoretical investigations.

De novo design approach based on nanorecognition toward development of functional molecules/materials and nanosensors/nanodevices

For the design of functional molecules and nanodevices, it is very useful to utilize nanorecognition (which is governed mainly by interaction forces such as hydrogen bonding, ionic interaction, π-H/π-π interactions, and metallic interactions) and nanodynamics (involving capture, transport, and release of electrons, photons, or protons). The manifestation of these interaction forces has led us to the design and realization of diverse ionophores/receptors, organic nanotubes, nanowires, molecular mechanical devices, molecular switches, enzyme mimetics, protein folding/unfolding, etc. In this review, we begin with a brief discussion of the interaction forces, followed by some of our representative applications. We discuss ionophores with chemo-sensing capability for biologically important cations and anions and explain how the understanding of hydrogen bonding and π-interactions has led to the design of self-assembled nanotubes from calix[4]hydroquinone (CHQ). The binding study of neutral and cationic transition metals with the redox system of hydroquinone (HQ) and quinone (Q) predicts what kind of nanostructures would form. Finally, we look into the conformational changes between stacked and edge-to-face conformers in π-benzoquinone-benzene complexes controlled by alternating electrochemical potential. The resulting flapping motion illustrates a promising pathway toward the design of mobile nanomechanical devices.

Conformational Stability of a Model Macrocycle Tetraamide: An ab Initio Study

Ab initio calculations are carried out to investigate the conformational stability of a model macrocyle tetraamide. The four amide groups in the selected model are present in the sequence: -(O=CNH)-Ph-(NHC=O)-CH=CH-(O=CNH)-Ph-(NHC=O)-CH=CH-. In this sequence, two phenyl rings and two ethene groups act as bridges between the amide units. Each amide motif bonds to a phenyl ring through its amide nitrogen and to an ethene group through its amide carbon. Four clearly distinct minimum-energy conformations are found upon full geometry optimization using the B3LYP/6-31+G(d) method. Frequency calculations using the same method confirm that the four conformations are indeed minima in the macrocycle potential energy surface. Relative to the most stable conformer, the other conformations are higher in energy by 0.86, 2.09, and 9.17 kcal/mol, respectively, at the MP2/6-31+G(d,p) level. The stability of the macrocycle conformations is correlated primarily to the existence and strength of intramolecular N-H...O=C hydrogen bonds. Additional stability to the conformations is found to come from weak Ph-H...O=C hydrogen bonding between a carbonyl oxygen and a hydrogen atom of a phenyl group. Solvent effects play an important role in the relative energies of the various conformations, as indicated by the simple SCRF = dipole model calculations for the case of aqueous solution.

All-cis Cyclic Peptides

Amide bonds -NH-CO- preferentially exist in trans conformations, the cis conformation being thermodynamically unfavored with respect to the trans by about 2 kcal/mol. Yet, the main reason most proteins or peptides cannot be made from cis-peptide plaques only lies in that connecting them into open chains appears to be sterically impracticable. It is possible, however, to build all-cis cyclic peptides in which all cis-plaques are efficiently locked. The present work examines, through quantum calculations, the structural and energetic issues associated with these peculiar arrangements. Systematic exploration at DFT-B3LYP level of the potential-energy surfaces for all-cis cyclopolyglycines cG(n)(c) (n = 2-10,15), and to a lesser extent, for all-cis cyclopolyalanines and all-cis cyclopolyphenylalanines confirms that all these structures are true minima. Optimal ring size occurs around eight peptide units, resulting in planar cG7(c), cG8(c), and cG9(c). In smaller systems, the ring strain is relieved through nonplanar cup-like distortions, particularly in cG6(c). From 10 peptide units and beyond, the ring framework distorts into a saddle-edge shape. These molecules disclose some molecular flexibility, as combinatorial tilting of the plaques may give sets of minima close in energy. Indexes based on isodesmic reactions are used to estimate the energy for joining all-cis or all-trans plaques into cyclic peptides. One of them, the mean plaque-junction energy (MPJE) suggests that within sensible sizes from six peptide units and beyond, all-cis plaque association is almost equally favorable as all-trans one. The frame of radiating cis-amide bonds can be considered as defining a new kind of peptidic material, endowed with specific self-assembling properties.

An ab initio theoretical prediction: An antiaromatic ring π-dihydrogen bond accompanied by two secondary interactions in a “wheel with a pair of pedals” shaped complex FH⋯C4H4⋯HF

By the counterpoise-correlated potential energy surface method (interaction energy optimization), the structure of the pi H-bond complex FH cdots, three dots, centered FH . . . C4H4 . . . HF has been obtained at the second-order Møller-Plesset perturbation theory (MP2/aug-cc-pVDZ) level. Intermolecular interaction energy of the complex is calculated to be -7.8 kcal/mol at the coupled-cluster theory with single, double substitutions and perturbatively linked triple excitations CCSD (T)/aug-cc-pVDZ level. The optimized structure is a "wheel with a pair of pedals" shaped (1mid R:1) structure in which both HF molecules almost lie on either vertical line passing through the middle-point of the C[Double Bond]C bond on either side of the horizontal plane of the C4 ring for cyclobutadiene. In the structure, an antiaromatic ring pi-dihydrogen bond is found, in which the proton acceptor is antiaromatic 4 electron and 4 center pi bond and the donors are both acidic H atoms of HF molecules. In accompanying with the pi-dihydrogen bond, two secondary interactions are exposed. The first is a repulsive interaction between an H atom of HF and a near pair of H atoms of C4H4 ring. The second is the double pi-type H bond between two lone pairs on a F atom and a far pair of H atoms.

Efficient Fluoride-Selective Fluorescent Host: Experiment and Theory

A new naphthalene derivative containing a urea group at the 1,8-position of naphthalene was synthesized and showed a unique absorption and fluorescence peak with fluoride ion. Calculations suggested that a new peak was attributed to the increased anionic character of urea nitrogen due to the strongly charged hydrogen bonding between fluoride and amide protons of the urea. The fluoride selectivity among halides (F(-), Cl(-), Br(-)) comes from the fact that the fluoride approaches much closer to the amide protons than other halides and resides in the cavity with fast dynamics. The nature of electronic transitions that were analyzed from the calculations by the collective electronic oscillator method also supports the anionic nature of the complex between host and fluoride.

Origin of the high affinity and selectivity of novel receptors for NH4+ over K+: charged hydrogen bonds vs cation-pi interaction

[structure: see text]Given the recent report of a novel pyrazole receptor exhibiting a high selectivity for NH4+ over K+, it would be interesting to investigate the origin of this selectivity and affinity so that better receptors could be designed. On the basis of extensive theoretical studies, we conclude that the origin arises from a subtle interplay of charged H-bonds and cation-pi interactions. The approach employed herein would be very useful in the rational design of novel functional molecular systems.

Ionophores and receptors using cation-pi interactions: collarenes

Cation-pi interactions are important forces in molecular recognition by biological receptors, enzyme catalysis, and crystal engineering. We have harnessed these interactions in designing molecular systems with circular arrangement of benzene units that are capable of acting as ionophores and models for biological receptors. [n]Collarenes are promising candidates with high selectivity for a specific cation, depending on n, because of their structural rigidity and well-defined cavity size. The interaction energies of [n]collarenes with cations have been evaluated by using ab initio calculations. The selectivity of these [n]collarenes in aqueous solution was revealed by using statistical perturbation theory in conjunction with Monte Carlo and molecular dynamics simulations. It has been observed that in [n]collarenes the ratio of the interaction energies of a cation with it and the cation with the basic building unit (benzene) can be correlated to its ion selectivity. We find that collarenes are excellent and efficient ionophores that bind cations through cation-pi interactions. [6]Collarene is found to be a selective host for Li+ and Mg2+, [8]collarene for K+ and Sr2+, and [10]collarene for Cs+ and Ba2+. This finding indicates that [10]collarene and [8]collarene could be used for effective separation of highly radioactive isotopes, 137Cs and 90Sr, which are major constituents of nuclear wastes. More interestingly, collarenes of larger cavity size can be useful in capturing organic cations. [12]Collarene exhibits a pronounced affinity for tetramethylammonium cation and acetylcholine, which implies that it could serve as a model for acetylcholinestrase. Thus, collarenes can prove to be novel and effective ionophores/model-receptors capable of heralding a new direction in molecular recognition and host-guest chemistry.