Self-association of an indole based guanidinium-carboxylate-zwitterion: formation of stable dimers in solution and the solid state

Demarcating Noncovalent and Covalent Bond Territories: Imine-CO2 Complexes and Cooperative CO2 Capture

Chemical bond territory is rich with covalently bonded molecules wherein a strong bond is formed by equal or unequal sharing of a quantum of electrons. The noncovalent version of the bonding scenarios expands the chemical bonding territory to a weak domain wherein the interplay of electrostatic and π-effects, dipole-dipole, dipole-induced dipole, and induced dipole-induced dipole interactions, and hydrophobic effects occur. Here we study both the covalent and noncovalent interactive behavior of cyclic and acyclic imine-based functional molecules (XN) with CO₂. All parent XN systems preferred the formation of noncovalent (nc) complex XN···CO₂, while more saturated such systems (XN') produced both nc and covalent (c) complexes XN'⁺-(CO₂)^-. In all such cases, crossover from an nc to c complex is clearly demarcated with the identification of a transition state (ts). The complexes XN'···CO₂ and XN'⁺-(CO₂)^- are bond stretch isomers, and they define the weak and strong bonding territories, respectively, while the ts appears as the demarcation point of the two territories. Cluster formation of XN with CO₂ reinforces the interaction between them, and all become covalent clusters of general formula (XN⁺-(CO₂)^-)_n. The positive cooperativity associated with the NH···OC hydrogen bond formation between any two XN'⁺-(CO₂)^- units strengthened the N-C coordinate covalent bond and led to massive stabilization of the cluster. For instance, the stabilizing interaction between the XN unit with CO₂ is increased from 2-7 kcal/mol range in a monomer complex to 14-31 kcal/mol range for the octamer cluster (XN'⁺-(CO₂)^-)₈. The cooperativity effect compensates for the large reduction in the entropy of cluster formation. Several imine systems showed the exergonic formation of the cluster and are predicted as potential candidates for CO₂ capture and conversion.

Experimental lipophilicity scale for coded and noncoded amino acid residues

Among other features, the polarity of amino acid residues is the key parameter for understanding their role in proteins. The wide occurrence of protein modifications in nature and the advent of genetic code engineering techniques created a need for an experimental polarity value integrating both coded (canonical) and noncoded (noncanonical) residues on one universal scale. To address this issue, this work reports on a polarity scale based on the experimental lipophilicity of methyl esters of N-acetylamino acids. The derivatization of amino acids was performed in two steps under mild conditions that allowed conversion of a wide array of amino acids into analytical derivatives. The partitioning/distribution between octan-1-ol and water/buffer was measured using the intensity of the NMR signal as a characteristic for the concentration. The reference set of twenty coded amino acids generated log P values spanning 5.1 units: from tryptophan being the most hydrophobic to aspartate being the most hydrophilic. Furthermore, lipophilicity was measured for a set of analogues of phenylalanine, tyrosine, tryptophan, methionine, proline, and lysine that are typical in nature and/or laboratory practice. The polarity scale reported here will aid the rationalization of amino acid replacements in proteins, and will guide further efforts in experimental genetic code engineering.

UV resonance Raman spectroscopy of the supramolecular ligand guanidiniocarbonyl indole (GCI) with 244 nm laser excitation

Ultraviolet resonance Raman (UVRR) spectroscopy is a powerful vibrational spectroscopic technique for the label-free monitoring of molecular recognition of peptides or proteins with supramolecular ligands such as guanidiniocarbonyl pyrroles (GCPs). The use of UV laser excitation enables Raman binding studies of this class of supramolecular ligands at submillimolar concentrations in aqueous solution and provides a selective signal enhancement of the carboxylate binding site (CBS). A current limitation for the extension of this promising UVRR approach from peptides to proteins as binding partners for GCPs is the UV-excited autofluorescence from aromatic amino acids observed for laser excitation wavelengths >260 nm. These excitation wavelengths are in the electronic resonance with the GCP for achieving both a signal enhancement and the selectivity for monitoring the CBS, but the resulting UVRR spectrum overlaps with the UV-excited autofluorescence from the aromatic binding partners. This necessitates the use of a laser excitation <260 nm for spectrally separating the UVRR spectrum of the supramolecular ligand from the UV-excited autofluorescence of the peptide or protein. Here, we demonstrate the use of UVRR spectroscopy with 244 nm laser excitation for the characterization of GCP as well as guanidiniocarbonyl indole (GCI), a next generation supramolecular ligand for the recognition of carboxylates. For demonstrating the feasibility of the UVRR binding studies without an interference from the disturbing UV-excited autofluorescence, benzoic acid (BA) was chosen as an aromatic binding partner for GCI. We also present the UVRR results from the binding of GCI to the ubiquitous RGD sequence (arginylglycylaspartic acid) as a biologically relevant peptide. In the case of RGD, the more pronounced differences between the UVRR spectra of the free and complexed GCI (1:1 mixture) clearly indicate a stronger binding of GCI to RGD compared with BA. A tentative assignment of the experimentally observed changes upon molecular recognition is based on the results from density functional theory (DFT) calculations.

Benzoylguanidines as Anion-Responsive Systems

A series of benzoylguanidinium salts was prepared and the changes in UV/Vis spectra, triggered by the presence of anions, were investigated. All compounds undergo deprotonation with basic anions like dihydrogenphosphate and acetate in acetonitrile. The most pronounced spectral changes were obtained by deprotonation of N¹ -benzoyl-N³ -(p-nitrophenyl) guanidinium chloride which shows the naked-eye visible color change from colorless to yellow. Measured pK_a (BH⁺ ) in acetonitrile ranges from 12-16, which is comparable to the pyridinium cations. The proton transfer equilibria were also tested in acetonitrile/water mixture where all but the most acidic derivatives showed pK_a (BH⁺ ) of 4-6 units which corresponds to apparent association constants of 10⁴ -10⁶  dm³  mol^-1 . UV/Vis spectra of neutral and protonated forms were modelled by the TD-DFT approach using CAM-B3LYP and PBE0 functionals and compared to CC2 results. In the case of CAM-B3LYP, a parameter ω, defining amount of long-range exchange correction, was varied to achieve the best agreement with the experimental spectra. The optimized ω parameters are 0.10 a₀ ^-1 for neutral benzoylguanidines and 0.20 a₀ ^-1 for neutral nitrobenzoyl and protonated systems. The larger ω parameter in the latter is ascribed to more pronounced charge transfer character of the HOMO-LUMO transition - the one responsible for the lowest energy absorption band.

Brønsted Acid-Mediated Domino One-Pot Dual C-C Bond Formation: Chemoselective Synthesis of Fused Tricyclic Ketones

A chemoselective synthesis of fused novel tricyclic motifs via a facile domino intramolecular cyclization is presented. The strategy enables the formation of dual C-C bond via intramolecular Friedel-Crafts alkylation followed by acylation to accomplish fused tricyclic ketones. Significantly, these fused tricyclic compounds are ubiquitous and constitute major structural cores of natural products.

Synthesis and preliminary investigations into novel 1,2,3-triazole-derived androgen receptor antagonists inspired by bicalutamide

A versatile and high yielding synthesis of novel androgen receptor (AR) antagonists is presented. Using this methodology, six 1,4-substituted-1,2,3-triazole derived bicalutamide mimics were synthesised in five steps and in isolated overall yields from 41% to 85%. Evaluation of these compounds for their anti-proliferative properties against androgen dependent (LNCaP) and independent (PC-3) cells showed promising IC50 values of 34-45 μM and 29-151 μM, respectively. The data suggest that the latter compounds may be an excellent starting point for the development of prostate cancer therapeutics for both androgen dependent and independent forms of this disease. Docking of these compounds (each enantiomer) in silico into the T877A mutated androgen receptor, as possessed by LNCaP cells, was also undertaken.

Deploying RNA and DNA with Functionalized Carbon Nanotubes

Carbon nanotubes internalize into cells and are potential molecular platforms for siRNA and DNA delivery. A comprehensive understanding of the identity and stability of ammoniumfunctionalized carbon nanotube (f-CNT)-based nucleic acid constructs is critical to deploying them in vivo as gene delivery vehicles. This work explored the capability of f-CNT to bind single- and double-strand oligonucleotides by determining the thermodynamics and kinetics of assembly and the stoichiometric composition in aqueous solution. Surprisingly, the binding affinity of f-CNT and short oligonucleotide sequences was in the nanomolar range, kinetics of complexation were extremely rapid, and from one to five sequences were loaded per nanotube platform. Mechanistic evidence for an assembly process that involved electrostatic, hydrogen-bonding and π-stacking bonding interactions was obtained by varying nanotube functionalities, oligonucleotides, and reaction conditions. ³¹P-NMR and spectrophotometric fluorescence emission data described the conditions required to assemble and stably bind a DNA or RNA cargo for delivery in vivo and the amount of oligonucleotide that could be transported. The soluble oligonucleic acid-f-CNT supramolecular assemblies were suitable for use in vivo. Importantly, key evidence in support of an elegant mechanism by which the bound nucleic acid material can be 'off-loaded' from the f-CNT was discovered.

Unexpected stable dimerisation of an anionic imidopyrrolecarboxylate in polar solution

The imidopyrrolecarboxylate 3(-) unexpectedly forms stable dimers (K(ass) = 130 M(-1) in CHCl(3)/DMSO, 1 : 1, v/v) despite the fact that two anions have to interact. The dimer is more stable than an analogous neutral amidopyrrolecarboxylic acid dimer (K(ass) < 10 M(-1)) underlining the importance of charged H-bonds compared to neutral ones.