A theoretical and experimental investigation of vicinal tricarbonyl systems and their hydrates

A concise treatment of pterins: some recent synthetic and methodology aspects and their applications in molecular sensors

A concise account of pterins in chemistry and biology and their applications in molecular sensors including their optical spectroscopic properties are described. Different natural, synthetic, biological and photophysical aspects are also discussed. Synthetic access to direct functionalised pterins and a recently reported new thiophene annulation technique are described for the synthesis of Form B of molybdenum cofactor. The receptor properties of fluorescent pterin molecules including selenopyrimidines which are rarely reported for their binding of anions and neutral molecules are also of major importance in this review. For such an old and still so young, unexplored pterin system on its power to be sensitive for physical studies especially the interaction with cations, anions and neutral molecules are fascinating and research in this area is relatively new and expected to increase fast. Pterin based receptors are for the first time put into a useful review for the advantage of those who want to explore pterin and modified pterin as chromogenic and fluorogenic sensors.

Predicting hydration propensities of biologically relevant α-ketoamides

Quantum chemical calculations coupled to experiments were used to predict covalent hydration propensities of biologically relevant α-ketoamides. Experimentally determined hydration equilibrium constants for related ketones and aldehydes were compared to computationally determined values to develop a method for predicting hydration equilibrium constants. This method was used on six newly synthesized α-ketoamides to experimentally verify computational predictions. A correlation between calculation and experiment was observed and applied to models of several pertinent APIs. Our results indicate that the keto form is favored for practically all α-ketoamides in biological environs.

Density functional theory (DFT) calculations on the structures and stabilities of [CnO2n+1]2– and [CnO2n+1]X2 polycarbonates containing chainlike (CO2)n units (n = 2–6; X = H or Li)

The structures and stabilities of chainlike (CO2)n (n = 2–6) polycarbonates, where adjacent C atoms are linked by C–O–C bonds, were investigated at the density functional theory (DFT) level (B3PW91/6–311G(2d,p)), including dicarboxylic dianions, [CnO2n+1]2–, and the corresponding acids, [CnO2n+1]H2, and Li salts, [CnO2n+1]Li2. At equilibrium, the most stable systems have Cs, C2, or C2v symmetries. In the gas phase, these dianions are generally metastable with respect to spontaneous ejection of one electron, yet in the presence of counterions they become stabilized, for example, as [CnO2n+1]2–(Li+)2 ion pairs. [CnO2n+1]2– linkages are also stabilized as dicarboxylic acids, [CnO2n+1]H2; we find the latter to have equilibrium conformations of higher symmetry than previously reported in the literature. To the best of our knowledge, none of the [CnO2n+1]X2 (X = Li or H) compounds with n ≥ 2 have been reported in the experimental literature (albeit, the alkyl esters C2O5R2 and C3O7R2 are commercially available). All CO bonds in C2O5X2 to C6O13X2 have single- to double-bond character (≈140–118 pm), indicating that the [CnO2n+1] moieties are held together by strong chemical forces (in contrast to the weakly bound complexes (CO2)n and (CO2)n–, n > 1). Vibrational frequencies were calculated to ensure all conformations were true minima. The IR and Raman intensities show that the high intensity C=O stretching modes (1750 ± 100 cm–1) will help in the spectral characterization of these compounds. Solvation calculations using the polarizable continuum model (PCM) find that C2O52– can be formed via CO32– + CO2 as well as CO3–[Formula: see text], each reaction having ΔG298 < 0 in practically all solvents. This result confirms the experimentally observed large solubility of CO2(g) in molten carbonates, CO3M2 (M = Li, Na, or K). In contrast, starting with n = 2, the reactions [CnO2n+1]2– + CO2 do not proceed spontaneously in any solvent (ΔG298 > 0).

Site of nucleophilic attack and ring opening of five-membered heterocyclic 2,3-diones: a density functional theory study

The site of nucleophilic addition to five-membered heterocyclic 2,3-diones (4-iminomethylfuran-2,3-dione A1 and 4-formyl-pyrrole-2,3-dione B1) is studied by density functional theory calculations (B3LYP/6-31G) with water as the nucleophile. Both uncatalyzed and water-assisted 1,2-addition to the lactone (lactam) and the keto carbonyl group, and conjugate addition to C5 of the heterocycle and the heteroatom of the 4-iminomethyl (formyl) moiety are considered. In addition, concerted and stepwise ring fission of the lactone (lactam) ring is also treated. The effect of solvation (aqueous solution) is taken into account by the polarizable continuum model (PCM) and the Poisson-Boltzmann SCRF method (PB-SCRF), as well as explicit water molecules. Only this latter approach yields meaningful activation free energies. Barriers for addition of H2O increase in the order 1,4-addition to C5 < addition to the lactone (lactam) carbonyl < hydration of the 3-keto group. No reaction path for concerted water-assisted ring opening could be found.

Hydration and Hydrolysis of alpha-Oxo Carboxylic Acid Derivatives and Conjugate Addition to alpha,beta-Unsaturated Carbonyl Compounds: A Density Functional Study

Hydration of the keto group as well as hydrolysis (ester and amide) of alpha-oxo carboxylic acid derivatives has been studied by density functional theory (B3LYP/6-31G and B3LYP/6-311G). Both uncatalyzed as well as water-assisted processes have been considered. Solvent effects were approximated by the self-consistent isodensity surface polarized continuum (SCIPCM) model. For hydrolysis reactions a concerted as well as a stepwise mechanism was calculated. In the latter one, addition of the nucleophile to a tetrahedral intermediate was found to be rate determining. In uncatalyzed processes both concerted and stepwise mechanisms are calculated to have comparable activation energies and free enthalpies. In catalyzed reactions the stepwise mechanism is predicted to be considerably more favorable. Hydration of the alpha-oxo group should be much more feasible than either ester or amide hydrolysis.