Self-catalytic mechanism of prebiotic reactions: from formamide to pterins and guanine.

Reaction pathway of prebiotic reactions for formation of the pteridines: pterin, xanthopterine, isoxanthopterine and leucopterine, as well as the purine nucleobase guanine from pure formamide are presented. In these reactions, formamide or its tautomer, formimidic acid, play the role of proton-carrying catalyst. All required raw materials, such as hydrogen cyanide, ammonia, water, formic acid, urea, 2-aminomalononitrile, glyoxal, glyoxylic acid and oxalic acid needed in the self-catalyzed reactions are obtained by partial decomposition of formamide. We show that the prebiotic formation of nucleobases and pterins is closely linked and they probably coexisted at the beginning of chemical evolution.

2-Carbamido-1,3-indandione - a Fluorescent Molecular Probe and Sunscreen Candidate.

The present work reports theoretical and experimental studies on the photophysical properties of two tautomeric forms of 2-carbamido-1,3-indandione (CAID). By means of UV-vis, steady-state and time-dependent fluorescence spectroscopy it is shown that both enol forms, 2-(hydroxylaminomethylidene)-indan-1,3-dione and 2-carboamide-1-hydroxy-3-oxo-indan, coexist in solution. On the base of spectroscopic studies of CAID interaction with human serum albumin and DNA sequences, it was shown that the compound has potential and it is suitable for use as fluorescent molecular probe for investigation of different biomolecules. CAID shows relatively high photostability within 3 h irradiation period. Such behavior of the investigated compound supposes possibilities for using of the CAID molecule as sunscreen because of strong absorption in UVA, UVB and UVC light spectra.

Synthesis of 3',4'-dihydro-2H,2'H,5H-spiro [imidazolidine-4,1'-naphthalene]-2,5-dione and its derivatives.

The synthesis of two novel compounds, 1-amino-3',4'-dihydro-2H,2'H,5H-spiro[imidazolidine-4,1'-naphthalene]-2,5-dione and 1,3-bis(hydroxymethyl)-3',4'-dihydro-2H,2'H,5H-spiro[imidazolidine-4,1'-naphthalene]-2,5-dione, was reported. The structures of the compounds were verified by (1)H, (13)C NMR and IR spectroscopy and quantum-chemical calculations at DFT level.

Solid-state tautomerism in 2-carboxyindan-1,3-dione.

The structure of 2-carboxyindan-1,3-dione was investigated using a combination of quantum-chemical calculations and solid-state NMR and IR spectroscopy. Due to poor solubility of the compound in different solvents, no single crystals could be obtained. Two dimeric structures formed from the tautomers of 2-carboxyindan-1,3-dione are likely to coexist in the solid state. The dimers interconvert via intramolecular proton transfer in one of the tautomeric forms constituting the dimers. The energy barrier of the intramolecular proton transfer reaction is calculated as 5.82 kcal mol(-1) at the MP2/6-31++G level of theory.

Binding Expedient of 2-carbamido-1,3-indandione to Nucleic Acids: Potential Fluorescent Probe.

Fluorescent and computational methods were used to elucidate the binding expedient of 2-carbamido-1,3-indandione (CAID) tautomers to nucleotides. The dependence of the fluorescence emission of CAID loaded nucleic acids sequences to compound concentration, temperature and time variation was investigated. It was found that the subject compound binds to nucleic acids but does not intercalate. According to our quantum-chemical calculations on the conjugation between CAID and nucleotides, the binding in the formed complexes may be through hydrogen bonds. Two possible types of complexes were considered-CAID to the phosphate group and CAID to the nucleobase. To estimate the binding affinity, the interaction energies of the formed complexes were calculated. Tautomer 2-carboamide-1-hydroxy-3-oxo-indane is preferred in the formation of complexes, and the phosphate group complexes were more stable. Generally, the guanosine and deoxyguanosine monophosphate complexes were the most preferred regardless of the complex type. Because of the lack of cytotoxic effect on untransformed cell lines of mouse embryo fibroblasts Balb/c 3T3 according to our previous report (Markova et al, (2017) Bulg Chem Commun, 49D, 221-226) and the affinity to nucleic acids, we can suggest that the subject compound could be suitable to be used as a novel type of fluorescent biomarker.

Chemical evolution: from formamide to nucleobases and amino acids without the presence of catalyst.

Abiotic synthesis of nucleobases and amino acids is of critical importance as it sheds light on potential prebiotic chemical reactions. During thermal decomposition of formamide in vacuum conditions, purine, cytosine, adenine, hypoxanthine, uracil, pterin, urea, urocanic acid, glycine, alanine and norvaline were detected. The compounds were obtained without catalyst by heating at 100-180 °C or microwave heating of formamide. Reaction network of self-catalyzed chemical reactions is suggested, showing how from only one parent molecule, nucleobases, urea and the amino acid glycine can be produced. The reaction pathways are theoretically determined using SCS-MP2 calculations.Communicated by Ramaswamy H. Sarma.

Tautomeric equilibria of 5-fluorouracil anionic species in water.

It has long been postulated that rare tautomeric or ionized forms of nucleic acid bases may play a role in mispair formation. Therefore, ab initio quantum chemical investigations on the tautomeric equilibrium in 5-fluorouracil (5FU) and its anions (deprotonated from N1, AN1, and from N3, AN3) and their tautomeric forms in water were performed. The effect of the water as solvent was introduced using solute-solvent clusters (four water molecules). The influence of the water molecules on the tautomeric reactions between different forms was considered by multiple proton transfer mechanisms. We show that when a water dimer is located in the reaction site between the two pairs of N-H and C═O groups, the assistive effect of the water molecules is strengthened. All calculations of the solute-water complexes were carried out at an MP2 level of theory and supplemented with correction for higher order correlation terms at CCSD(T) level, using the 6-31+G(d,p) basis set. The ab initio calculated frequencies and Raman intensities of 5FU and its anions AN1, AN3, and dianion are in good agreement with the experimental Raman frequencies in aqueous solution at different pH. In order to establish the pH-induced structural transformation in the molecule of 5FU, further (1)H, (19)F, and (13)C NMR spectra in water solution for pH = 6.9-13.8 were acquired and the chemical shift alterations were determined as a function of pH. On the basis of NMR spectroscopic data obtained for 5FU in aqueous solution at alkaline pH, we suggest the existence of a mixture of the anionic tautomeric forms predicted by our theoretical calculations.

Tautomerism of Inosine in Water: Is It Possible?

Syn- and anti-conformers of four tautomer structures of inosine were studied in the gas phase and in solvent water to investigate the possibility of hydrogen bonding and tautomeric conversion. It was found that in the gas phase and in water solution the most stable is the syn-conformer of the 6-keto tautomer followed by its anti-conformer and syn-conformer of the 6-enol form. In the gas phase, the percent content of syn- and anti-conformers is 83.77 and 12.86%, respectively, whereas syn-enol tautomer is calculated to be 2.54%. However, in water solution the syn-conformer of the keto tautomer is 99.9%. The water-assisted proton transfer process in inosine was investigated using ab initio MP2 and SCS-MP2 quantum chemical approaches. Solute-solvent clusters containing an inosine molecule and five water molecules embedded in the "bulk" solvent treated as polarizable continuum (the CPCM/MP2/6-31+G(d,p) level of theory) were explored. The energy barrier of the water-assisted proton transfer reaction in inosine is found to be 12.9 kcal mol-1 and the rate constant ( k = 6.68 × 101 s-1) is sufficiently large to generate the 6-enol tautomer. From the reaction profile of the proton transfer we can conclude that the process is realized through the asynchronous concerted mechanism.

Hybrid MC/QC simulations of water-assisted proton transfer in nucleosides. Guanosine and its analog acyclovir.

To provide an in-depth insight into the molecular basis of spontaneous tautomerism in DNA and RNA base pairs, a hybrid Monte Carlo (MC)-quantum chemical (QC) methodology is implemented to map two-dimensional potential energy surfaces along the reaction coordinates of solvent-assisted proton transfer processes in guanosine and its analog acyclovir in aqueous solution. The solvent effects were simulated by explicit inclusion of water molecules that model the relevant part of the first hydration shell around the solute. The position of these water molecules was estimated by carrying out a classical Metropolis Monte Carlo simulation of dilute water solutions of the guanosine (Gs) and acyclovir (ACV) and subsequently analyzing solute-solvent intermolecular interactions in the statistically-independent MC-generated configurations. The solvent-assisted proton transfer processes were further investigated using two different ab initio MP2 quantum chemical approaches. In the first one, potential energy surfaces of the 'bare' finite solute-solvent clusters containing Gs/ACV and four water molecules (MP2/6-31+G(d,p) level) were explored, while within the second approach, these clusters were embedded in 'bulk' solvent treated as polarizable continuum (C-PCM/MP2/6-31+G(d,p) level of theory). It was found that in the gas phase and in water solution, the most stable tautomer for guanosine and acyclovir is the 1H-2-amino-6-oxo form followed by the 2-amino-6-(sZ)-hydroxy form. The energy barriers of the water-assisted proton transfer reaction in guanosine and in acyclovir are found to be very similar - 11.74 kcal mol-1 for guanosine and 11.16 kcal mol-1 for acyclovir, and the respective rate constants (k = 1.5 × 101 s-1, guanosine and k = 4.09 × 101 s-1, acyclovir), are sufficiently large to generate the 2-amino-6-(sZ)-hydroxy tautomer. The analysis of the reaction profiles in both compounds shows that the proton transfer processes occur through the asynchronous concerted mechanism.

Anti-conjunctivitis effect of fresh juice of xGraptoveria (Crassulaceae): A phytochemical and ethnobotanical study.

AIM: The parent of xGraptoveria, Graptopetalum paraguayense, is used in Chinese folk medicine for alleviating hepatic disorders, detumescence and detoxication, lowering of blood pressure, inhibition of cancer cells, exerting diuretic effects, relieving pain and infections. No data are available regarding its anti-conjunctivitis effect. The aim of this preliminary study is to test the anti-conjunctivitis properties of xGraptoveria (Crassulaceae) and to identify its bioactive constituents. MATERIALS AND METHODS: Fresh watery juice of leaves of xGraptoveria was extracted with n-butanol and the extract was analyzed using gas chromatography-mass spectrometry (GC/MS). The ethnobotanical appraisal of the anti-conjunctivitis properties of xGraptoveria was based on 11 interviews about the symptoms against which this plant demonstrated positive effect. RESULTS: Fresh juice of xGraptoveria leaves applied directly to the irritated eye 2 times per day cured conjunctivitis in all reported cases. The main groups of organic compounds identified by GC/MS analysis in the fresh extracted leaf juice of xGraptoveria were: Alkylamines, hydroxycarboxylic acids, aliphatic and aromatic carboxylic acids, amino acids, alcohols, aromatic and aliphatic hydrocarbons. CONCLUSION: In this preliminary study, it is suggested that xGraptoveria exerts anti-conjunctivitis activity, through synergistic effect of different chemical compounds, most probably alkylamines and mainly hydroxycarboxylic, aliphatic, and aromatic carboxylic acids.

Synthesis, cytotoxicity, antibacterial and antitumor activity of platinum(II) complexes of 3-aminocyclohexanespiro-5-hydantoin.

New platinum(II) complexes of 3-aminocyclohexanespiro-5-hydantoin (achsh) were prepared and characterized. Ab initio calculation of the structure and the measurements of IR and NMR spectra of [Pt(NH(3))(achsh)Cl(2)] were also performed. Quantum-chemical and spectroscopic studies indicated a cis-square planar structure with a hydantoin ligand coordinated via the NH(2) group. The complexes were evaluated for in vitro cytotoxicity in murine erythroleukemia (MEL) cells, clone F4N, as well as for in vivo antitumor activity toward murine L1210 leukemia. The complexes exerted significantly lower in vitro and in vivo toxicities compared with those of cisplatin (cis-diamminedichloroplatinum(II), DDP). The complex [Pt(NH(3))(achsh)Cl(2)] exhibited antitumor activity against L1210 leukemia, comparable to that of cisplatin, resulting at a dose of 72 mg/kg in a %T/C (increased survival time) of 191%. This complex, as well as cisplatin, induced apoptosis in F4N cells, and exerted antibacterial activity as assessed in 10 bacterial strains.

Physicochemical characterization and in vitro behavior of daunorubicin-loaded poly(butylcyanoacrylate) nanoparticles.

The design, preparation and characterization of poly(butylcyanoacrylate) nanoparticles as a drug-delivery system for daunorubicin is reported. A range of light scattering [photon correlation spectroscopy (PCS)], spectroscopic [(1)H nuclear magnetic resonance ((1)H NMR), Fourier transform infrared (FTIR), chromatographic [gel permeation chromatography (GPC)] and quantum chemical techniques have been employed for the physicochemical characterization of drug-loaded nanoparticles and to clarify the mechanisms of drug immobilization in the polymer matrix. The presence of daunorubicin in the polymerization medium was found to affect both the degree of polymerization and the compactness of the resulting nanoparticles. The GPC, FTIR and (1)H NMR results confirmed cytostatic immobilization in the polymer matrix, with evidence for the presence of three types of inclusion: physically entrapped, polymer-associated (due to hydrogen bonds and/or dipole-charge interactions with the polymer chains), and polymer surface-adsorbed daunorubicin. The developed colloidal delivery system has the capacity for sustained in vitro release of daunorubicin. Preliminary in vitro assays were carried out on two cell lines, DLKP and DLKP-A, which display different levels of drug resistance, to evaluate the cytotoxicity of the drug-loaded nanoparticles.

Intramolecular hydrogen-bonding interactions in 2-nitrosophenol and nitrosonaphthols: ab initio, density functional, and nuclear magnetic resonance theoretical study.

Intramolecular hydrogen bonding (IHB) interactions and molecular structures of 2-nitrosophenol, nitrosonaphthols, and their quinone-monooxime tautomers were investigated at ab initio and density functional theory (DFT) levels. The geometry optimization of the structures studied was performed without any geometrical restrictions. Possible conformations with different types of the IHB of the tautomers were considered to understand the nature of the HB among these conformers. The effect of solvent on hydrogen bond energies, conformational equilibria, and tautomerism in aqueous solution were studied. Natural bond orbital analysis was performed to study the IHB in the gaseous phase and in aqueous medium. The NMR 1H, 13C, 15N, and 17O chemical shifts in the gaseous phase and in solution for the studied compounds were calculated using the gauge-including atomic orbitals approach implemented in the Gaussian 03 program package. The optimized geometrical parameters and 1H NMR chemical shifts are in good agreement with previous theoretical and experimental data.

Ab initio investigation on the second-order nonlinear optical responses in keto-enol equilibria of salicylideneanilines.

The keto-enol (K-E) tautomerization equilibrium, more precisely, the keto-amine/enol-imine equilibrium, has been investigated for a series of substituted salicylideneanilines in view of designing compounds with a contrast of second-order nonlinear optical properties. Substituting the salicylidene ring by an acceptor group or the other ring by a donor prevents the K form from being stable, whereas in the other cases, the K form can easily be converted to the E form due to the small activation barrier, figuring out in most cases that the K form is metastable. For a representative set of donor/acceptor substituents, the E and K forms present a sufficiently large contrast of beta to allow its detection by using electric-field-induced second harmonic generation or hyper-Rayleigh scattering. The largest beta values are mainly associated with species bearing a donor in the para position of the salicylidene ring and an acceptor on the other ring whereas the largest beta values are generally found for the E form.

Theoretical and spectroscopic study of 2-substituted indan-1,3-diones: a coherent picture of the tautomeric equilibrium.

The structures of some 2-substituted indan-1,3-diones are investigated in the gas phase and solution using quantum chemical calculations and spectral (NMR, IR, and UV) measurements. The influence of the substituent at the 2-position on the tautomeric equilibrium of 2-substituted indan-1,3-diones in solvents with different polarity is evaluated. It is shown that the equilibrium in 2-formyl-indan-1,3-dione and 2-acetyl-indan-1,3-dione is shifted to the 2-hydroxyalkylidene-indan-1,3-dione tautomer, while 2-carboxyamide-indan-1,3-dione exists as a mixture of two tautomers, 2-(hydroxyaminomethylidene)-indan-1,3-dione and 2-carboamide-1-hydroxy-3-oxo-indan, with extremely fast proton transfer between them. The situation for 2-carboxy-indan-1,3-dione is quite different - on the basis of the analysis of the obtained results, the possible existence of an anionic form of 2-carboxy-indan-1,3-dione in solution can be inferred.

Oxo-hydroxy tautomerism of 5-fluorouracil: water-assisted proton transfer.

Post-Hartree-Fock ab initio quantum chemical calculations were performed for 5-fluorouracil in the gas phase and in a three-water cluster. Full geometry optimizations of the 5-fluorouracil-water complexes were carried out at the MP2/6-31+G(d,p) level of theory. MP4/6-31+G(d,p)//MP2/6-31+G(d,p) and MP4/6-31++G(d,p)//MP2/6-31+G(d,p) single-point calculations were performed to obtain more accurate energies. In water solution, 5-fluorouracil exists mainly in the 2,4-dioxo form (A). We propose that the populations of the 2-hydroxy-4-oxo (B) and 4-hydroxy-2-oxo (D) tautomers are 1 x 10(-4)% and 3.9 x 10(-8)%, respectively, on the basis of the relative stabilities of the tautomers calculated at the MP4/6-31++G(d,p)//MP2/6-31+G(d,p) level of theory. A profound difference between isolated and hydrated 5-fluorouracil is noted for the height of the tautomerization barrier. In the absence of water, the process of proton transfer is very slow. The addition of water molecules decreases the barrier by 2.3 times, making the process much faster. The minimum energy path (MP2/6-31+G(d,p)) for water-assisted proton transfer in trihydrated 5-fluorouracil was followed. CNDO/S-CI calculations predict singlet pi-pi(*) electron transitions at 312 nm for B and at 318 nm for D. The fluorescence spectrum of 5-fluorouracil in water confirms the presence of the hydroxy tautomer.

Ab initio study of 2,4-substituted azolidines. II. Amino-imino tautomerism of 2-aminothiazolidine-4-one and 4-aminothiazolidine-2-one in water solution.

The relative stabilities of the tautomers of 2-aminothiazolidine-4-one and 4-aminothiazolidine-2-one were calculated at the MP2/6-31+G(d,p) level by considering their mono- and trihydrated complexes. Single-point calculations at the MP4/6-31+G(d,p)//MP2/6-31+G(d,p) level of theory were performed to obtain more accurate energies. The values of proton transfer barriers in the isolated, mono- and trihydrated tautomers of 2-aminothiazolidine-4-one (2AT) and 4-aminothiazolidine-2-one (4AT) were calculated for two different mechanisms of tautomerisation. In the absence of water, the process of proton transfer should not occur. Addition of water molecules decreases the barrier making the process faster, as the participation of two water molecules in a proton transfer reaction is more favorable than the participation of only one water molecule. To estimate the effect of the medium (water) on the relative stabilities of the tautomers of the studied compounds we applied the polarizable continuum model (PCM). (13)C NMR chemical shieldings were calculated using the GIAO approach at MP2/6-31+G(d,p) optimized geometries. HF and the DFT B3LYP functional with 6-31+G(d,p) basis set were employed. The quantum chemical results for the chemical shifts in gas phase and in polar solvents (water and DMSO) were compared with experimental data. TD DFT B3LYP/aug-cc-pVTZ calculations were performed to predict the absorption maxima of tautomers A and B of 2AT and 4AT.