π-Extended push-pull azo-pyrrole photoswitches: synthesis, solvatochromism and optical band gaps.

A new family of push-pull biphenyl-azopyrrole compounds 3b-g and 4b-d was efficiently obtained via a Suzuki cross-coupling reaction between 2-(4'-iodophenyl-azo)-N-methyl pyrrole (1a) or 3-(4'-iodophenyl-azo)-1,2,5-trimethyl pyrrole (2a) and 4'-substituted phenyl boronic acids in excellent yields. The influence of the π-biphenyl backbone and pyrrole pattern substitution was correlated with their optical properties. Solvatochromic studies via UV-visible spectrophotometry revealed that the inclusion of a 4'-nitro-biphenyl fragment favors a red-shift of the main absorption band in these azo compounds compared with their non-substituted analogues. Likewise, optical band-gaps were estimated by means of electronic absorption spectra and correlated with TD-DFT studies. The pyrrole pattern substitution and the π-conjugated backbone exhibit a clear influence on their thermal isomerization kinetics at room temperature. In all cases, biphenylazo-pyrrole compounds lead to the formation of J-type aggregates in binary MeOH : H2O solvents. Under these conditions, compounds 3b-c undergo a water-assisted cis-to-trans isomerization at room temperature.

Formation of carbon nanodots with different spin states in mechanically processed mixtures of ZnO with carbon nanoparticles: an electron paramagnetic resonance study.

Mixtures of zinc oxide with carbon nanoparticles, ZnO + xC (x = 0.1%, 1% and 3% by weight), were subjected to mechanical processing (MP) in a hermetically sealed grinding chamber. Using electron paramagnetic resonance (EPR) spectroscopy, we monitored the evolution of spin centers in CNPs. While the initial CNPs were EPR silent, their short-duration MP (tMP) gave rise to emergence of low-intensity carbon signal. Increasing the sample temperature at tMP > 9 min induced CNP oxidation, which lead to a dramatic increase in the intensity of C signal. The oxidation process also manifested itself in the appearance of a photoluminescence (PL) band at ∼2.8 eV, which is characteristic for carbon nanodots with an average size of ∼2.7 nm. A limited amount of oxygen in the grinding chamber lead to different ways of carbon nanodot oxidation, depending on carbon content in the samples, which in turn influenced the characteristics of C EPR signals observed. The number of spins calculated per one CNP (NSOP) was found to depend on carbon content in ZnO + xC samples. Based on a detailed analysis of EPR spectral lines, we suggest the existence of a broad variety of relaxation mechanisms for forming C paramagnetic centers.

Cross-linking of C60 films with 1,8-diaminooctane and further decoration with silver nanoparticles.

We applied the direct solvent-free functionalization of fullerene C60 with aliphatic bifunctional amine, 1,8-diaminooctane, to prepare chemically cross-linked C60 thin films capable of binding silver nanoparticles. The gas-phase diamine treatment of C60 reduced dramatically the fullerene solubility in toluene, indicating the transformation of pristine C60 into a different solid phase with cross-linked fullerene molecules. Compared to the spectra of pristine C60 film and powder samples, Fourier-transform infrared, UV-Visible, Raman, and 13C nucleic magnetic resonance spectra of the functionalization products exhibited new features, which point to a breaking of C60 ideal structure during the formation of new covalent bonds and to the appearance of sp3 hibridization. The covalent functionalization with 1,8-diaminooctane allowed for a stable and homogeneous deposition of silver nanoparticles of ca. 5-nm diameter onto the functionalized films through the coordination bonding between metal atoms and nitrogen donor atoms of the fullerene derivatives. The proposed mechanism of Ag nanoparticle binding was supported by density functional theory calculations using the hybrid BLYP functional in conjunction with the double numerical basis set DND.

Catalysis of peptide formation by inorganic oxides: high efficiency of alumina under mild conditions on the Earth-like planets.

Amino acid condensation catalyzed by inorganic oxides is a widely recognized way for prebiotic peptide formation. Silica and alumina are widely distributed in the Earth-like planets' crust as minerals of different complexity, and thus are attractive model catalysts for the studies of abiotic peptide synthesis. Experiments performed in other laboratories have shown that this process can be efficient at > 80 degrees C, which is not easy to find on the planetary surface in combination with sufficient concentrations of amino acids and necessary catalysts. In the present work we tested catalytic activity of three forms of alumina (which proved to be an efficient catalyst for this process) in the intermolecular condensation of L-alanine. We expanded the temperature interval down to 55 degrees C and used the simplest permanent heating procedure, without employing fluctuating drying/wetting conditions. The most important finding is that even under the lowest temperature considered (i.e. 55 degrees C), short peptide formation can be detected already after 10-30 days of heating. This fact implies that the abiotic peptide formation might occur in a wide variety of planetary environments, without need for high temperatures, given the presence of amino acid building blocks and alumina-containing minerals.

Survivability of biomolecules during extraterrestrial delivery: new results on pyrolysis of amino acids and poly-amino acids.

The hypothesis on exogenous origin of organic matter on the early Earth is strongly supported by the detection of a large variety of organic compounds (including amino acids and nucleobases) in carbonaceous chondrites. Whether such complex species can be successively delivered by other space bodies (comets, asteroids and interplanetary dust particles) is unclear and depends primarily on capability of the biomolecules to survive high temperatures during atmospheric deceleration and impacts to the terrestrial surface. Recent simulation experiments on amino acid and nucleic acid base pyrolysis under oxygen-free atmosphere demonstrated that simple representatives of these (considered thermally unstable) compounds can survive at 1-10% level a rapid heating at 500-600 degrees C. In the present work, we report on new data on the pyrolysis of amino acids and their homopolymers and discuss implications of their thermal behavior for extraterrestrial delivery.

Quantum chemical calculations of infrared spectra for the identification of unknown compounds by GC/FTIR/MS in exobiological simulation experiments.

Gas chromatography/Fourier transform IR spectroscopy/mass spectrometry (GC/FTIR/MS) is a powerful tool for the separation and unambiguous identification of complex mixtures of organic compounds, where the use of two kinds of spectra allows to significantly increase identification reliability. The simplest situation is when acquired spectra can be found in IR and MS databases, or appropriate standards are available; but this is not always the case. Some simulation experiments related to the origins of life and exobiology (e.g., simulation of amino acid pyrolysis during atmospheric entry of space bodies) can be a typical example when one encounters with numerous unknown compounds. To assist their identification by GC/FTIR/MS, recently we suggested quantum chemical calculations of infrared spectra in order to compare them to IR spectra acquired experimentally. The present work summarizes the results obtained by semi-empirical and ab initio methods, discusses their advantages and limitations, considering as test compounds some cyclic amides and amidines derived from amino acids, saturated and unsaturated nitriles (including those of interest for the Titan atmospheric chemistry), acetylenes and some other nitrogen compounds.

Some observations on amino acid racemization under pyrolytic temperatures and inorganic oxide-catalyzed intermolecular condensation.

The problem of homochirality is of crucial importance for the origins of Life. While most laboratory studies are focused on the search of physical and chemical sources of handedness in the Universe, they reflect only one aspect of the problem: the origin of homochiral biomolecules. At the same time, any space environments where biomolecules are expected to form and where they have to pass through before the first primitive forms of Life emerge, include strong irradiation or/and high temperatures. This automatically implies the possibility of losing the optical activity, i.e. racemization. The simulation experiments performed by our group deal with the following two aspects of amino acid abiotic chemistry: (1) amino acid pyrolysis associated with their extraterrestrial delivery; and (2) peptide formation from amino acids catalyzed by inorganic oxides. According to our observations, the racemization phenomena are very common in the systems considered, not only under pyrolytic temperatures, but in some cases also under rather mild conditions (<100 degrees C). Our results put additional constraints on the environments where the chirality of biomolecules can be efficiently preserved.

Calculated gas-phase infrared spectra of 2,2,5,5,8,8-hexamethylhexahydroimidazo [1,2-a]-pyrazine-3,6-dione: relative performance of Hartree-Fock and hybrid density functional theory methods.

Geometric parameters and IR spectra of 2,2,5,5,8,8-hexamethylhexahydroimidazo[1,2-a]pyrazine-3,6-dione were computed by the HF, B3LYP, B3P86 and B3PW91 methods with the 6-31G(d) basis set. All the computation methods produce a boat conformation of the six-membered ring with the orientation opposite to the one experimentally observed, that is obviously due to incapability of such calculations to take into account mutual influence of the molecules in a crystal package. Quality of predicting the interatomic distances observed experimentally decreases in the series HF, B3LYP, B3PW91 and B3P86; for bond angles, in the series B3LYP, P3PW91, B3P86 and HF. At the same time, the IR spectra computed are in a good agreement with the observed FTIR spectrum. The correlation between the calculated and experimental vibration frequencies is characterized by the coefficients higher than 0.9999 for all three DFT methods; for HF it is slightly lower than 0.9995. The calculated absolute band intensities satisfactory match the observed relative intensities as well. Optimal uniform scaling factors calculated are 0.8973, 0.9593, 0.9540 and 0.9552 for HF, B3LYP, B3P86 and B3PW91, respectively.

(C-rac-5,5,7,12,12,14-Hexamethyl-1,4,8,11-tetraazacyclotetradecane-kappa4N)(nicotinato-O,O')nickel(II) perchlorate.

In the title compound, [Ni(C(6)H(4)NO(2))(C(16)H(36)N(4))]ClO(4), the macrocyclic unit adopts a folded conformation, allowing the two carboxyl O atoms to occupy two neighbouring coordination sites and thus form an additional four-membered chelate ring. The less crowded side of the macrocycle (that with the two asymmetric C-H groups) is directed towards the nicotinate anion and the asymmetric C-CH(3) groups are directed away from it. The macrocyclic NH groups neighbouring the C-CH(3) groups are also directed away from the nicotinate anion, while those NH groups which are near to the geminal methyl groups are directed towards the nicotinate anion. Although the complex does not include water molecules, three types of hydrogen bond were found, involving NH groups of the macrocyclic ligand, pyridine N atoms and O atoms of the perchlorate anions.

PM3, AM1, MNDO and MINDO3 semi-empirical IR spectra simulations for compounds of interest for Titan's chemistry: diazomethane, methyl azide, methyl isocyanide, diacetylene and triacetylene.

Four semi-empirical methods (PM3, AM1, MNDO and MINDO3) have been tested to find the best auxiliary tool for the gas chromatography/Fourier transform IR spectroscopy/mass spectrometry (GC/FTIR/MS) identification of five compounds of interest for Titan's atmospheric chemistry as test compounds: diacetylene, triacetylene, diazomethane, methyl azide, methyl isocyanide. Of the four methods, MINDO3 can be considered as the most appropriate method to facilitate the identification of such and similar compounds, since (1) the simulated IR spectra best match the experimental spectra for four compounds of five studied; and (2) MINDO3 provides the best linearity between the calculated and experimental frequencies (correlation coefficient of 0.995; a scaling factor of 0.84 can be applied to afford better correspondence between the calculated and experimental wavenumbers). None of the semi-empirical methods tested is able to predict (even approximately) infrared band intensities, and therefore a spectral intensity pattern.

PM3, AM1, MINDO3 semi-empirical IR spectra simulations for some nitriles of interest for Titan's chemistry.

A set of the semi-empirical methods (PM3, AM1, MNDO and MINDO3) has been tested to find the best auxiliary tool for the identification of nitriles by gas chromatography/Fourier transform IR spectroscopy/mass spectrometry, considering five nitriles of interest for Titan's chemistry as test compounds: acetonitrile, acrylonitrile, cyanoacetylene, 2-butynenitrile and dicyanoacetylene. Of the four semi-empirical methods, MNDO can be considered as the most advantageous auxiliary tool for the gas chromatography/Fourier transform IR spectroscopy/mass spectrometry (GC/FTIR/MS) identification of nitriles of interest for Titan's atmospheric chemistry, since (1) the simulated IR spectra best match the experimental (in some cases AM1 gives comparable results); (2) it provides the best linearity between the calculated and experimental frequencies (correlation coefficient of 0.990); a scaling factor of 0.90 can be applied to afford better correspondence between the calculated and experimental wavenumbers. At the same time, none of the methods is able to predict infrared intensities and a spectral intensity pattern.

Transport of extraterrestrial biomolecules to the Earth: problem of thermal stability.

The idea of extraterrestrial delivery of organic matter to the early Earth is especially attractive at present and is strongly supported by the detection of a large variety of organic compounds, including amino acids and nucleobases, in carbonaceous chondrites. Whether these compounds can be delivered by other space bodies is unclear and depends primarily on capability of the biomolecules to survive high temperatures during atmospheric deceleration and impacts to the terrestrial surface. In the present study we estimated survivability of simple amino acids (alpha-aminoisobutyric acid, L-alanine, L-valine and L-leucine), purines (adenine and guanine) and pyrimidines (uracil and cytosine) under rapid heating to temperatures of 400 to 1000 degrees C under N2 or CO2 atmosphere. We have found that most of the compounds studied cannot survive the temperatures substantially higher than 700 degrees C; however at 500-600 degrees C, the recovery can be at a per cent level (or even 10%-level for adenine, uracil, alanine, and valine). Implications of the data for extraterrestrial delivery of the biomolecules are discussed.

Behavior of amino acids when volatilized in the presence of silica gel and pulverized basaltic lava.

To evaluate the types of amino acid thermal transformations caused by silicate materials, we studied the volatilization products of Aib, L-Ala, L-Val and L-Leu under temperatures of up to 270 degrees C in the presence of silica gel as a model catalyst and pulverized basaltic lava samples. It was found that silica gel catalyzes nearly quantitative condensation of amino acids, where piperazinediones are the major products, whereas lava samples have much lower catalytic efficiency. In addition bicyclic and tricyclic amidines and several products of their subsequent thermal decomposition have been identified using the coupled technique of GC-FTIR-MS and HPLC-PB-MS, with auxiliary computer simulation of IR spectra and NMR spectroscopy. The decomposition is due to dehydrogenation, elimination of the alkyl substituents and dehydration as well as cleavage of the bicyclic ring system. The imidazole ring appears to be more resistant to thermal decomposition as compared to the pyperazine moiety, giving rise to the formation of different substituted imidazolones. The amidines were found to hydrolyze under treatment with concentrated HCl, releasing the starting amino acids and thus behaving as amino acid anhydrides. The thermal transformations cause significant racemization of amino acid residues. Based on our observations, the formation of amidine-type products is suggested to be rather common in the high-temperature experiments on amino acid condensation.

Possible role of volcanic ash-gas clouds in the Earth's prebiotic chemistry.

Volcanic ash-gas clouds represent versatile local atmospheric environments appropriate for abiotic synthesis of rather complex organic molecules due to the simultaneous presence of various gaseous reagents, catalytically active inorganic particles, electric discharges, pressure and temperature gradients. They are relatively readily attainable for the scientists, contrary to objects or events of space origin (interstellar and planetary dust, meteoritic/cometary impacts, etc.), providing excellent opportunities for in situ studies and grounded simulating experiments. This paper reviews the available data on this environment, its most important chemical and physical parameters. Based on this analysis, it is suggested in brief experimental conditions for the simulation.

Dust in the Universe: implications for terrestrial prebiotic chemistry.

In the present review we analyze the available literature on the distribution of dust in the Universe, methods of its observation and determination of the chemical composition, and the roles for terrestrial prebiotic chemistry. The most plausible natural sources of dust on the Earth in the prebiotic era are sedimentation of interplanetary dust, meteoritic and cometary impacts, volcanic eruptions, and soil microparticulates; the interplanetary medium being among the most powerful supplier of the dust matter. Two fundamental roles of dust particles for the origins of life are considered: (1) catalytic formation of prebiotic compounds; and (2) delivery of organic matter to the Earth by space dust particles. Due to the fact that there is only approximate information on the chemical composition and properties of interstellar, circumstellar, and major part of interplanetary dust, even the simulating experiments are difficult to perform. Until these gaps are filled, it seems reasonable to focus efforts of the scientists dealing with dust-driven catalytic formation of prebiotically important compounds on the volcanic and meteoritic/cometary impact environments.

Adsorption of small biological molecules on silica from diluted aqueous solutions: quantitative characterization and implications to the Bernal's hypothesis.

To describe quantitatively the adsorption of prebiotically important compounds of low molecular weight (amino acids, short linear peptides, cyclic dipeptides, the Krebs's cycle and other carboxylic acids, nucleosides and related phosphates) on silica surface from diluted neutral aqueous solutions, equilibrium constants (K) and free energies (-delta G) of adsorption were determined from the retention values measured by means of high-performance liquid chromatography on a silica gel column and from the isotherms measured under static conditions. For most carboxylic acids (including amino acids and linear peptides) -delta G values were negative and K < 1, thus showing very weak adsorption. Cyclic dipeptides (2,5-piperazinediones) exhibited higher adsorbability; -delta G > 0 and K > 1 were found for most of them. Influence of the structure of alpha-substituent on the adsorbability is analyzed. A linear dependence of -delta G on the number of aliphatic carbon atoms in a sorbate molecule was found for the series of aliphatic bifunctional amino acids, related dipeptides and 2,5-piperazinediones, as well as for the row from glycine to triglycyl glycine. The adsorption of nucleosides and their phosphates is characterized by much higher K and -delta G values (of the order of 10(2) and 10(4), respectively). The adsorption data available from our work and literature are summarized and discussed with implications to the Bernal's hypothesis on the roles of solid surfaces in the prebiotic formation of biopolymers from monomeric 'building blocks'.

Free energies of amino acid adsorption on silica in neutral aqueous medium as estimated from high-performance liquid-chromatographic retention data.

Equilibrium constants (K) and free energies (-ΔG) of amino acid adsorption on silica in a neutral aqueous medium were calculated from the retention values measured by means of high-performance liquid chromatography on a silica gel column. For most amino acids (with the exception of proline) -ΔG values were negative andK < 1, thus showing very low adsorption. Influence of the structure of theα-substituent on adsorbability is analyzed. A linear dependence of -ΔG on the number of aliphatic carbon atoms was shown for the series: glycine-alanine-valine-leucine-isoleucine.

Condensation of vaporous amino acids in the presence of silica. Formation of bi- and tricyclic amidines.

Amino acids (alanine, valine, norvaline, leucine, and 2-aminoisobutyric acid) were subjected to repeated (5-9 times) sublimation in the presence of silica at temperature of 220-240 degrees C. The major amino acid condensation products were diketopiperazines (DKPs) in yields of 27-89%. Mixtures of by-products have been isolated from the DKPs by means of chloroform extraction. On the basis of fast atom bombardment mass spectrometric studies of the mixtures it is proposed that under these conditions further dehydration proceeds resulting in bicyclic (BCA) and tricyclic (TCA) amidine derivatives of DKPs; the BCA formation has been confirmed by means of IR and 1H NMR spectroscopy in the case of 2-aminoisobutyric acid. During the sublimation, thermal destruction of the cyclic products was also observed accompanied by the cycle degradation and cleavage of alkyl substituents. The BCAs and TCAs are considered as possible sources of linear di- and tripeptides.

Growth of peptide chains on silica in absence of amino acid access from without.

Changes in IR spectra during thermal treatment of chemisorption products of glycine and valine vapours on dehydrated silica surfaces have been studied. Peptide products were formed from these chemisorbed species. A scheme of peptide chain growth on the silica surface is suggested based on the idea of ester type "activated intermediates".