Chirality, photochemistry and the detection of amino acids in interstellar ice analogues and comets

The primordial appearance of chiral amino acids was an essential component of the asymmetric evolution of life on Earth. In this tutorial review we will explore the original life-generating, symmetry-breaking event and summarise recent thoughts on the origin of enantiomeric excess in the universe. We will then highlight the transfer of asymmetry from chiral photons to racemic amino acids and elucidate current experimental data on the photochemical synthesis of amino and diamino acid structures in simulated interstellar and circumstellar ice environments. The chirality inherent within actual interstellar (cometary) ice environments will be considered in this discussion: in 2014 the Rosetta Lander Philae onboard the Rosetta space probe is planned to detach from the orbiter and soft-land on the surface of the nucleus of comet 67P/Churyumov-Gerasimenko. It is equipped for the in situ enantioselective analysis of chiral prebiotic organic species in cometary ices. The scientific design of this mission will therefore be presented in the context of analysing the formation of amino acid structures within interstellar ice analogues as a means towards furthering understanding of the origin of asymmetric biological molecules.     

DFT studies of squarylium and core‐substituted squarylium dye derivatives: understanding the causes of the additional shorter wavelength absorption in the latter

Recent reports indicate that the core‐substituted squarylium (CSQ) dyes (obtained when one oxygen atom of the SQ moiety is replaced by an electron withdrawing group or sulfur) show bathochromic shift of the absorption maxima and an additional shorter wave length absorption in visible when compared to parent SQ dyes. To investigate this interesting property of these dyes which will be more suitable for applications in DSSC, a comparative study using computational techniques of some selected SQ and CSQ derivatives has been carried out. The effect of this core substitution on geometries is studied. The ground state charge distribution is analyzed by natural population analysis. It is noticed that the biradical character, which is normally large in SQ derivatives, is reduced in CSQ due to the substitution and the zwitterionic character is increased. The absorption maxima for both parent SQ and CSQ dyes obtained with TD‐DFT methods using various functional like B3LYP, M06‐2X and CAM‐B3LYP methods do not match the experimental results. However, results obtained using SAC‐CI method are better. Charge transfer (CT) data based on Mulliken charges of both ground and excited states is obtained from SAC/SAC‐CI studies. It is seen that on excitation substantial CT from the side groups to the central core is taking place in parent SQ molecules. In contrast, intense CT occurs from –X to side groups through central core in the case of CSQ molecules. This study will be helpful in designing and synthesizing new CSQ dyes which makes them suitable for solar cell applications. Copyright © 2012 John Wiley & Sons, Ltd.     

Dynamics and mechanism of DNA repair in a biomimetic system: flavin-thymine dimer adduct

To mimic photolyase for efficient repair of UV-damaged DNA, numerous biomimetic systems have been synthesized, but all show low repair efficiency. The molecular mechanism of this low-efficiency process is still poorly understood. Here we report our direct mapping of the repair processes of a flavin-thymine dimer adduct with femtosecond resolution. We followed the entire dynamic evolution and observed direct electron transfer (ET) from the excited flavin to the thymine dimer in 79 ps. We further observed two competitive pathways, productive dimer ring splitting within 435 ps and futile back-ET in 95 ps. Our observations reveal that the underlying mechanism for the low repair quantum yield of flavin-thymine dimer adducts is the short-lived excited flavin moiety and the fast dynamics of futile back-ET without repair.     

Theoretical insights into the mechanism of carbon monoxide (CO) release from CO-releasing molecules

We used density functional theory to investigate the capacity for carbon monoxide (CO) release of five newly synthesized manganese-containing CO-releasing molecules (CO-RMs), namely CORM-368 (1), CORM-401 (2), CORM-371 (3), CORM-409 (4), and CORM-313 (5). The results correctly discriminated good CO releasers (1 and 2) from a compound unable to release CO (5). The predicted Mn-CO bond dissociation energies were well correlated (R(2) ≈0.9) with myoglobin (Mb) assay experiments, which quantified the formation of MbCO, and thus the amount of CO released by the CO-RMs. The nature of the Mn-CO bond was characterized by natural bond orbital (NBO) analysis. This allowed us to identify the key donor-acceptor interactions in the CO-RMs, and to evaluate the Mn-CO bond stabilization energies. According to the NBO calculations, the charge transfer is the major source of Mn-CO bond stabilization for this series. On the basis of the nature of the experimental buffers, we then analyzed the nucleophilic attack of putative ligands (L' = HPO(4)(2-), H(2)PO(4)(-), H(2)O, and Cl(-)) at the metal vacant site through the ligand-exchange reaction energies. The analysis revealed that different L'-exchange reactions were spontaneous in all the CO-RMs. Finally, the calculated second dissociation energies could explain the stoichiometry obtained with the Mb assay experiments.     

Substituents destabilize the molecule by increasing biradicaloid character and stabilize by intramolecular charge transfer in the derivatives of benzobis(thiadiazole) and thiadiazolothienopyrazine: a computational study

Keeping in view the possible applications of singlet open-shell molecules as semiconductors, non-classical derivatives of the heterocyclic rings benzobis(thiadiazole) (BBT) and its positional isomer thiadiazolothienopyrazine (TTP) are characterized using DFT methodologies. M06-2X, B3LYP and BHandHLYP functionals were used to optimize the geometries and estimate the vertical transition energies. It is observed that unlike the BHandHLYP functional (50% exchange), which gives rise to spin-contaminated solutions for all molecules in the series, M06-2X (54% exchange) affords a wavefunction either with no instability or negligible instability for most of the molecules. The results are compared with the earlier reported experimental data and those obtained herein using the spin-flip (SF)-5050 method. It is found that B3LYP does not fare well while on the other hand the M06-2X and SF-50-50 are in good agreement with the experimental results. It is seen that M06-2X TD-DFT for the molecules can be carried out without major spin contamination and also that the more time-consuming CI can be avoided for the calculation of transition energies. The biradical nature of the molecules is estimated by the singlet-triplet gap. Intramolecular charge transfer is calculated. It is found that the ring substituents donate charge in the ground state, creating a zwitterionic structure. Thus the substituents play an interesting dual role, decreasing the stability of the molecule by increasing the biradical character (small HOMO-LUMO gap), and stabilization of this ground state by intramolecular charge transfer.     

Selenoglycosides in silico: ab initio-derived reparameterization of MM4, conformational analysis using histo-blood group ABH antigens and lectin docking as indication for potential of bioactivity

The identification of glycan epitopes such as the histo-blood group ABH determinants as docking sites for bacterial/viral infections and signals in growth regulation fuels the interest to develop non-hydrolysable mimetics for therapeutic applications. Inevitably, the required substitution of the linkage oxygen atom will alter the derivative’s topology. Our study addresses the question of the impact of substitution of oxygen by selenium. In order to characterize spatial parameters and flexibility of selenoglycosides, we first performed ab initio calculations on model compounds to refine the MM4 force field. The following application of the resulting MM4R version appears to reduce the difference to ab initio data when compared to using the MM4 estimator. Systematic conformational searches on the derivatives of histo-blood group ABH antigens revealed increased flexibility with acquisition of additional low-energy conformer(s), akin to the behavior of S-glycosides. Docking analysis using the Glide program for eight test cases indicated potential for bioactivity, giving further experimental investigation a clear direction to testing Se-glycosides as lectin ligands.     

Effect of wall thickness on the end corrections of the extended inlet and outlet of a double-tuned expansion chamber

Simple expansion chambers, the simplest of the muffler configurations, have very limited practical application due to the presence of periodic troughs in the transmission loss spectrum which drastically lower the overall transmission loss of the muffler. Tuned extended inlet and outlet can be designed to nullify three-fourths of these troughs, making use of the plane wave theory. These cancellations would not occur unless one altered the geometric lengths for the extended tube in order to incorporate the effect of evanescent higher-order modes (multidimensional effect) through end corrections or lumped inertance approximation at the area discontinuities or junctions. End corrections of the extended inlet and outlet have been studied by several researchers. However the effect of wall thickness of the inlet/outlet duct on end correction has not been studied explicitly. This has significant effect on the tuning of an extended inlet/outlet expansion chamber. It is investigated here experimentally as well as numerically (through use of 3-D FEM software) for stationary medium.     

Alternate and Efficient Method for the Total Synthesis of Egonol via Sonogashira Coupling Reaction

Efficient method for the total synthesis of egonol in five steps via Sonogashira coupling reaction is reported.