Tereza Varnali

Scytonemin: molecular structural studies of a key extremophilic biomarker for astrobiology

Ab initio calculations for scytonemin, an important ultraviolet (UV)-radiation protective biomolecule synthesized by extremophilic cyanobacteria in stressed terrestrial environments, are reported for the first time. Vibrational spectroscopic assignments for the previously studied Raman spectra assist in the identification of the major features in the observed data. Calculations of the electronic absorption spectra confirm the capability of this molecule to absorb in all three regions of the UV, UVA, UVB and UVC, and also illustrate the need for a dimeric species in this respect. The presence of significant steric hindrance between the two halves of the dimeric molecule about the C—C bridging bond in scytonemin forces the molecule significantly out of planarity, contrary to assumptions made in the literature; however, it appears that the monomer is capable of absorbing to only a limited extent in the UVB and UVC regions only, so conferring a special emphasis upon the need for the dimerization to remove the lower-energy UV radiation whilst still affording protection for the chlorophyll with transmission of the visible radiation required for photosynthesis. The observation of vibrational band wavenumber coincidences for the first time between the infrared and Raman spectra confirm the non-planar structural prediction from the calculations. The results of this study provide information about the protective chemical strategies of terrestrial extremophilic cyanobacteria and provide a basis for the search for molecules of this type in the astrobiological exploration of Mars.

Ab initio calculations of scytonemin derivatives of relevance to extremophile characterization by Raman spectroscopy.

The recognition that scytonemin, the radiation protectant pigment produced by extremophilic cyanobacterial colonies in stressed terrestrial environments, is a key biomarker for extinct or extant life preserved in geological scenarios is critically important for the detection of life signatures by remote analytical instrumentation on planetary surfaces and subsurfaces. The ExoMars mission to seek life signatures on Mars is just one experiment that will rely upon the detection of molecules such as scytonemin in the Martian regolith. Following a detailed structural analysis of the parent scytonemin, we report here for the first time a similar analysis of several of its methoxy derivatives that have recently been extracted from stressed cyanobacteria. Ab initio calculations have been carried out to determine the most stable molecular configurations, and the implications of the structural changes imposed by the methoxy group additions on the spectral characteristics of the parent molecule are discussed. The calculated electronic absorption bands of the derivative molecules reveal that their capability of removing UVA wavelengths is removed while preserving the ability to absorb the shorter wavelength UVB and UVC radiation, in contrast to scytonemin itself. This is indicative of a special role for these molecules in the protective strategy of the cyanobacterial extremophiles.

Iron-scytonemin complexes: DFT calculations on new UV protectants for terrestrial cyanobacteria and astrobiological implications.

Cyanobacterial colonies produce the radiation-protectant biomolecule scytonemin as part of their response strategy for survival in environmentally stressed conditions in hot and cold deserts. These colonies frequently use sandstone rocks as host matrices for subsurface colonization, which is accompanied by a zone of depletion of iron and transportation of iron compounds to the mineral surface. It is suggested that an iron-scytonemin complex could feature in this survival strategy and facilitate the movement of iron through the rock. Calculations were carried out on several hypothetical iron-scytonemin complexes to evaluate the most stable structure energetically and examine the effect of the complexation of the biomolecule upon the electronic absorption characteristics of the radiation-protectant species. The implications for extraterrestrial planetary detection and analytical monitoring of an iron-scytonemin complex are assessed.

Associated species of dimethylsulfoxide: Semiempirical modeling

Quantum chemical calculations have been carried to gain insight into the self-association of dimethylsulfoxide (DMSO), the interaction of DMSO with a solvent, and the protonation of DMSO. Different species that may be present in DMSO solutions have been modeled semiempirically.

Geometrical consequences of resonance-assisted hydrogen bonding in 2-nitrovinyl alcohol and indication of a slight attractive O⋯H interaction in 2-nitroethanol. An ab initio molecular orbital investigation

Abstract Ab initio molecular orbital calculations on 2-nitrovinyl alcohol and 2-nitroethanol and their parent structures have been performed with a 6-31G∗∗ basis set, including electron correlation using second-order Moller-Plesset perturbation theory. There is resonance-assisted hydrogen bonding in 2-vinyl alcohol, as witnessed by a 1.75 A long O…H interaction and considerable bond length changes in the rest of the molecule, as compared with nitroethylene and vinyl alcohol. Slight bond length changes in 2-nitroethanol point to some attractive O…H interaction even in 2-nitroethanol.

Reduced and oxidised scytonemin: Theoretical protocol for Raman spectroscopic identification of potential key biomolecules for astrobiology

Scytonemin is an important UV-radiation protective biomolecule synthesised by extremophilic cyanobacteria in stressed terrestrial environments. Scytonemin and its reduced form have been both isolated experimentally and the Raman spectrum for scytonemin has been assigned and characterised experimentally both in extracts and in living extremophilic cyanobacterial colonies. Scytonemin is recognised as a key biomarker molecule for terrestrial organisms in stressed environments. We propose a new, theoretically plausible structure for oxidised scytonemin which has not been mentioned in the literature hitherto. DFT calculations for scytonemin, reduced scytonemin and the new structure modelled and proposed for oxidised scytonemin are reported along with their Raman spectroscopic data and λmax UV-absorption data obtained theoretically. Comparison of the vibrational spectroscopic assignments allows the three forms of scytonemin to be detected and identified and assist not only in the clarification of the major features in the experimentally observed Raman spectral data for the parent scytonemin but also support a protocol proposed for their analytical discrimination. The results of this study provide a basis for the search for molecules of this type in future astrobiological missions of exploration and the search for extinct and extant life terrestrially.

Conformational equilibria of α-substituted carbonyl compounds. Study of solvent effects

Abstract PM3 computations have been performed to study confonnational equilibria of a series of α-substituted carbonyl compounds in solution. The solvent is taken into account in the calculations by using cavity models. The compounds studied are a series of substituted acetaldehydes CH2R-CHO and cyclohexanones C6H9OR (R = F, Cl, Br, CN, NO;). The predicted solvent effects are in agreement with available experimental data. The discussion emphasizes the role played by the multipole moments and the necessity of going beyond the ellipsoidal cavity shape approximation in the case of substituted cyclohexanones.

STRUCTURES AND ENERGETICS OF PROTON-BOUND FORMIC ACID-WATER CLUSTERS, (HCOOH)N(H2O)H+

Abstract Semiempirical and ab initio calculations have been performed on proton-bound mixed clusters (HCOOH)n(H2O)H+ with n = 1–8. Energetically competitive structures were deduced: open-chain structures with a H2O unit at the end are favored energetically for lower members (n

AB INITIO STUDY ON THE CONFORMATIONAL BEHAVIOUR OF ETHANE-1,1-DIOL and ETHANE-1,1,2-TRIOL IN SOLUTION

Ab initio optimizations at the HF/6–31G level and single-point calculations at the MP2/6–31G**//6–31G level were performed on ethane-1,1-diol and ethane-1,1,2-triol. Their conformational properties are discussed in terms of the anomeric effect, gauche effect and internal O–H interactions. The results showed a parallel behaviour with ethane-1,2-diol. The solvent effect was taken into account using the SCRF theory with a general cavity shape which is defined by the molecular surface.

Raman spectroscopic identification of scytonemin and its derivatives as key biomarkers in stressed environments.

Raman spectroscopy has been identified as an important first-pass analytical technique for deployment on planetary surfaces as part of a suite of instrumentation in projected remote space exploration missions to detect extant or extinct extraterrestrial life signatures. Aside from the demonstrable advantages of a non-destructive sampling procedure and an ability to record simultaneously the molecular signatures of biological, geobiological and geological components in admixture in the geological record, the interrogation and subsequent interpretation of spectroscopic data from these experiments will be critically dependent upon the recognition of key biomolecular markers indicative of life existing or having once existed in extreme habitats. A comparison made with the characteristic Raman spectral wavenumbers obtained from standards is not acceptable because of shifts that can occur in the presence of other biomolecules and their host mineral matrices. In this paper, we identify the major sources of difficulty experienced in the interpretation of spectroscopic data centring on a key family of biomarker molecules, namely scytonemin and its derivatives; the parent scytonemin has been characterized spectroscopically in cyanobacterial colonies inhabiting some of the most extreme terrestrial environments and, with the support of theoretical calculations, spectra have been predicted for the characterization of several of its derivatives which could occur in novel extraterrestrial environments. This work will form the foundation for the identification of novel biomarkers and for their Raman spectroscopic discrimination, an essential step in the interpretation of potentially complex and hitherto unknown biological radiation protectants based on the scytoneman and scytonin molecular skeletons which may exist in niche geological scenarios in the surface and subsurface of planets and their satellites in our Solar System.