Search for Chirality in Hydrogenated Magnesium Nanosilicates: A DFT and TD-DFT Investigation
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Kamil B. Stelmach↗
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Remote Enantioselection Transmitted by an Achiral Peptide Nucleic Acid Backbone
short homochiral segment of DNA into a PNA helix could have guaranteed that the next short segment of DNA to be incorporated would have the same handedness as the first. Once two segments of the same handedness were present, the probability that a third segment would have the same handedness would increase, and so on. Evolution could then slowly dilute out the PNA part. This scenario would ultimately allow the formation of a chiral oligonucleotide by processes that are largely resistant to enantiomeric crossinhibition. It is important to note that the ligation of homochiral dinucleotides on a nucleic acid template would probably be at least as enantiospecific as the reaction that we have studied. The disadvantage of using chiral monomers as components of a replicating system arises from the difficulty of generating a first long homochiral template from a racemic mixture of monomers, although results of experiments designed to overcome this difficulty by employing homochiral tetramers have been reported.l l The probability of obtaining a homochiral n-mer from achiral substrates is approximately 1P-I if the nontemplate-directed extension of the primer is not enantioselective. Hence, it would be very hard to get started with a homochiral 40-mer, for example. No such difficulty exists in a scenario that originates with an achiral genetic material and in which the incorporation of very few chiral monomers in this achiral background gradually progresses towards homochirality. It seems possible that some PNA sequences could act as catalysts, analogous to ribozymes, even though PNA lacks clear metal binding sites. Although such catalysts could not be enantioselective, the incorporation of as few as two chiral nucleotides could then impose chiral specificity on the system. Furthermore, such patch chimeras could help to bridge the gap in catalytic potential between PNA and RNA, while guaranteeing enantioselectivity.
Kozlov, Igor A.↗
Bacterial Utilization of L-sugars and D-amino Acids
The fact that organotrophic organisms on Earth use L-amino acids and D-sugars as an energy source is recognized as one of the universal features of life. The chirality of organic molecules with asymmetric location of group- radicals was described a relatively long time ago. In 1848, Louis Pasteur discovered chiral molecules when he investigated the way that crystals of sodium ammonium paratartrate rotated the plane of polarization of light. He found that the crystal structures represented the underlying asymmetry of molecules that existed in either lea-handed or right-handed forms (enantiomers). Pasteur observed that abiotic (chemical) processes produced mixtures with equal numbers (racemic) of the two forms but that living organisms possessed a molecular asymmetry that included only one of the enantiomers (homochirality). He speculated that the origin of the asymmetry of chiral biomolecules might hold the key to the nature of life. All of the amino acids in proteins (except for Glycine which is symmetrical) exhibit the same absolute steric configuration as L-glyceraldehyde. D-amino acids are never found in proteins, although they do exist in nature and are often found in polypeptide antibiotics. Constitutional sugars of cells, opposite to the amino acids, are the D-enantiomers, and the appearance of L-sugars in Nature is extremely rare. Notwithstanding this fact, the metabolism of some bacteria does have capability to use amino acids and sugars with alternative chirality. This property may be caused by the function of specific enzymes belonging to the class of isomerases (racemases, epimerases, isomerases, tautomerases). In our laboratory, we have investigated several anaerobic bacterial strains, and have found that some of these bacteria are capable of using D-amino acids and L-sugars. Strain BK1 is capable of growth on D-arginine, but its growth characteristics on L-arginine are approximately twice higher. Another alkaliphilic strain SCAT(sup T) (= ATCC BAA-1084(sup T)= JCM 12857(sup T) = DSM 17722(sup T) = CIP 107910(sup T)) was found to be capable of growth on L-ribose and L-arabinose. It is interesting that this strain was incapable of growth on D-arabinose, which suggests the involvement of some alternative mechanism of enzyme activity. In this paper, we describe the preliminary results of these microbiological studies and discuss some possible implications.
Pikuta, Elena↗
Magnetic Helicity Condensation and the Solar Cycle
Solar filaments exhibit a global chirality pattern where dextral/sinistral filaments, corresponding to negative/ positive magnetic helicity, are dominant in the northern/southern hemisphere. This pattern is opposite to the sign of magnetic helicity injected by differential rotation along east–west oriented polarity inversion lines, posing a major conundrum for solar physics. A resolution of this problem is offered by the magnetic helicity-condensation model of Antiochos. To investigate the global consequences of helicity condensation for the hemispheric chirality pattern, we apply a temporally and spatially averaged statistical approximation of helicity condensation. Realistic magnetic field configurations in both the rising and declining phases of the solar cycle are simulated. For the helicity-condensation process, we assume convective cells consisting of positive/negative vorticities in the northern/southern hemisphere that inject negative/positive helicity. The magnitude of the vorticity is varied as a free parameter, corresponding to different rates of helicity injection. To reproduce the observed percentages of dominant and minority filament chiralities, we find that a vorticity of magnitude 2.5 x 10(exp −6)/s is required. This rate, however, is insufficient to produce the observed unimodal profile of chirality with latitude. To achieve this, a vorticity of at least 5 x 10(exp −6)/s is needed. Our results place a lower limit on the small-scale helicity injection required to dominate differential rotation and reproduce the observed hemispheric pattern. Future studies should aim to establish whether the helicity injection rate due to convective flows and/or flux emergence across all latitudes of the Sun is consistent with our results.
Mackay, Duncan H.↗
New estimates of asymmetric decomposition of racemic mixtures by natural beta-radiation sources
Some recent calculations that appeared to invalidate the Vester-Ulbricht hypothesis, which suggests that the chirality of biological molecules originates from the beta-radiolysis of prebiotic racemic mixtures, are reexamined. These calculations apparently showed that the radiolysis-induced chiral polarization can never exceed the chiral polarization produced by statistical fluctuations. It is here shown that several overly restrictive conditions were imposed on these calculations which, when relaxed, allow the radiolysis-induced polarization to exceed that produced by statistical fluctuations, in accordance with the Vester-Ulbricht hypothesis.
Hegstrom, R. A.↗
Freely Suspended Smectic Filaments and the Structure of the B7 Phase of MHOBOW
Our recent discovery of the spontaneous formation of chiral domains in fluid smectic phases of achiral bow-shaped molecules opens up a wide variety of possibilities for new liquid crystal phases and phenomena. The basic, spontaneously chiral layer structure of the highest temperature fluid smectic phases, the B2 and B7, are shown. One of the most intriguing aspects of this structure is the plethora of possible phases coming from different stacking sequences of the polar ordering and tilt directions. The four possibilities of next-nearest neighbor alternation are shown. In the original material studied, NOBOW, the ground states found are antiferroelectric, either the racemic SmC(sub S)P(sub A) or the chiral SmC(sub A)P(sub A). We are currently studying MHOBOW, synthesized by D. Walba which, by virtue of its methyl hexyloxy tail has a tendency to form anticlinic layer interfaces, in the hope of finding a phase with a ferroelectric ground state, either SmC(sub A)P(sub S) or SmC(sub S)P(sub A), which can be obtained in NOBOW only by applying a field. Preliminary observations of MHO-BOW have made its study, from the point of view of understanding novel LC structures, extremely high priority. The following truly remarkable characteristics have been revealed: (i) The smectic phase grows out of the isotropic in the form of helical ribbons. The resulting planar aligned textures of focal conics with layers normal to glass plates exhibit bizarre modulations, including stripes and checker-boards. These have also been seen in other materials suggesting that this is a new phase (tentatively called B7), which is a fluid smectic with some kind of in-layer structure. (ii) It is virtually impossible to make freely suspended films of MHOBOW. Rather it makes the freely suspended filaments which preliminary x-ray scattering experiments reveal to have the nested cylinder layer structure indicated; (iii) The powder x-ray diffraction exhibits four resolution-limited smectic layering peaks, very close in layer spacing, which vary continuously with T. This is further evidence for a more complex three dimensional structure than NOBOW, which has a typical single layering reflection. (iv) The x-ray structure factor of the layering peak of the filaments is extraordinarily complex and rich. Varying in qL (the scattering vector component along the filament axis) from a double slit-like pattern to modulated layer-like patterns, as qH (the scattering vector component normal to the filament axis) is varied over the range where the four powder peaks are located. These results suggest some kind of mosaic structure, perhaps with different layer spacings corresponding to the different stacking sequences. Recent x-ray diffraction experiments show that the peaks are modulated in intensity upon translation along a filament, in domains of several hundred microns dimension. These preliminary experiments suggest that the B7 is a fluid smectic with extremely unusual and fascinating structures. Of all of the many hundreds of fluid smectic materials we have attempted to study in the freely suspended film geometry over the years, only a few have failed to form films, and none showed any great tendency to form filaments, although this clearly should be a possible freely suspended smectic LC morphology. On several occasions in the past we have intentionally tried to make filaments from a variety of smectics without success. Thus the smectic filament formation property makes the B7 phase unique. It seems quite likely that the stability of filaments is related to the in-plane structure. The filaments exhibit other interesting structural and optical features. They are birefringent with a local optic axis which is oblique and which can vary continuously along filament and which can be manipulated with an electric field applied normal to the fiber, as if the field were causing a rotation of the optic axis about the fiber axis. Rapid displacement of the ends of the fiber toward one another causes a macroscopic helixing at low T and causes thick regions to transiently appear at high T, a 1D analog of island formation on a rapidly compressed film.
Clark, N.↗
Micro-Detection System for Determination of the Biotic or Abiotic Origin of Amino Acids
The research carried out under this PIDDP involves the development of a breadboard version of a spacecraft-based system for the detection of amino acid chirality (molecular handedness) on solar system bodies. Chirality provides an unambiguous way of distinguishing between abiotic and biotic origins since only one mirror-image form is used in the functional molecules of life. Recent advances in a variety of nano-fabrication technologies have resulted in concepts for enabling miniaturized chemical and biological analytical systems. These are complete application-specific systems that integrate fluid micro handling systems for extracting and reacting target molecules, micro-separation technologies for enhanced sensitivity and resolution, and advanced detection technologies. This effort makes use of a relatively new technology that shows demonstrated promise for spacecraft-based amino acid analysis: microchip-based capillary electrophoresis (μCE). The μCE system is capable of analyzing the type of amino acids present as well as the relative amounts of their mirror image forms. The system we developed will be able to chirally resolve all of the major amino acids found in extraterrestrial material (Gly, Ala, Val, Pro, Asp, Glu, a-aminoisobutyric acid, and isovaline) at sub-part-per-billion levels. The -CE analysis requires that the amino acids be extracted from the sample and derivatized for either optical or electrochemical detection. In our implementation, the amino acids are released from the sample by sublimation and prepared for μCE analysis using a microfluidic circuit. In addition, we have investigated the use of a microfluidic circuit for the release of amino acids from samples in which sublimation has proven to be problematic.
Jeffrey L Bada↗
Racemization and the origin of optically active organic compounds in living organisms
The organic compounds synthesized in prebiotic experiments are racemic mixtures. A number of proposals have been offered to explain how asymmetric organic compounds formed on the Earth before life arose, with the influence of chiral weak nuclear interactions being the most frequent proposal. This and other proposed asymmetric syntheses give only sight enantiomeric excess and any slight excess will be degraded by racemization. This applies particularly to amino acids where half-lives of 10(5)-10(6) years are to be expected at temperatures characteristic of the Earth's surface. Since the generation of chiral molecules could not have been a significant process under geological conditions, the origins of this asymmetry must have occurred at the time of the origin of life or shortly thereafter. It is possible that the compounds in the first living organisms were prochiral rather than chiral; this is unlikely for amino acids, but it is possible for the monomers of RNA-like molecules.
NASA Discipline Exobiology↗
Selective adsorption of L- and D-amino acids on calcite: Implications for biochemical homochirality
The emergence of biochemical homochirality was a key step in the origin of life, yet prebiotic mechanisms for chiral separation are not well constrained. Here we demonstrate a geochemically plausible scenario for chiral separation of amino acids by adsorption on mineral surfaces. Crystals of the common rock-forming mineral calcite (CaCO(3)), when immersed in a racemic aspartic acid solution, display significant adsorption and chiral selectivity of d- and l-enantiomers on pairs of mirror-related crystal-growth surfaces. This selective adsorption is greater on crystals with terraced surface textures, which indicates that d- and l-aspartic acid concentrate along step-like linear growth features. Thus, selective adsorption of linear arrays of d- and l-amino acids on calcite, with subsequent condensation polymerization, represents a plausible geochemical mechanism for the production of homochiral polypeptides on the prebiotic Earth.
Calcium Carbonate/metabolism↗
Instrument for Solvent Extraction and Analysis (ISEE) of Organics from Regolith Simulant Using Supercritical Fluid Extraction and Chromatography
ISEE is an instrument with the potential to perform extractions from regolith found on the surface of asteroids and planets, followed by characterization and quantitation of the extracts using supercritical fluid extraction (SFE) and chromatography (SFC). SFE is a developed technique proven to extract a wide range of organic compounds. SFC is similar to High Performance Liquid Chromatography (HPLC) but has the advantage of performing chiral separations without needing to derivatize the chiral compounds. CO2 will be the solvent for both stages as it is readily available in the Mars atmosphere. ISEE will capture CO2 from the environment, and use it for SFE and SFC. If successful, this would allow ISEE to perform analysis of organic compounds without using consumables. This paper will present results on a preliminary, proof-of-principle effort to use SFE and SFC to extract and analyze lunar regolith simulant spiked with organic compounds representing a range of organics that ISEE would expect to characterize. An optimization of variables for the extraction of the organics from the spiked regolith was successfully developed, using 138 bar pressure and 40 C temperature. The extraction flow rate was optimized at 2% SLPM with 30% methanol modifier. The extractions were successful with a value of 77.3+/- 0.9% of organics extracted. However, the recovery of organics after the extraction was very low with only 48.5+/-14.2%. Moreover, three columns were selected to analyze multiple samples at a time; two of them are Viridis HSS C18 SB and Torus DIOL, and the third column, specific for chiral separations, has not yet been selected yet.
Franco, Carolina↗
Possible Mechanism(s) in the Photo-Magnetic Production of Enantiomer Excesses.
Among the multitude of organic compounds identified in carbonaceous chondrites are sugar acids ((HO-R)xCOOH), i.e., oxidized counterparts of the common aldehyde sugars (e.g., glyceraldehyde, erythrose, ribose, glucose, etc.). In the historical study of extraterrestrial compounds chiral analyses are particularly significant in origins-of-life studies. Chiral compounds are composed of two non-superposable mirror images or "enantiomers", analogous to a left and right hand. Such molecules are important in contemporary life because biological polymers (proteins, nucleic acids, etc.) are homochiral, i.e., their chiral monomers usually consist of only one of the two enantiomers. It has been shown, at least in one lab setting, that abiotic syntheses of significantly sized RNA polymers do not proceed if the monomers are present in racemic (50:50) amounts. The latter results may argue for, at least, significant enantiomer excesses in organic compounds before the origin of nucleic acids and life. Therefore, the finding that amino acids and sugar acids in carbonaceous chondrites possess enantiomeric excesses may aid in understanding one source of precursors to homochirality. Note: Attachment contains full abstract.
G. Cooper↗
Asymmetric adsorption by quartz - A model for the prebiotic origin of optical activity
One mechanism previously proposed for the abiotic accumulation of molecules of one chirality in nature is asymmetric adsorption on the chiral surfaces of optically active quartz crystals. Earlier literature in this field is reviewed, with the conclusion that previous investigations of this phenomenon, using optical rotation criteria, have afforded ambiguous results. We now have studied the adsorption of radioactive D- and L-alanine on powdered d- and l-quartz, using change in radioactivity level as a criterion for both gross and differential adsorption, d-Quartz preferentially adsorbed D-alanine from anhydrous dimethyl-formamide solution, and l-quartz L-alanine. The differential adsorption varied between 1.0 and 1.8%. The implications of these observations are discussed from the viewpoint of early chemical evolution and the origin of optically active organic compounds in nature.
Bonner, W. M.↗
Nonbonded interactions in membrane active cyclic biopolymers. IV - Cation dependence
Interactions of valinomycin and form of its analogs in several conformations with the central ions Li(+), Na(+), K(+), Rb(+) and Cs(+) are investigated as part of a study of the specific preference of valinomycin for potassium and the mechanisms of carrier-mediated ion transport across membranes. Ion binding energies and conformational potential energies are calculated taking into account polarization energy formulas and repulsive energy between the central ion and the ligand atoms for conformations representing various stages in ion capture and release for each of the two ring chiralities of valinomycin and its analogs. Results allow the prediction of the chirality and conformation most likely to be observed for a given analog, and may be used to synthesize analogs with a desired rigidity or flexibility. The binding energies with the alkali metal cations are found to decrease with increasing ion size, and to be smaller than the corresponding ion hydration energies. It is pointed out that the observed potassium preference may be explainable in terms of differences between binding and hydration energies. Binding energies are also noted to depend on ligand conformation.
Radhakrishnan, R.↗
On the stereoselective aminoacylation of RNA
Gabbay and Kleinman (1970) have found that stereospecific complex formation (noncovalent) occurs between nucleic acids and a number of derivatives of amino acids. However, until recently, chiral selection in any nonenzymatic RNA-aminoacylation reaction was unknown. Profy and Usher (1984) reported that aminoacylation of the 'internal' 2-prime-ester occurred with a significant amount of stereoselection. Profy and Usher (1984) have also observed that aminoacylation of the 'internal' 2-prime-hydroxyl groups of polyribonucleotides by the imidazolide of N-3,5-dinitrobenzoylalanine occurs with chiral selection. In order to obtain further information regarding the considered phenomena, a systematic investigation was initiated of the factors which contribute to the observed stereoselectivity of the aminoacylation reaction. In the present paper, the effect of a change in the amino acid from alanine to leucine is considered along with an investigation of the D- and L-alanyl internal' 2-prime esters of the dinucleoside monophosphate of 3-prime,5-prime-ApA.
Usher, D. A.↗
The evolution of nucleotides
Examples of chiral selection in nonenzymatic aminoacylation of internal 2-prime hydroxyl groups of oligo- and polynucleotides are discussed as an evidence for the early evolution of bionucleotides. Some factors that could influence the degree of this chiral selection and its direction are discussed. These include the structure of the aminoacyl component, the structure of the nucleoside component, and the reaction conditions. Investigation of the mechanism of this reaction was aided by the use of 3-prime inosine methyl phosphate (as a simplified model for a dinucleoside monophosphate) and proton NMR spectroscopy of t-butoxycarbonyl-alanyl esters of nucleosides as models for the transition state of the aminoacylation reaction itself.
Usher, D. A.↗
Enantiomeric Cross-Inhibition in the Synthesis of Oligonucleotides on a Nonchiral Template
Prebiotic syntheses of chiral monomers always yield racemic mixtures. Living systems, however, utilize L-amino acids and D-nucleotides in their biopolymers. The generation of optical asymmetry by selection and amplification in an autocatalytic process is, therefore, an important element in many theories of the origin of life. Replication of polynucleotides in template-directed syntheses is an obvious candidate for such an amplification step in a pre-'RNA world'. A serious objection to this suggestion is the observation that the efficiency of template-directed syntheses of RNA is limited by enantiomeric cross-inhibition. Peptide Nucleic Acids (PNAs), amide-linked, nonchiral analogues of RNA, have been 'copied' into RNA and constitute an alternative to chiral polynucleotides as an informational replicating system. Here, we use PNA as model for a hypothetical, nonchiral precursor of RNA in experiments re-examining enantiomeric cross-inhibition. We find that enantiomeric cross-inhibition is as serious in the polymerization of nucleotides on a PNA template as it is on a conventional RNA or DNA template.
Schmidt, Jurgen G.↗
Electronic Structure and Properties of Deformed Carbon Nanotubes
A theoretical framework based on Huckel tight-binding model has been formulated to analyze the electronic structure of carbon nanotubes under uniform deformation. The model successfully quantifies the dispersion relation, density of states and bandgap change of nanotubes under uniform stretching, compression, torsion and bending. Our analysis shows that the shifting of the Fermi point away from the Brillouin zone vertices is the key reason for these changes. As a result of this shifting, the electronic structure of deformed carbon nanotubes varies dramatically depending on their chirality and deformation mode. Treating the Fermi point as a function of strain and tube chirality, the analytical solution preserves the concise form of undeformed carbon nanotubes. It predicts the shifting, merging and splitting of the Van Hove singularities in the density of states and the zigzag pattern of bandgap change under strains. Four orbital tight-binding simulations of carbon nanotubes under uniform stretching, compression, torsion and bending have been performed to verify the analytical solution. Extension to more complex systems are being performed to relate this analytical solution to the spectroscopic characterization, device performance and proposed quantum structures induced by the deformation. The limitations of this model will also be discussed.
Yang, Liu↗
Organic Chemistry of Carbonaceous Meteorites
Chiral and carbon-isotopic analyses of isovaline have been carried out on numerous samples of the Murchison and one sample of the Murray carbonaceous chondrite. The isovaline was found to be heterogeneous with regard to enantiomeric excess (ee) both between samples and within a single Murchison sample. L-Excesses ranging from 0 to 15% were observed. The isovaline delta(sup 13) C was found to be about +18%. No evidence was obtained suggesting terrestrial contamination in the more abundant L-enantiomer. A correlation was observed between isovaline (also alpha - aminoisobutyric acid) concentration and PCP content of five CM chondrites. It is suggested that isovaline, along with other meteoritic a-methyl amino acids with ee, are of presolar origin. The possible formation of ee in extraterrestrial amino acids by exposure to circularly polarized light or by magnetochiral photochemistry is discussed. Key words: Murchison meteorite, Murray meteorite, amino acids, isovaline, chirality, carbon isotopes, PCP.
Cronin, John R.↗