R2PI Study of intermolecular hydrogen bond in solvent-free chiral complexes.

One- and two-color, mass selected R2PI spectra of the S(1)<--S(0) transitions in the bare (+)-(R)-1-phenyl-1-ethanol (E(R)) and its complexes with different solvent molecules (solv) (-)-(R)-2-butanol (B(R)) or (+)-(S)-2-butanol (B(S)) and (-)-(R)-2-butylamine (A(R)) or (+)-(S)-2-butylamine (A(S)), have been recorded after a supersonic molecular beam expansion. The one-color R2PI excitation spectra of the diastereomeric complexes are characterized by significant shifts of their band origin relative to that of bare E(R). The extent and the direction of these spectral shifts are found to depend on the structure and the configuration of solv and are attributed to different short-range interactions in the ground and excited states of the complexes. In analogy with other diastereomeric complexes, the phenomenological binding energy of the homochiral cluster is found to be greater than that of the heterochiral one.     

Thermodynamic Features of Structural Motifs Formed by β-L-RNA

This is the first report to provide comprehensive thermodynamic and structural data concerning duplex, hairpin, quadruplex and i-motif structures in β-L-RNA series. Herein we confirm that, within the limits of experimental error, the thermodynamic stability of enantiomeric structural motifs is the same as that of naturally occurring D-RNA counterparts. In addition, formation of D-RNA/L-RNA heterochiral duplexes is also observed; however, their thermodynamic stability is significantly reduced in reference to homochiral D-RNA duplexes. The presence of three locked nucleic acid (LNA) residues within the D-RNA strand diminishes the negative effect of the enantiomeric, complementary L-RNA strand in the formation of heterochiral RNA duplexes. Similar behavior is also observed for heterochiral LNA-2′-O-methyl-D-RNA/L-RNA duplexes. The formation of heterochiral duplexes was confirmed by ¹H NMR spectroscopy. The CD curves of homochiral L-RNA structural motifs are always reversed, whereas CD curves of heterochiral duplexes present individual features dependent on the composition of chiral strands.     

Circular dichroism of host-guest complexes of achiral pyridino- and phenazino-18-crown-6 ligands with the enantiomers of chiral aralkyl ammonium salts

Circular dichroism (CD) spectroscopy was used for distinguishing different types of chiral interactions in host-guest complexes of achiral pyridino- and phenazino-18-crown-6 ligands with chiral aralkyl ammonium salts. The general feature of the CD spectra of many homochiral (e.g., (R,R)-host and (R)-guest) and heterochiral (e.g., (R,R)-host and (S)-guest) alpha-(1-naphthyl)ethylamine hydrogenperchlorate salt (NEA) complexes with chiral pyridino- and phenazino-18-crown-6 hosts is exciton interaction. The most interesting example is the coupling of the transitions of the chiral guest NEA with the energetically close transitions of the achiral phenazino-18-crown-6 host 6. The CD spectrum of the complex is predominated by exciton coupling between the (1)B(b) transition of the chiral guest and the (1)B(b) transition of the achiral host. The redshifted intense spectra of the complexes of (R)- or (S)-1-phenylethylamine hydrogenperchlorate salt (PEA) with the achiral diester-pyridino-18-crown-6 host 4 are indicative of merging the pi electron systems into one joint charge transfer chromophore. The appearance of weak bands with alternating sign in the spectrum of PEA complexes of the achiral "parent" pyridino-18-crown-6 host (1) indicates the presence of two or more conformers. The CD spectra of the complexes of achiral phenazino-18-crown-6 host 6 with PEA are also determined by pi-pi interaction. In addition to charge transfer bands, CD bands are also induced in the long-wavelength spectral region of the achiral host. The weak pi-pi interaction between the achiral phenazino-18-crown-6 host and methyl phenylglycinate hydrogenperchlorate (PGMA) or methyl phenylalaninate hydrogenperchlorate (PAMA) does not result in a definite spectral effect in the (1)L(a) region of the spectrum of the chiral guest, but its existence is proven by the weak CD bands induced in the long-wavelength spectral region of the achiral host.     

The model structure of the hammerhead ribozyme formed by RNAs of reciprocal chirality

RNA-based tools are frequently used to modulate gene expression in living cells. However, the stability and effectiveness of such RNA-based tools is limited by cellular nuclease activity. One way to increase RNA’s resistance to nucleases is to replace its D-ribose backbone with L-ribose isomers. This modification changes chirality of an entire RNA molecule to L-form giving it more chance of survival when introduced into cells. Recently, we have described the activity of left-handed hammerhead ribozyme (L-Rz, L-HH) that can specifically hydrolyse RNA with the opposite chirality at a predetermined location. To understand the structural background of the RNA specific cleavage in a heterochiral complex, we used circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy as well as performed molecular modelling and dynamics simulations of homo- and heterochiral RNA complexes. The active ribozyme-target heterochiral complex showed a mixed chirality as well as low field imino proton NMR signals. We modelled the 3D structures of the oligoribonucleotides with their ribozyme counterparts of reciprocal chirality. L- or D-ribozyme formed a stable, homochiral helix 2, and two short double heterochiral helixes 1 and 3 of D- or L-RNA strand thorough irregular Watson–Crick base pairs. The formation of the heterochiral complexes is supported by the result of simulation molecular dynamics. These new observations suggest that L-catalytic nucleic acids can be used as tools in translational biology and diagnostics.     

Theoretical studies of infrared signatures of proton-bound amino acid dimers with homochiral and heterochiral moieties

Proton-bound homochiral and heterochiral dimers, X-H⁺-X, of five amino acids (X = Ser, Ala, Thr, Phe, and Arg) are investigated theoretically using quantum chemical density functional theory (DFT) calculations and molecular dynamics simulations with the aim to unveil diastereomer-specific mid-infrared (mid-IR) absorption bands in the spectral range of 1000 to 1800 cm⁻¹. The theoretical calculations performed in this work imply that all systems, except Ala₂H⁺, have distinct mid-IR absorption bands in homochiral and heterochiral configurations, which make them appropriate systems to be studied experimentally with mid-IR spectroscopy. We show that intermolecular interaction with the side chain, in the form of hydrogen bonding or cation-π interaction, is necessary for chiral effects to be present in the mid-IR spectra of proton-bound dimers of amino acids. We also report new conformers for Ala₂H⁺, Thr₂H⁺, Phe₂H⁺, and Arg₂H⁺, which were not found in earlier studies of these dimers.     

A study of the oxidation of butan-1-ol and propan-2-ol by nicotinamide-adenine dinucleotide catalysed by yeast alcohol dehydrogenase.

1. The kinetics of oxidation of butan-1-ol and propan-2-ol by NAD+, catalysed by yeast alcohol dehydrogenase, were studied at 25 degrees C from pH 5.5 to 10, and at pH 7.05 from 14 degrees to 44 degrees C, 2. Under all conditions studied the results are consistent with a mechanism whereby some dissociation of coenzyme from the active enzyme-NAD+-alcohol ternary complexes occurs, and the mechanism is therefore not strictly compulsory order. 3. A primary 2H isotopic effect on the maximum rates of oxidation of [1-2H2]butan-1-ol and [2H7]propan-2-ol was found at 25 degrees C over the pH range 5.5-10. Further, in stopped-flow experiments at pH 7.05 and 25 degrees C, there was no transient formation of NADH in the oxidation of butan-1-ol and propan-2-ol. The principal rate-limiting step in the oxidation of dependence on pH of the maximum rates of oxidation of butan-1-ol and propan-2-ol is consisten with the possibility that histidine and cysteine residues may affect or control catalysis.     

Cyclopenta[g]quinazoline-based antifolates: the effect of the chirality at the 6-position on the inhibition of thymidylate synthase (TS).

Cyclopenta[g]quinazoline-based inhibitors of thymidylate synthase (TS) possess a chiral centre at the 6-position of the molecule. The effect of this chirality on the inhibition of TS was investigated by synthesising compounds 6S-1a-c, 6R-1a-c. It was shown, in particular with the diastereoisomers 6S-1c, 6R-1c, that the inhibitory activity against TS is mainly due to the 6S diastereoisomer rather than the 6R diastereoisomer, which is virtually inactive.     

Factors affecting cephalosporin C biosynthesis

Summary Caprolactam, butan-2-one, butan-2-ol, and butan-1, 3-diol were found to have a stimulating effect on the biosynthesis of cephalosporin C by a mutant strain ofCephalosporium. Caprolactam was shown to have a synergistic effect, when added to the fermentation medium together with each of the other three compounds.     

Chiral Selection in Oligoadenylate Formation in the Presence of a Metal ion Catalyst or Poly(U) Template

The lead ion-catalyzed oligomerization of 5′-phosphorimidazolides of D-, L- or racemic DL-adenosine (D-ImpA, L-ImpA and DL-ImpA) gave oligoadenylates up to a pentamer. The oligomers resulting from racemic ImpA were comparable in yields and length to those from chiral D- or L-ImpA. A complex mixture of homochiral and heterochiral oligomers was formed in the reaction from racemic ImpA. Total dimer product from racemic ImpA by the lead ion catalyst showed homochiral selectivity. The reaction catalyzed by uranyl ion yielded oligoadenylates up to 15mer from chiral D- or L-ImpA in over 95% yield. A complex mixture of isomeric oligoadenylates was formed from racemic DL-ImpA in the presence of uranyl ion catalyst in comparable yields to those from D- or L-ImpA. The analysis of the dimer product from DL-ImpA showed that the homochiral 2′ –5′ linked dimer was selectively formed. D-ImpA polymerized effectively on a poly(U) template, which is exclusively composed of D-uridine, yielding oligoadenylates up to a pentamer. In contrast, L-ImpA or racemic DL-ImpA polymerized far less efficiently on the poly(U) template, demonstrating that chiral selection takes place in the poly(U) template-directed oligoadenylate formation.     

Spontaneous resolution of 2,3-bis-fluoren-9-ylidenesuccinic acid induced by achiral guest inclusion

The racemic title host compound (1) formed homochiral inclusion crystals (conglomerate) of 1 with acetone, while heterochiral inclusion crystals (racemate) were obtained when complexed with ethyl acetate. Upon treatment of the homochiral inclusion crystals of 1 with gaseous acetyl chloride in the solid state, optically active 2,3-bis(fluorenylidene)succinic anhydride (3) was obtained in high optical purity.     

Chirally sensitive collision induced dissociation of proton‐bound diastereomeric complexes of tryptophan and 2‐butanol

In this work we report the stereo‐dependent collision‐induced dissociation (CID) of proton‐bound complexes of tryptophan and 2‐butanol. The dissociation efficiency was measured as a function of collision energy in single collision mode. The homochiral complex was found to be less stable against CID than a heterochiral one. Additional gas dependence measurements were performed with diastereomeric complexes that confirm the findings.     

Conformational investigation of alpha,beta-dehydropeptides. Part. IV. Beta-turn in saturated and alpha,beta-unsaturated peptides Ac-Pro-Xaa-NHCH3: NMR and IR studies.

Solution conformations of three series of model peptides, homochiral Ac-Pro-L-Xaa-NHCH3 and heterochiral Ac-Pro-D-Xaa-NHCH3 (Xaa = Val, Phe, Leu, Abu, Ala) as well as alpha,beta-unsaturated Ac-Pro-delta Xaa-NHCH3 [delta Xaa = delta Val, (Z)-delta Phe, (Z)-delta Leu, (Z)-delta Abu] were investigated in CDCl3 and CH2Cl2 by 1H-, 13C-NMR, and FTIR spectroscopy. NH stretching absorption spectra, solvent shifts delta delta for NH (Xaa) and NHCH3 on going from CDCl3 to (CD3)2SO, diagnostic interresidue proton NOEs, and trans-cis isomer ratios were examined. These studies performed showed the essential difference in conformational propensities between homochiral peptides (L-Xaa) on the one hand and heterochiral (D-Xaa) and alpha,beta-dehydropeptides (delta Xaa) on the other. Former compounds are conformationally flexible with an inverse gamma-bend, a beta-turn, and open forms in an equilibrium depending on the nature of the Xaa side chain. Conformational preferences of heterochiral and alpha,beta-dehydropeptides are very similar, with the type-II beta-turn as the dominating structure. There is no apparent correlation between conformational properties and the nature of the Xaa side chain within the two groups. The beta-turn formation propensity seems to be somewhat greater in alpha,beta-unsaturated than in heterochiral peptides, but an estimation of beta-folded conformers is risky.     

Diastereoisomerically pure pyrazole-3,5-dicarboxylate-bridged dinuclear ruthenium(II) and osmium(II) complexes of 2,2-bipyridine: structural, electrochemical and spectral studies

Pyrazole-3,5-dicarboxylate-bridged dinuclear ruthenium(II) and osmium(II) complexes of 2,2^′-bipyridine of composition [(bpy)₂Ru(pzdc)Ru(bpy)₂](ClO₄) · H₂O (1) and [(bpy)₂Os(pzdc)Os(bpy)₂](ClO₄) · H₂O (2) have been obtained in high yield and have been separated to their homochiral (ΛΛ/ΔΔ) rac (1a, 2a) and heterochiral (ΛΔ/ΔΛ) meso (1b, 2b) diastereoisomers. The distinctive structural features of these diastereoisomers have been characterized by 1-D and 2-D ¹H NMR spectroscopy. The X-ray crystal structure of rac-[(bpy)₂Os(pzdc)Os(bpy)₂](ClO₄) · H₂O (2a) has been determined. The electrochemical and electronic spectral studies have established that there remain difference in properties and hence difference in intermetallic communication between the diastereoisomeric forms in each case.     

A study of the kinetics and mechanism of yeast alcohol dehydrogenase with a variety of substrates

1. The kinetics of oxidation of ethanol, propan-1-ol, butan-1-ol and propan-2-ol by NAD(+) and of reduction of acetaldehyde and butyraldehyde by NADH catalysed by yeast alcohol dehydrogenase were studied. 2. Results for the aldehyde-NADH reactions are consistent with a compulsory-order mechanism with the rate-limiting step being the dissociation of the product enzyme-NAD(+) complex. In contrast the results for the alcohol-NAD(+) reactions indicate that some dissociation of coenzyme from the active enzyme-NAD(+)-alcohol ternary complexes must occur and that the mechanism is not strictly compulsory-order. The rate-limiting step in ethanol oxidation is the dissociation of the product enzyme-NADH complex but with the other alcohols it is probably the catalytic interconversion of ternary complexes. 3. The rate constants describing the combination of NAD(+) and NADH with the enzyme and the dissociations of these coenzymes from binary complexes with the enzyme were measured.     

Kinetic analysis of artificial peptide self-replication. Part II: the heterochiral case

A kinetic model has been designed to describe and to analyze the stereoselective behavior of a recently discovered heterochiral template-directed peptide self-replicator by Ghadiri and co-workers [Nature 409 (2001) 797-801]. It turned out that previous assumptions stating that exclusively homochiral species participate in a stereoselective and autocatalytic pathway and that heterochiral species originate only from uncatalyzed background reactions could not be validated by our model. On the contrary, excellent fitting of experimental data indicated that the whole combinatorial variety of possible cross-catalytic processes involving L- and D- peptide species play an important role and need to be taken into account. The system shows no net creation of chiral matter but only a redistribution of the initially present chiral material. Both, the separation of an optically inactive meso-type template dimer and a slight chiroselective autocatalytic effect, contribute to a predicted amplification of enantiomeric excess that, in some cases, can simultaneously result in a substantial amount of optically active matter.     

Mass Spectrometry Study and Infrared Spectroscopy of the Complex Between Camphor and the Two Enantiomers of Protonated Alanine: The Role of Higher‐Energy Conformers in the Enantioselectivity of the Dissociation Rate Constants

The properties of the protonated complexes built from S camphor and R or S alanine were studied in a Paul ion trap at room temperature by collision‐induced dissociation (CID) and infrared multiple‐photon dissociation spectroscopy (IRMPD), as well as molecular dynamics and ab initio calculations. While the two diastereomer complexes display very similar vibrational spectra in the fingerprint region, in line with similar structures, and almost identical calculated binding energies, their collision‐induced dissociation rates are different. Comparison of the IRMPD results to computed spectra shows that the SS and SR complexes both contain protonated alanine strongly hydrogen‐bonded to the keto group of camphor. The floppiness of this structure around the NH⁺…O = C hydrogen bond results in a complex potential energy surface showing multiple minima. Calculating the dissociation rate constant within the frame of the transition state theory shows that the fragmentation rate larger for the heterochiral SR complex than the homochiral SS complex can be explained in terms of two almost isoenergetic low‐energy conformers in the latter that are not present for the former. Chirality 25:436‐443, 2013. © 2013 Wiley Periodicals, Inc.     

Progress in demonstrating total homochiral selection in montmorillonite-catalyzed RNA synthesis

The Na⁺-montmorillonite-catalyzed reactions of 5′-phosphorimidazolides of nucleosides generates RNA oligomers. The question arises as to how chiral selectivity was introduced into this biopolymer from a simple chemical system. We have demonstrated homochiral selection in quaternary reactions of a racemic mixture of d,l-ImpA and d,l-ImpU on Na⁺-montmorillonite. The dimer, trimer, tetramer and pentamer fractions were investigated for homochiral selection. The products were collected via ion exchange HPLC and their terminal 5′-phosphate was cleaved by alkaline phosphatase. These fractions were analyzed by reverse phase HPLC for the identification of homochiral and heterochiral isomers. Encouraged by favorable homochiral excesses of dimer (63.5 ± 0.8%) and trimer (74.3 ± 1.7%), the study was extended to the analysis of higher oligomers. The tetramer and pentamer of the quaternary reaction were separated into 26 and 22 isomers, respectively, on a reverse phase column. Their co-elution with those formed in the binary reactions of d-ImpA and d-ImpU on Na⁺-montmorillonite revealed 92.7 ± 2.0% and 97.2 ± 0.5% homochirality of the tetramer and pentamer, respectively. These results suggest that Na⁺-montmorillonite not only catalyzes the prebiotic synthesis of RNA but it also facilitates homochiral selection.     

Biotransformations of R-(+)-pulegone and menthofuran in vitro: chemical basis for toxicity

Incubation of R-(+)-pulegone(I) with PB-induced rat liver microsomes in the presence of NADPH resulted in the formation of menthofuran (II) and 2-Z-[2'-keto-4'-methylcyclohexylidene] propanol (III, 9-hydroxy pulegone) as the major and minor metabolites, respectively. When isopulegone (IV) was used as the substrate, the major metabolite formed was shown to have identical GC-MS fragmentation pattern to that of synthetic 2-[2'-keto-4'-methylcyclohexyl]prop-2-en-1-ol (V) and the minor metabolite was shown to be menthofuran (II). Transformation of menthofuran (II) by microsomes in the presence of NADPH yielded a metabolite identified as 2-Z-(2'-keto-4'-methyl cyclohexylidene) propanal (VI, pulegone-8-aldehyde). Formation of this alpha, beta -unsaturated aldehyde was further confirmed by trapping it as cinnoline derivative by adding semicarbazide to the assay medium. The toxicity mediated by pulegone is discussed in the light of these observations.     

Phospholipase D stimulation is required for sphingosine-1-phosphate activation of actin stress fibre assembly in human airway epithelial cells.

In human airway epithelial cells, sphingosine-1-phosphate (SPP) and lysophosphatidic acid (LPA) stimulated the production of phosphatidic acid (PA), which was inhibited by the primary alcohol butan-1-ol, but not by the inactive butan-2-ol, clearly indicating phospholipase D (PLD) involvement. Both SPP and LPA stimulated actin stress fibre formation, which was also butan-2-ol-insensitive and inhibited by butan-1-ol. SPP-induced PLD activation and cytoskeletal remodelling were insensitive to brefeldin A and toxin B from Clostridium difficile, which conversely blocked the effect of LPA, suggesting that the monomeric GTPases ADP ribosylation factor (ARF) and Rho are involved in LPA, but not in SPP responses. Pertussis toxin inhibited SPP- but not LPA-induced effects. PLD activation and stress fibre formation by both lysolipids were abolished by the tyrosine kinase inhibitor genistein. Addition of PA to cells caused a massive stress fibre assembly. In conclusion, PLD is one of the signalling components linking SPP-receptor activation to assembly of actin stress fibres.