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Since our work on corrin synthesis was intended to be a model study for the construction of the ligand system of vitamin B12 (cf. Part I of this series), the choice of an A/D component that would contain an angular Me group at the junction between rings A and D seemed crucial. Such a Me group was expected to direct (through its steric impact) a regioselective functionalization of the two carbonyl groups of a corresponding dilactam structure that appeared to be the obvious type of intermediate in the construction of an A/D component. The target A/D structure envisaged originally was the methyl ester derivative 1a (cf. Fig. 1). However, observations in an early phase of our work made it clear that we better aim at the nitrile derivative 1b, instead of the corresponding methyl ester. Nitrile 1b was in fact synthesized, but not used as A/D component, because, on the way to its synthesis, the opportunity emerged to prepare structure 2. As A/D component, 2 differs from 1b by the isomeric positioning of the angular Me group, it could be prepared regio- as well as stereoselectively and, therefore, much more efficiently than 1b.

The N,O-acetal and N,O-ketal derivatives (oxazolidinones) formed from proline, and aldehydes or ketones are well-known today, and they are detectable in reaction mixtures involving proline catalysis, where they have been considered ‘parasitic dead ends’. We disclose results of experiments performed in the early 1970's, and we describe more recent findings about the isolation, characterization, and reactions of the oxazolidinone derived from proline and cyclohexanone. This oxazolidinone reacts (THF, room temperature) with the electrophiles β-nitrostyrene and chloral (=trichloroacetaldehyde), to give the Michael and aldol adduct, respectively, after aqueous workup (Scheme 5). The reactions occur even at −75° when catalyzed with bases such as 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) or EtN(i-Pr)2 (DIPEA) (10%; Table 1). It is shown by NMR (Figs. 1 and 3) and IR analysis (Figs. 2 and 4) that the primarily detectable product (before hydrolysis) of the reaction with the nitro-olefin is again an oxazolidinone. When dissolved in hydroxylic solvents such as MeOH, ‘hexafluoroisopropanol’ ((CF3)2CHOH; HFIP), AcOH, CF3COOH, or in LiBr-saturated THF, the ring of the oxazolidinone from cyclohexanone and proline opens up to the corresponding iminium ion (Tables 2–4), and when treated with strong bases such as DBU (in (D8)THF) the enamino-carboxylate derived from proline and cyclohexanone is formed (Scheme 8). Thus, the two hitherto putative participants (iminium ion and enamine) of the catalytic cycle (Scheme 9) have been characterized for the first time. The commonly accepted mechanism of the stereoselective C,C- or C,X-bond-forming step (i.e., A–D) of this cycle is discussed and challenged by thoughts about an alternative model with a pivotal role of oxazolidinones in the regio- and diastereoselective formation of the intermediate enamino acid (by elimination) and in the subsequent reaction with an electrophile (by trans-addition with lactonization; Schemes 11–14). The stereochemical bias between endo- and exo-space of the bicyclo[3.3.0]octane-type oxazolidinone structure (Figs. 5 and 6) is considered to possibly be decisive for the stereochemical course of events. Finally, the remarkable consistency, with which the diastereotopic Re-face of the double bond of pyrrolidino-enamines (derived from proline) is attacked by electrophiles (Schemes 1 and 15), and the likewise consistent reversal to the Si-face with bulky (Aryl)2C-substituents on the pyrrolidine ring (Scheme 16) are discussed by invoking stereoelectronic assistance from the lone pair of pyramidalized enamine N-atoms.

An X-ray structure analysis of the title compound reveals that this purinoid exists in the crystal as two tautomers which interact with each other in the mode of a reverse-Watson–Crick base pair.

Pyranosyl-RNA (qp-RNAq) is an oligonucleotide system isomeric to natural RNA and composed of the very same building blocks as RNA. Its generational, chem., and informational properties are deemed to be those of an alternative nucleic acid system that could have been a candidate in Nature's evolutionary choice of the mol. basis of genetic function. We consider the study of the chem. of p-RNA as etiol. relevant in the sense that knowledge of its structural, chem., and informational properties on the chem. level offers both a perspective and ref. points for the recognition of specific structural assets of the RNA structure that made it the (supposedly) superior system among possible alternatives and, therefore, the system that became part of biol. as we know it today. The paper describes the chem. synthesis of b-D- (and -L)-ribopyranosyl-(4'->2')-oligonucleotide sequences, presents a resume of their structural and chem. properties, and cautiously discusses what we may and may not have learned from the pyranosyl isomer of RNA with respect to the conundrum of RNA's origin. [on SciFinder (R)]

Among the members of a family of diastereoisomeric pentopyranosyl-(4′2′)-oligonucleotide systems derived from D-ribose, D-xylose, L-lyxose, and L-arabinose, the α-arabinopyranosyl system shows by far the strongest WatsonCrick base pairing. The system is, in fact, one of the strongest oligonucleotide-type base-pairing systems known. It undergoes efficient cross-pairing with all the other members of the pentopyranosyl family, but not with RNA and DNA. The paper describes the synthesis and pairing of the properties of α-L-arabinopyranosyl-(4′2′)-oligonucleotides.

Our studies of α-L-Threofuranosyl-(3′→2′)-oligonucleotides (‘TNA') are part of a systematic experimental inquiry into the base-pairing properties of potentially natural nucleic acid alternatives taken from RNA's close structural neighborhood. TNA is an efficient Watson-Crick base-pairing system and has the capability of informational cross-pairing with both RNA and DNA. This property, together with the system's constitutional and (presumed) generational simplicity, warrants special scrutiny of TNA in the context of the search for chemical clues to RNA's origin.

The solution structure of the duplex formed by α-L-arabinopyranosyl-(4′2′)-(CGAATTCG) was studied by NMR. The resonances of all H-, P- and most C-atoms could be assigned. Dihedral angles and distance estimates derived from coupling constants and NOESY spectra were used as restraints in a simulated annealing calculation, which generated a well-defined bundle of structures for the six innermost nucleotide pairs. The essential features of the resulting structures are an antiparallel, WatsonCrick-paired duplex with a strong backbone inclination of ca. −50° and, therefore, predominant interstrand base stacking. The very similar inclination and rise parameters of arabinopyranosyl-(4′2′)-oligonucleotides and p-RNA explain why these two pentapyranosyl isomers are able to cross-pair.

To determine whether the remarkable chemical properties of the pyranosyl isomer of RNA as an informational Watson-Crick base-pairing system are unique to the pentopyranosyl-(4′2′)-oligonucleotide isomer derived from the RNA-building block D-ribose, studies on the entire family of diastereoisomeric pyranosyl-(4′2′)-oligonucleotide systems deriving from D-ribose, L-lyxose, D-xylose, and L-arabinose were carried out. The result of these extended studies is unambiguous: not only pyranosyl-RNA, but all members of the pentopyranosyl-(4′2′)-oligonucleotide family are highly efficient Watson-Crick base-pairing systems. Their synthesis and pairing properties will be described in a series of publications in this journal. The present paper describes the α-L-lyxopyranosyl-(4′2′)-system.

Cyclic nucleo-δ-amino acids that constitute monomers of a conformationally constrained nucleo-δ-peptide base-pairing system have been prepared. Their synthesis starts with an enantioselectively catalyzed chirogenic Diels-Alder reaction, proceeds via a regioselective e-iodolactamization process, and ends with a regio- as well as diastereoselective introduction of nucleobases through SN2-type opening of a transiently formed N-acylaziridine ring. Extensive use of X-ray crystal-structure analysis has been made to support structure assignments.

Amidotriphosphate (0.1 M) in aqueous solution at near neutral pH in the presence of magnesium ions (0.25 M) converts glycolaldehyde (0.025 M) within days at room temperature into glycolaldehyde phosphate in (analytically) nearly quantitative yields (76% in isolated product). This robust phosphorylation process was observed to proceed at concentrations as low as 30 microM glycolaldehyde and 60 microM phosphorylation reagent under otherwise identical conditions. In sharp contrast, attempts to achieve a phosphorylation of glycolaldehyde with cyclotriphosphate ('trimetaphosphate') as phosphorylating reagent were unsuccessful. Mechanistically, the phosphorylation of glycolaldehyde with amidotriphosphate is an example of intramolecular delivery of the phosphate group.

Why Pentose- and Not Hexose-Nucleic Acids? Purine-Purine Pairing in homo-DNA: Guanine,Isoguanine, 2,6-Diaminopurine, and Xanthine This paper concludes the series of reports in this journal [1–4] on the chemistry of homo-DNA, the constitutionally simplifie dmodel system of hexopyranosyl-(6′ → 4′)-oligonucleotide systems stidued in our laboratory as potentially natural-nucleic-acid alternatives in the context of a chemical aetiology of nucleic-acid structure. The report describes the synthesis and pairing properties of homo-DNA oligonucleotides which contain as nucleobases exclusively purines, and gives, together with part III of the series [3], a survey of what we know today about purine-purine pairingin homo-DNA. In addition, the paper discusses those aspects of the chemistry of homo-DNA which, we think, influence the way how some of the structural features of DNA (and RNA) are to be interpreted on a qualitative level. Purine-purine pairing occurs in the homo-DNA domain in great variety. Most prominent is a novel tridentate Watson-Crick pair between guanine and isoguanine, as well as one between 2,6-diaminopurine and xanthinone, both giving rise to very stable duplexes containing the all-purine strands in antiparallel orientation. For the guanine-isoguanine pair, constitutional assignment is based on temperature-dependent UV and CD spectroscopy of various guanine- and isoguanine-containg duplexes in comparison with duplexes known to be paired in the reverse guanine is replaced by 7-carbauguanine. Isoguanine and 2,6-diaminopurine also have the capability of self-pariring in the reverse-Hoogsteen mode, as previously observed for adenine and guanine [3]. In this type of pairing, the interchangeably. Fig. 36 provides an overall survey of the relative strength of pairing in all possible purine-purine combinations. Watson-Crick pairing of isoguanine with guanine demands the former to participate in its 3H-tautomeric form; hitherto this specific tautomer had not been considered in the pairing chemistry of isoguanine. Whereas (cumulative) purine-purine pairing in DNA (reverse-Hoogsten or Hoogsteen) seems to occur in triplexes and tetrapalexes only, its occurrence in duplexes in a characteristic feature of homo-DNA chemistry. The occurrence of purine-purine Watson-Crick base pairs is probably a consequence of homo-DNA's quasi-linear ladder structure [1][4]. In a double helix, the distance between the two sugar C-atoms, on which a base pair is anchored, is expected to be constrained by the dimensions of the helix; in a linear duplex, however, there would be no restrictions with regard to base-pair length. Homo-DNA's ladder-like model also allows one to recognize one of the reasons why nucleic-acid duplexes prefer to pair in antiparallel, rather than parallel strand orientation: in homo-DNA duplexes, (averaged) backbone and base pair axes are strongly inclined toward one another [4]; the stronger this inclination, the higher the preference for antiparallel strand orientation is expected to be (Fig. 16). In retrospect, homo-DNA turns out to be one of the first artificial oligonucleotide systems (cf. Footnote 65) to demonstrate in a comprehensive way that informational base pairing involving purines and pyrimidines is not a capability unique to ribofuranosyl systems. Stability and helical shape of pairing complexes are not necessary conditions of one another; it is the potential for extensive conformational cooperativity of hte backbone structure with respect to the constellational demands of base pairing and base stacking that determines whether or nor a given type of base-carrying backbone structure is an informational pairing system. From the viewpoint of the chemical aetiology of nucleic-acid structure, which inspired our investigations on hexopyranosyl-(6′ → 4′)-oligonucleotide systems in the first place, the work on homo-DNA is only an extensive model study, because homo-DNA is not to be considered a potential natural-nucleic-acid altenratie. In retrospect, it seems fortunate that the model study was carried out, because without it we could hardly have comprehended the pairing behavior of the proper nucleic-acid alternatives which we have studied later and which will be discussed in Part VI of this series. The English footnotes to Fig. 1–49 provide an extension of this summary.

Replication (single-turnover) of pyranosyl-RNA (p-RNA) sequences can be accomplished reliably by template-directed ligation of 2',3'-cyclophosphates of short oligomers. The ligation process was studied using (mostly) octamers as templates and tetramers as ligands. The transcription of the sequence pr(GGGCGGGC) into the (antiparallel) complementary sequence pr(GCCCGCCC) by ligation of 2 mols. of pr(GCCC)-2',3'-cp was investigated in detail. In aq. 1.5 M LiCl soln. of pH 8.5 at room temp. (0.45 mM ligand, 0.15 mM template), the reaction proceeds in up to 60% yield within a week. It is limited by concomitant hydrolysis of cyclophosphate groups of both reactant and ligation product as the only efficient side reaction, the latter occurring .apprx.3 times more slowly than ligation. No ligation at all is obsd. in the absence of template. The reaction is highly regioselective: the (4'->2') phosphodiester junction is formed exclusively; no isomeric (4'->3') junctions are found. For ligation to occur, template and ligand must be homochiral and must have the same sense of chirality; with chiro-diastereoisomeric tetramer-2',3'-cyclophosphates contg. a single enantio-ribopyranosyl unit, no ligation is obsd., except to a minor extent in the case of the diastereoisomer that has that unit at the 4'-end. Observations made in expts. involving 6 different octamer templates contg. isomeric base sequences indicate that the ligation process does not tolerate a mismatch at ligation sites. However, ligation still takes place when a mismatch occurs at either end of the (octamer) template. Ligation efficiencies differ widely, depending on the nature, as well as the sequence, of participating bases. These differences can be understood qual. by considering the relative stability of ternary pre-ligation complexes, together with the differences in interstrand base stacking at ligation sites. Dominance of the latter over intrastrand base stacking is the feature of the p-RNA structure that appears to det. most of the characteristic properties of p-RNA. As regards the etiol. context of this work on nucleic-acid alternatives, it is essential that the chem. properties found for p-RNA be compared with the corresponding properties of RNA. In the RNA series, the 2 ligations of the replicative cycle r(GGGCGGGC) .tautm. r(GCCCGCCC) using the corresponding ribofuranosyl-tetramer 2',3'-cyclophosphates as ligands are found to proceed also, though somewhat less efficiently than in the p-RNA series; however, the ligation step produces exclusively the unnatural (5'->2') phosphodiester junctions instead of the natural (5'->3') junctions. This is in sharp contrast to p-RNA, where template-controlled 2',3'-cyclophosphate ligations produce the 'correct' phosphodiester junctions. [on SciFinder (R)]

Chemistry of α-Aminonitriles. Regioselective Synthesis and Crystal Structure of Uroporphyrinogen (Type I) Octanitrile A regioselective synthesis of uroporphyrinogen-octanitrile (type I) based on the strategy of multiple use of (dimethylmethylidene)ammonium iodide for stepwise regioselective functionalization of the pyrrole nucleus is described. This uroporphyrinogen derivative is remarkably stable and beautifully crystallizes in space group P1 with one molecule per unit cell. The crystal structure of the compound shows interesting conformational characteristics which are interpreted to be caused by subtle stereoelectronic effects. The English Footnotes to Schemes 1-3 and Figs. 1-12 provide an extension of this summary.

The soln. structure of the duplex formed by self-pairing of the p-RNA octamer b-D-ribopyranosyl-(2'->4')-(CGAATTCG) was studied by NMR techniques and, independently, by mol.-dynamics calcns. The resonances of all non-exchanging protons, H-bearing C-atoms, P-atoms, and of most NH protons were assigned. Dihedral angle and distance constraints derived from coupling consts. and NOESY spectra are consistent with a single dominant conformer and corroborate the main structural features predicted by qual. conformational anal. The duplex displays Watson-Crick pairing with antiparallel strand orientation. The dihedral angles b and e in the phosphodiester linkages differ considerably from the idealized values. Model considerations indicate that these deviations from the idealized model allow better inter strand stacking and lessen unfavorable interactions in the backbone. The av. base-pair axis forms an angle of ca. 40 Deg with the backbone. The resulting inter strand p-p stacking between either 2 purines, or a purine and a pyrimidine, but not between 2 pyrimidines, constitutes a characteristic structural feature of the p-RNA duplex. A 1000-ps mol.-dynamics (MD) calcn. with the AMBER force field resulted in an av. structure of the same conformation type as derived by NMR. For the backbone torsion angle e, dynamically averaged coupling consts. from the MD calcn. agree well with the exptl. values, but for the angle b, a systematic difference of ca. 25 Deg remains. The 2 base pairs at the ends of the duplex are calcd. to be highly labile, which is consistent with the high exchange rate of the corresponding imino protons found by NMR. [on SciFinder (R)]

The natural genesis of life on Earth is a hypothesis of evolutionary science; it is the task of synthetic organic chemistry to test this hypothesis experimentally. The aim of an experimental aetiological chemistry is not primarily to delineate the pathways along which our (‘natural’) life on Earth could have originated, but to provide decisive experimental evidence, through the realization of model systems (‘artificial chemical life’), that life can arise as a result of the organization of organic matter.

A review and discussion, with 42 refs. Base pairing in p-RNA (b-D-ribopyranosyl-(4'->2')-oligonucleotides) is not only stronger than in DNA and RNA, but also more selective in the sense that it is strictly confined to the Watson-Crick mode. Homopurine sequences (tested up to decamers) exist as single strands under conditions where they undergo reverse-Hoogsteen self-pairing in homo-DNA or Hoogsteen self-pairing in DNA. This exceptional pairing selectivity is rationalized as hinging on 2 structural features of p-RNA: the large inclination between backbone axis and base-pair axes in p-RNA duplexes, and the higher rigidity of the p-RNA backbone compared with RNA, DNA, and homo-DNA. The most important consequence of the pairing selectivity refers to the potential of p-RNA to replicate. Replicative copying of sequence information by nonenzymic template-controlled ligation is not hampered by self-pairing of guanine-rich templates, as it is known to be the case in the RNA series. Two replicative cycles are demonstrated in which G-rich p-RNA-octamer templates induce sequence-selective ligation of tetramer-2'-phosphate derivs. to complementary C-rich octamer sequences, and in which the latter, with comparable efficiency, induce corresponding ligation reactions back to the original G-rich octamers. Ligation is most satisfactorily achieved after pre-activation of the 2'-phosphate groups as 2',3'-cyclophosphate derivs.; in this version, the process does not proceed as oligocondensation, but as a genuine oligomerization. This is of considerable promise for the search for potentially natural conditions under which homochiral p-RNA strands might self-assemble and self-replicate. [on SciFinder (R)]

Glycolaldehyde phosphate, sorbed from highly dilute, weakly alkaline solution into the interlayer of common expanding sheet structure metal hydroxide minerals, condenses extensively to racemic aldotetrose-2,4-diphosphates and aldohexose-2,4,6-triphosphates. The reaction proceeds mainly through racemic erythrose-2,4-phosphate, and terminates with a large fraction of racemic altrose-2,4,6-phosphate. In the absence of an inductive mineral phase, no detectable homogeneous reaction takes place in the concentration- and pH range used. The reactant glycolaldehyde phosphate is practically completely sorbed within an hour from solutions with concentrations as low as 50 micrometers; the half-time for conversion to hexose phosphates is of the order of two days at room temperature and pH 9.5. Total production of sugar phosphates in the mineral interlayer is largely independent of the glycolaldehyde phosphate concentration in the external solution, but is determined by the total amount of GAP offered for sorption up to the capacity of the mineral. In the presence of equimolar amounts of rac-glyceraldehyde-2-phosphate, but under otherwise similar conditions, aldopentose-2,4,-diphosphates also form, but only as a small fraction of the hexose-2,4,6-phosphates.

Oxiranecarbonitrile in basic aq. soln. at room temp. reacts regioselectively with inorg. phosphate to give the cyanohydrin of 2-oxoethyl phosphate ('glycolaldehyde phosphate'), a source of (the hydrate of) the free aldehyde, preferably in the presence of formaldehyde. In aq. phosphate soln. buffered to nearly neutral pH, oxiranecarbonitrile produces the phosphodiester of glycolaldehyde as its bis-cyanohydrin in good yield. In contrast to mono- and dialkylation, trialkylation of phosphate with oxiranecarbonitrile is difficult, and the triester deriv. is highly sensitive to hydrolysis. Glycolaldehyde phosphate per se is of prebiotic interest, since it has been shown to aldomerize in basic aq. soln. regioselectively to rac-hexose 2,4,6-triphosphates and in the presence of formaldehyde mainly to rac-pentose 2,4-diphosphates with, under appropriate conditions, rac-ribose 2,4-diphosphate as the major reaction product. However, the question as to whether oxiranecarbonitrile itself has the potential of having been a prebiol. natural constituent remains unanswered. Backbone structures of hexopyranosyl-oligonucleotides with phosphodiester linkages specifically between the positions 6' -> 4', 6' -> 2', or 4' -> 2' of the sugar residues can formally be derived via the (hypothetical) aldomerization pathway, a combinatorial intermol. aldomerization of glycolaldehyde phosphate and bis(glycolaldehyde)-phosphodiester in a 1:1 ratio. The constitutional relationships revealed by this synthetic anal. has played a decisive role as a selection criterion in the pursuit of exptl. studies toward a chem. etiol. of the natural nucleic acids' structure. The discussion delineates how the anal. contributed to the conception of the structure of p-RNA. [on SciFinder (R)]

Chemistry of α-Amino Nitriles . Exploratory Experiments on Thermal Reactions of α-Amino Nitriles The paper extends a previously published report [4] on chemical properties of α-amino nitriles and of members of the C3H4N2 ensemble (Scheme 1) as observed in experiments carried out under non-aqueous conditions. The reactions investigated and the observations made are summarized in some detail in the English footnotes (*) referring to Schemes 1–17 and Fig. 1.

Why Pentose- and Not Hexose-Nucleid Acids? Part IV. ‘Homo-DNA’: 1H-, 13C-, 31P-, and 15N-NMR-Spectroscopic Investigation of ddGlc(A-A-A-A-A-T-T-T-T-T) in Aqueous Solution From a comprehensive NMR structure analysis, it is concluded that the ‘homo-DNA’ oligonucleotide ddGlc(A-A-A-A-A-T-T-T-T-T) in 3 mM D2O solution (100 mM NaCl, 50 mM phosphate buffer, pH 7.0, T = 50°) forms a duplex of C2-symmetry, with its self-complementary oligonucleotide strands in antiparallel orientation. The 2′,3′-dideoxy-β-D-glucopyranosyl rings are in their most stable chair conformation, with all three substituents equatorial and with the adenine as well as the thymine bases in the anti-conformation. The base pairing is of the Watson-Crick type; this pairing mode (as opposed to the reverse-Hoogsteen mode) was deduced from the observation of inter strand NOEs between the adenine protons HC(2) and the pyranose protons Hα–C(2′) of the sequentially succeeding thymidine nucleotides of the opposite strand, a correlation which discriminates between the Watson-Crick and the reverse-Hoogsteen pairing mode. The NOEs of the NH protons with either the adenine protons HC(2) or HC(8), that are normally used to identify the pairing mode in DNA duplexes, cannot be observed here, because the NH signals are very broad. This line broadening is primarily due to the fact that the exchange of the imino protons with the solvent is faster than for corresponding DNA duplexes. Computer-assisted modeling of the [ddGlc(A5-T5)]2 duplex with the program CONFOR [23], using the linear (idealized) homo-DNA single-strand conformation (α = −60°, β = 180°, γ = 60°, δ = 60°, ϵ = 180°, ζ = −60°, see [1] [3]) as the starting structure, resulted in two duplex models A and B (see Figs. 27–32, Scheme 9, and Table 4) which both contain quasi-linear double strands with the base-pairing axis inclined relative to the strand axes by ca. 60° and 45°, respectively, and with base-pair stacking distances of ca. 4.5 A. While neither of the two models, taken separately, can satisfy all of the NMR constraints, the NMR data can be rationalized by the assumption that the observed duplex structure represents a dynamic equilibrium among conformers which relate to models A and B as their limiting structure. The required rapid equilibrium appears feasible, since the models A and B are interconvertible by two complementary 120° counter rotations around the α-axis and the γ-axis, respectively, of the phosphodiester backbone. The models A and B correspond to the two types of linear (idealized) single-strand backbone conformation derived previously by qualitative conformational analysis without and with allowance for gauche-trans-phosphodiester conformations, respectively [1] [3]. Refinement of the models A and B with the use of the program AMBER [27] by energy minimization in a water bath and molecular-dynamics simulations (2 ps, 300° K) resulted in two dynamic structures (Figs. 33 and 34, Table 4). These have roughly the same energy, closely resemble the starting structures A and B, and satisfy - as an ensemble - all of the NMR constraints without violating any van der Waals distances by more than 0.2 A. Extensive fluctuations in base-pair distance and deviations from base-pair coplanarity, as well as the presence of water molecules in the cavities between some of the base pairs, were observed in both dynamic structures A and B, which, on the other hand, did not mutually interconvert within the short simulation time period used. These model properties, together with the conjectured equilibrium between the two structure types A and B, lead to the hypothesis of a homo-DNA duplex containing a ‘partially molten’ pairing core. This proposal could qualitatively account for a high rate of the NH exchange, as well as for part of the previously established [3] deficits in both enthalpic stabilization and entropic destabilization of homo-DNA duplexes relative to corresponding DNA duplexes. The phenomenon of the higher overall stability of homo-DNA duplexes vs. DNA duplexes (e.g, [ddGlc(A5-T5)]2, Tm = 59° vs. [d(A5-T5)]2, Tm = 33°, both at c ≈ 50 μM [3]) can then be seen as the result not only of a higher degree of conformational preorganization of the homo-DNA single strand toward the conformation of the duplex backbone [1] [3], but also of the entropic benefit of greater disorder in the central pairing zone of the homo-DNA duplex. This view of the structure of a homo-DNA duplex relates its characteristic properties to a central structural feature: the average base-pair distance in the models of homo-DNA is too large for regular base stacking (ca. 4.5 A vs. ca. 3.5 A in DNA). This difference in the distances between adjacent base pairs is a direct consequence of the quasi-linearity of the homo-DNA double strand as opposed to the right-handed twist of the helical DNA duplexes [1] [3], which is directly related to the specific conformational properties of pyranose rings as opposed to furanose rings [1]. Thus, the structural hypothesis derived from the NMR analysis of [ddGlc(A5-T5)]2 relates the conformational differences between homo-DNA and DNA directly to the sugar ring size, which is the essential constitutional difference between the two types of structure. The English footnotes to Figs. 1–34, Schemes 1–9, and Tables 1–4 provide an extension of this summary.

A review with 39 refs. Qual. conformational anal. of the entirety of conceivable hexo- and pentopyranosyl oligonucleotide systems derived from the diastereoisomeric aldohexoses (CH2O)6 and aldopentoses (CH2O)5 predicts the existence of a variety of pairing systems which have not been exptl. investigated so far. In particular, the anal. foresees the existence of a ribopyranosyl isomer of RNA ('p-RNA'), contg. the phosphodiester linkage between the positions C(4') and C(2') of neighboring ribopyranosyl units. Double strands of p-RNA oligonucleotides are expected to have a linear structure and to show purine-pyrimidine and purine-purine (Watson-Crick) pairing comparable in strength to that obsd. in homo-DNA. Exptl., synthetic b-D-ribopyranosyl (4'->2')-oligonucleotides derived from adenine and uracil confirm this prognosis: adenine-uracil pairing in p-RNA duplexes is stronger than in the corresponding RNA duplexes. Importantly, adenine in p-Ribo(A8) does not show (reverse-Hoogsteen) self-pairing, in sharp contrast to its behavior in the homo-DNA series. The sheer existence of strong and selective pairing in a system that is constitutionally isomeric to RNA and can be predicted to have a linear structure has implications for the problem of RNA's origin. In this context, a comprehensive exptl. study of the pairing properties of p-RNA, of its potential for constitutional assembly, self-replication, and intra-duplex isomerization to RNA seems mandatory. [on SciFinder (R)]

Why Pentose-And Not Hexose-Nucleic Acids? Part III. Oligo(2′,3′-dideoxy-β-D-glucopyranosyl)nucleotides. (‘Homo-DNA’): Base-Pairing Properties1 The paper presents results of a comprehensive investigation on the pairing properties of homo-DNA oligonucleotides, the preparation of which has been described in Part II of this series [2]. The investigation was carried out by using established methods described in the literature for the characterization of oligonucleotides in the natural series, such as determination of melting temperatures of oligonucleotide duplexes by temperature-dependent of melting temperatures, determination of pairing stoichiometry by ratio-dependent UV spectroscopy of binary mixtures of pairing partners, temperature-dependent CD spectroscopy, gel electrophoresis under non-denaturing conditions, and – in selected cases – 1H – and31P-NMR spectroscopy. The systematic comparison of the paring properties of homo-DNA oligonucleotides with corresponding DNA nucleotides (up to dodecamers) indicates that homo-DNA is a highly efficient, autonomous, artificial pairing system with a pairing behavior that is in part similar to, but also, in part, strikingly different from, the pairing behavior of DNA. The pairing properties established so far are listed below in a manner that reflects the sequence of subtitles in Chapt.2 of the text; they were determined under the conditions: H2O, 0.15M NaCl, 0.01M Tris-HCl buffer, pH 7, oligonucleotide concentrations in the μM range, 1:1 ratio of single strands in the case of non-selfcompementary sequences.

Glycolaldehyde phosphate, sorbed from highly dilute, weakly alkaline solution into the interlayer of common expanding sheet structure metal hydroxide minerals, condenses extensively to racemic aldotetrose-2, 4-diphophates, and aldohexose-2, 4, 6-triphosphates. The reaction proceeds mainly through racemic erythrose-2, 4-phosphate, and terminates with a large fraction of racemic altrose-2, 4, 6-phosphate. In the absence of an inductive mineral phase, no detectable homogeneous reaction takes place in the concentration- and pH range used. The reactant glycolaldehyde phosphate is practically completely sorbed within an hour from solutions with concentrations as low as 50 micron; the half-time for conversion to hexose phosphates is of the order of two days at room temperature and pH 9.5. Total production of sugar phosphates in the mineral interlayer is largely independent of the glycolaldehyde phosphate concentration in the external solution, but is determined by the total amount of GAP offered for sorption up to the capacity of the mineral. In the presence of equimolar amounts of rac-glyceraldehyde-2-phosphate, but under otherwise similar conditions, aldopentose-2, 4, -diphosphates also form, but only as a small fraction of the hexose-2, 4, 6-phosphates.

Why Pentose and Not Hexose Nucleic Acids? Part II. Preparation of Oligonucleotides Containing 2′,3′-Dideoxy-β-D-glucopyranosyl Building Blocks(7) This paper describes the preparation of the 2′,3′-dideoxy-β-D-glucopyranosyl-( = 2′,3′-dideoxy-β-D-erythro-hexopyranosyl)-derived nucleosides of the five bases adenine, cytosine, guanine, thymine, and uracil ( = ‘homo-de-oxyribonucleosides’) as well as the synthesis of oligonucleotides derived from them. The methods used for both nucleoside and oligonucleotide synthesis closely follow the known methods of synthesis in the corresponding series of natural 2′-deoxyribonucleosides and oligonucleotides. The efficient methods of automated DNA synthesis proved to be fully applicable to the synthesis of homo-DNA oligonucleotides, the only change necessary for achieving satisfactory coupling yields being a slight lengthening of the coupling time. Homo-DNA oligonucleotides with chain lengths of up to twelve nucleoside units were assembled on solid support either manually or on a commercial DNA synthesizer in scales of 0.4 μmol to as much as 200 μmol and were purified by either reversed-phase or ion-exchange HPLC to single-peak purity according to both chromatographic systems (estimated purity > 95%). The choice of the specific base sequences to be synthesized was determined primarily by the constitutional problems of base pairing that emerged from experimental observations made in the course of systematic studies of the pairing properties of homo-DNA oligonucleotides. About 100 homo-DNA sequences were prepared for this purpose. Their pairing properties will be described in Part III of this series; the present paper is restricted to the characterization of the purity and constitutional integrity of a few selected (single-stranded) oligonucleotides by 1H-, 31P-, and 13C-NMR spectroscopy as well as by FAB and time-of-flight mass spectroscopy. The English Footnotes to Schemes 1–9, Fig. 1–12, and Table 1 provide an extension of this summary.

Why Pentose and Not Hexose Nucleic Acids? Part I. Introduction to the Problem, Conformational Analysis of Oligonucleotide Single Strands Containing 2′,3′-Dideoxyglucopyranosyl Building Blocks (‘Homo-DNA’), and Reflections on the Conformation of A- and B-DNA Summary in collaboration with Prof. Dr. C.E. Wintner, Haverford College, Haverford, PA 19041-1392; academic guest, ETH, March and June/July, 1991. Chemical rationalization of the structure of a biomolecule can be sought through consideration of two criteria: first, the relationship between the structure and its biological function; and second, the structure's potential for constitutional self assembly. The latter criterion convers the judgment, by chemical reasoning, of the chance of its preformation, that is, a synthetic event which must have been undergone by any molecular structure in order to have been selected (or to have selected itself) to become a biomolecule. One way to further the task of rationalizing a biomolecule's structure by experimental means is the design, synthesis, and study of structural alternatives which might have become biomolecules on the basis of either criterion, but which do not, in fact, appear in Nature today. In the formation of sugar phosphates from glycolaldehyde phosphate under basic conditions, straightforward and selective formation of rac-hexose 2,4,6-triphosphates is observed in the absence of formaldehyde, while rac-pentose 2,4-diphosphates are dominant, when (0.5 equiv.) formaldehyde is present [1]. This and other observations indicate that hexose sugars should be regarded to have had a chance of preformation comparable with that of pentose sugars. Why, then, did Nature choose pentoses and not hexoses as the sugar building blocks of nucleic acids? The reason must be functional; it must be the case that pentose nucleic acids are biologically superior to potential hexose alternatives. To the extent that biological function is a consequence of molecular structure and reactivity, the origin of this superiority should be decipherable through chemical experiment, that is, through synthesis of hexose nucleic acids, systematic study of their chemical properties, and comparison of these properties with those of their natural counterparts. This has been the object of the present investigation, initiated in 1986. The paper introduces a series of papers which will describe the results of a model study, namely, the synthesis, pairing properties and structure of homo-DNA oligonucleotides.

The structure of a derivative of coenzyme F430 from methanogenic bacteria, the bromide salt of 12,13-diepi-F430 pentamethyl ester (5, X = Br), was determined by X-ray structure analysis. It reveals a more pronounced saddle-shaped out-of-plane deformation of the macrocycle than any hydroporphinoid Ni complex investigated so far. The crystal structure confirms the constitution proposed for coenzyme F430 (2) and shows that in the epimer 5, the three stereogenic centers in ring D, C(17), C(18), and C(19), have the (17S)-, (18S)-, and (19R)-configuration, respectively. Deuteration and 2D-NMR studies independently demonstrate that native coenzyme F430 (2) has the same configuration in ring D as the epimer 5. Therefore, our original tentative assignment of configuration at C(19) and C(18) [1] has to be reversed. This completes the assignment of configuration for all stereogenic centers in coenzyme F430, which has the structure shown in Formula2.

The rearrangement of methyl 2-(methylthio)benzenesulfonate (1) to the zwitterionic 2-(dimethyl-sulfonium)benzenesulfonate (2) is known to proceed in solution by intermolecular Me transfers. The same rearrangement has been observed to occur in crystalline 1, but the crystal structure shows that the molecular packing is not conducive to intermolecular Me transfer. The reaction has been carried out with mixed crystals composed of 1 and deuteriomethylated (D6)-l. By fast-atom-bombardment mass spectroscopy, it has been shown that the product consists of a 1:2:1 mixture of the non-, tri-, and hexadeuterated species, the mixture expected, if the solid-state reaction proceeds by intermolecular Me transfers. From this result, together with the slower rates of conversion in the single crystal compared with the melt, it can be concluded that the reaction must occur not topochemically but rather at defects such as microcavities, surfaces, and other irregularities in the ordered crystal arrangement.

2-Aminopropenenitrile in solvents such as MeCN, MeOH, or H2O is photoisomerized by UV light to racemic aziridine-2-carbonitrile (rac-2); the larger part of the starting material, however, fragments to HCN and MeCN. The observed photocyclization constitutes a structural connection within an ensemble of C3H4N2 compounds considered to be potentially relevant to prebiotic chemistry.

Chemistry of α-Aminonitriles. Aziridine-2-carbonitrile, a Source of Racemic O′-Phosphoserinenitrile and Glycolaldehyde Phosphate Racemic aziridine-2-carbonitrile (rac-1) in MeCN solution reacts regioselectively (> 90%) with 2 equiv. of TsOH at room temperature to form the hydrotosylate of racemic O3-tosylserinenitrile (rac-2) via β-ring opening (Scheme 2). A similar regioselective reaction takes place between rac-l and H3PO4 to produce racemic O3-phosphoserinenitrite (rac-3) which is in turn a source of glycolaldehyde phosphate (=formylmethyl dihydrogenphosphate) under the conditions of a ‘retro-Strecker’ reaction in aqueous solution (Scheme 6). These experiments document a close structural relationship between the simplest of the sugar phosphates and an α-aminonitrile precursor. The English Footnotes (*) referring to Schemes 1-7 are intended to provide an extension of this summary.

Glycoaldehyde phosphate aldomerizes in aq. NaOH to a product mixt. contg. the racemates of two diastereomeric tetrose 2,4-diphosphates and 8 hexose 2,4,5-triphosphates. The aldomerization of glycoaldehyde in the presence of formaldehyde is a variant of the formose reaction. It avoids the formation of complex formose product mixts., because C(2)-phosphorylated aldoses cannot undergo aldose-ketose tautomerization. This work, with its demonstration of an intrinsic kinetic preference for ribose 2,4-diphosphate and allose 2,4,5-triphosphate formation, adds a piece of factual chem. information to ongoing discussion about the origin of ribonucleic acids. [on SciFinder (R)]

Chemistry of α-Aminonitriles I: Introduction and Pathways to Uroporphyrinogen-octanitriles. An introduction to experimental studies on the chemistry of α-aminonitriles potentially relevant to the problems of prebiotic chemistry is presented. The framework of conditions wherein the investigation is chosen to be carried out implies both molecular oxygen and - whenever feasible - water to be excluded from reaction conditions. This study focusses on 2-amino-2-propenenitrile (3) (Scheme 6) as central starting material of reaction sequences which aim at the nitrile forms of proteinogenic amino acids as well as at the aza forms of building blocks of biological cofactor molecules as their targets (Scheme 5). Schemes 13,16,23 as well as 25 and 26 summarize reaction sequences by which 3 is transformed within the defined framework of conditions into the thermodynamic (statistically controlled) mixture of the four isomeric uroperphyrinogen-octanitriles 57–60. HPLC's of such mixtures document the dominance of the least symmetrical isomer whose constitutional pattern of peripheral substituents happens to be the one percent in all biological porphinoids. Preparative procedures for the synthesis of 3(Scheme 9), the β,β-disubstituted pyrrol-nitriles 30,53 and 54 (Scheme 19) as well as the porphyrinogenoctakis(propionitrile) and-octakis(acetonitrile) 65 and 66, respectively (Scheme 24) are given.

Experiments on a simulation of the photochemical A/D-secocorrin corrin cycloisomerization by redox processes. Electrochemical oxidation of nickel(II)-1-methylidene-2,2,7,7,12,12-hexamethyl-15-cyano-1,19-secocorrinate perchlorate Can the act of light excitation in the photochemical A/D-secocorrin corrin cycloisomerization be replaced by redox reactions in the dark? Electrochemical oxidation of nickel(II)-A/D-secocorrinate 4 in acetonitrile containing a trace of water produces the secocorrinoxide–nickel-complex 5 (structure determined by X-ray analysis) in almost quantitative yield. This two-electron oxidation involves a hydrogen shift from the methylene group C(19) in ring D to the methylidene carbon atom at ring A in the radical cation intermediate. Since the same type of hydrogen shift occurs in the photochemical A/D-secocorrin corrin cycloisomerization, a close parallelism in their chemical reactivity seems to exist between electronically excited A/D-secocorrins and corresponding radical cations. Formation of the corrin complex 2 (M = Ni+) could be achieved (so far only in modest yields) by electrochemical one-electron oxidation of 4 in acetonitrile/acetanhydride/acetic acid 8:1:1 followed by one-electron reduction. – The transformation of the oxide nickel complex 5 to the corrinoid complex 10 – a new member in the family of dehydrocorrins – is also recorded.

Photochemical and non-photochemical A/D-secocorrincorrin-cyclizations of 19-carboxy- and 19-formyl-1-methylidene-1,19-secocorrinates. Decarboxylation (and deformylation) of nickel(II)-19-carboxy-(resp. 19-formyl)-corrinates Nickel (II) 1-methylidene-2,2,7,7,12,12-hexamethyl-15-cyano-19-carboxy-1,19-secocorrinate can be induced to cyclize with concomitant decarboxylation to the corresponding corrinate (Scheme 9). Experiments with deuterated derivatives (Scheme 10) indicate that in this decarboxylative A/D-secocorrincorrin-cyclization the ring closure step precedes decarboxylation. In accord therewith is the finding that the corresponding intermediate nickel(II) 19-carboxy-corrinate (synthesized via photochemical cyclization of the corresponding cadmium complex, Schemes 6 and 9) decarboxylates under very mild conditions. Nickel(II) 1-methylidene-2,2,7,7,12,12-hexamethyl-15-cyano-19-formyl-1,19-secocorrinate cyclizes smoothly to the corresponding 19-formyl-corrinate in the presence of acetic acid/triethylamine. The formyl group of the cyclization product can be eliminated hydrolytically in essentially quantitative yield by treatment with 2N KOH in ethanolic solution (Scheme 11). The non-photochemical (AD)-cyclization of 19-formyl-1,19-secocorrinoids represents formation of the corrin chromophore at the oxidation level of porphyrinogens and exemplifies how a C1-fragment that eventually leaves the ligand can fulfill a specific function in the (AD)-ring closure to a corrin.

β,γ-unsaturated δ-hydroxy-cyclohexene carboxylic acids undergo a smooth decarboxylative elimination when treated with DMF-dineopentylacetal in an unpolar solvent. The reaction provides a method for the regiospecific preparation of 1,3-cyclohexadiene derivatives under non-isomerizing conditions, starting from easily accessible and structurally variable intermediates.

Magnesium transfer from the iodo-magnesium salt of 3,5-di-t-butyl-4-hydroxy-toluene (BHT) into methyl pheophorbide a is a fast process in methylenechloride/ether solution at ambient temperature. This procedure for the introduction of magnesium into labile chlorin ligands has made possible the preparation of a crystalline 132, 173-cyclochlorophyllide a-enol. Concomitant use of the lithium salt of BHT facilitates the more critical insertion of magnesium into methyl bacteriopheophorbide a. The preparative success of these magnesium transfers depends crucially upon the solvent system used. Under conditions where the complexation of methyl pheophorbide a with iodo-magnesium-BHT is essentially complete within 2 minutes at 12° in methylenechloride/ether solution, strong inhibition of the magnesium transfer is observed by cosolvents such as pyridine, dimethylacetamide, dioxan or tetrahydrofuran.

The Ag+-induced α-chloro-aldonitrone/olefin reaction in polar solvents can proceed by substitution, thereby providing a method for the preparation of β, γ-unsaturated aldehydes. Positional as well as configurational retention of the olefinic double bond are mechanistically significant and preparatively useful characteristics of this process. Substitution also occurs with great ease at nucleophilic aromatic nuclei; this offers a simple preparative route to certain β-aryl-aldehydes. The results illustrate a general aspect of the chemistry of α-chloro-aldonitrones: the N-alkenyl-N-alkyl-nitrosonium-ions derived from them can serve as preparative equivalents of the elusive corresponding α-acyl-carbonium-ions.

Preparation and Properties of some Hydrocorphinoid Nickel(II)-Complexes Corphin derivatives synthesized earlier in our laboratory have been used for the preparation of tetrahydro- and hexahydrocorphinoid nickel(II)-complexes containing novel chromophore systems. The UV./VIS. and 1H- and 13C-NMR. spectral data of these complexes were relevant to the structure determination of Factor F430 described in the following paper.

An X-ray structure analysis and magetic as well as electrochemical data for synthetic corrinioid and corphinoid nickel(II) complexes document the pronounced axial electrophilicity of the nickel(II) ion when complexed by ligands of the type occurring in coenzyme F430.