Chemical evolution: the mechanism of the formation of adenine under prebiotic conditions.

Fundamental building blocks of life have been detected extraterrestrially, even in interstellar space, and are known to form nonenzymatically. Thus, the HCN pentamer, adenine (a base present in DNA and RNA), was first isolated in abiogenic experiments from an aqueous solution of ammonia and HCN in 1960. Although many variations of the reaction conditions giving adenine have been reported since then, the mechanistic details remain unexplored. Our predictions are based on extensive computations of sequences of reaction steps along several possible mechanistic routes. H(2)O- or NH(3)-catalyzed pathways are more favorable than uncatalyzed neutral or anionic alternatives, and they may well have been the major source of adenine on primitive earth. Our report provides a more detailed understanding of some of the chemical processes involved in chemical evolution, and a partial answer to the fundamental question of molecular biogenesis. Our investigation should trigger similar explorations of the detailed mechanisms of the abiotic formation of the remaining nucleic acid bases and other biologically relevant molecules.

Aromaticity and antiaromaticity in fulvenes, ketocyclopolyenes, fulvenones, and diazocyclopolyenes.

The structures, energies, natural charges, and magnetic properties of 3-, 5-, 7-, and 9-membered cyclic polyenes 1-4, respectively, with exocyclic methylene, keto, ketenyl, and diazo substituents (a-d, respectively) were computed at the B3LYP/6-311G+ **//B3LYP/6-311+G** level to elucidate their aromatic and antiaromatic properties. The corresponding conjugated cyclic cations le and 3e were also studied. The criteria used are isomerization energies (ISE), magnetic susceptibility exaltations (lambda), aromatic stabilization energies (ASE), nucleus independent chemical shifts (NICS), and bond length alternation (deltaR). Planar C2v structures were found to be the lowest energy minima with the exceptions of diazocyclopropene (1d), cycloheptafulvenone (3c), diazocycloheptatriene (3d), and all of the cyclononatetraene derivatives (4). The fulvenes (1a-4a) have modest aromatic or antiaromatic character, and are used as standards for comparison. By these criteria the ketenylidene and diazo cyclopropenes and cycloheptatrienes 1,3-c,d and oxo cyclopentadiene and cyclononatetraene 2,4b are antiaromatic, while the 5- and 9-ring ketenyl and diazo compounds and 3- and 7-ring ketones are aromatic. The degree of aromatic/antiaromatic character decreases with ring size. The consistent agreement with Hückel rule predictions for all the criteria shows their utility for the evaluation of the elusive properties of aromaticity and antiaromaticity.

Stability and three-dimensional aromaticity of closo-NB(n-1)H n azaboranes, n = 5-12.

Computations on all the possible positional isomers of the closo-azaboranes NB(n)()(-)(1)H(n)() (n = 5-12) reveal substantial differences in the relative energies. Data at the B3LYP/6-311+G level of density functional theory (DFT) agree well with expectations based on the topological charge stabilization, with the qualitative connectivity preferences of Williams, and with the Jemmis-Schleyer six interstitial electron rules. The energetic relationship involving each of the most stable positional isomers, 1-NB(4)H(5), NB(5)H(6), 2-NB(6)H(7), 1-NB(7)H(8), 4-NB(8)H(9), 1-NB(9)H(10), 2-NB(10)H(11), NB(11)H(12), was based on the energies (DeltaH) of the model reaction: NBH(2) + (n-1)BH(increment) --> NB(n)()H(n)()(+1) (n = 4-11). This evaluation shows that the stabilities of closo-azaboranes NB(n)()(-)(1)H(n)() (n = 5-12) increase with increasing cluster size from 5 to 12 vertexes. The "three-dimensional aromaticity" of these closo-azaboranes NB(n)()(-)(1)H(n)() (n = 5-12) is demonstrated by their the nucleus-independent chemical shifts (NICS) and their magnetic susceptibilities (chi), which match one another well. However, there is no direct relationship between these magnetic properties and the relative stabilities of the positional isomers of each cluster. As expected, other energy contributions such as topological charge stabilization and connectivity can be equally important.

Amination of pyridylketenes: experimental and computational studies of strong amide enol stabilization by the 2-pyridyl group.

Laser flash photolyses of 2-, 3-, and 4-diazoacetylpyridines 8 give the corresponding pyridylketenes 7 formed by Wolff rearrangements, as observed by time-resolved infrared spectroscopy, with ketenyl absorptions at 2127, 2125, and 2128 cm(-1), respectively. Photolysis of 2-, 3-, and 4-8 in CH(3)CN containing n-BuNH(2) results in the formation of two transients in each case, as observed by time-resolved IR and UV spectroscopy. The initial transients are assigned as the ketenes 7, and this is confirmed by IR measurements of the decay of the ketenyl absorbance. The ketenes then form the amide enols 12, whose growth and decay are monitored by UV. Similar photolysis of diazoacetophenone leads to phenylketene (5), which forms the amide enol 17. For 3- and 4-pyridylketenes and for phenylketene, the ratios of rate constants for amination of the ketene and for conversion of the amide enol to the amide are 3.1, 7.7, and 22, respectively, while for the 2-isomer the same ratio is 1.8 x 10(7). The stability of the amide enol from 2-7 is attributed to a strong intramolecular hydrogen bond to the pyridyl nitrogen, and this is supported by the DFT calculated structures of the intermediates, which indicate this enol amide is stabilized by 12.8 kcal/mol relative to the corresponding amide enol from phenylketene. Calculations of the transition states indicate a 10.9 kcal/mol higher barrier for conversion of the 2-pyridyl amide enol to the amide as compared to that from phenylketene.

Stability and Three-Dimensional Aromaticity of closo-Monocarbaborane Anions, CB(n)()(-)(1)H(n)(-), and closo-Dicarboranes, C(2)B(n)()(-)(2)H(n)().

Comprehensive ab initio calculations RMP2(fc)/6-31G on the closo-monocarbaboranes, CB(n)()(-)(1)H(n)()(-) (n = 5-12), and the closo-dicarboranes, C(2)B(n)()(-)(2)H(n)() (n = 5-12), show that the relative energies of all the positional isomers agree with the qualitative connectivity considerations of Williams and with the topological charge stabilization rule of Gimarc. The reaction energies (DeltaH) of the most stable positional isomers, 1-CB(4)H(5)(-), CB(5)H(6)(-), 2-CB(6)H(7)(-), 1-CB(7)H(8)(-), 5-CB(8)H(9)(-), 1-CB(9)H(10)(-), 2-CB(10)H(11)(-), CB(11)H(12)(-), as well as 1,5-C(2)B(3)H(5), 1,6-C(2)B(4)H(6), 2,4-C(2)B(5)H(7), 1,7-C(2)B(6)H(8), 4,5-C(2)B(7)H(9), 1,10-C(2)B(8)H(10), 2,3-C(2)B(9)H(11), and 1,12-C(2)B(10)H(12) (computed using the equations, CBH(2)(-) + (n - 1)BH(increment) --> CB(n)()H(n)()(+1)(-) (n = 4-11) and C(2)H(2) + nBH(increment) --> C(2)B(n)()H(n)()(+2) (n = 3-10)), show that the stabilities of closo-CB(n)()(-)(1)H(n)()(-) and of closo-C(2)B(n)()(-)(2)H(n)() generally increase with increasing cluster size from 5 to 12 vertexes. This is a characteristic of three-dimensional aromaticity. There are variations in stabilities of individual closo-CB(n)()(-)(1)H(n)()(-) and closo-C(2)B(n)()(-)(2)H(n)() species, but these show quite similar trends. Moreover, there is rough additivity for each carbon replacement. The rather large nucleus independent chemical shifts (NICS) and the magnetic susceptibilities (chi), which correspond well with one another, also show all closo-CB(n)()(-)(1)H(n)()(-) and closo-C(2)B(n)()(-)(2)H(n)() species to exhibit "three-dimensional aromaticity". However, the aromaticity ordering based on these magnetic properties does not always agree with the relative stabilities of positional isomers of the same cluster, when other effects such as connectivity and charge considerations are important.

The Large closo-Borane Dianions, B(n)()H(n)()(2-) (n = 13-17) Are Aromatic, Why Are They Unknown?

The relative stabilities of the unknown larger closo-borane dianions B(n)()H(n)()(2)(-) (n = 13-17), were evaluated at the B3LYP/6-31G level of density functional theory by comparing the average energies, E/n, and also by the energies using the model equation: B(n)()(-)(1)H(n)()(-)(1)(2)(-) + B(6)H(10) --> B(n)()H(n)()(2)(-) + B(5)H(9) (n = 6-17). Starting with the small closo-borane, B(5)H(5)(2)(-), the sequential addition of BH groups is represented by formal transfer from B(6)H(10) to build up larger and larger clusters. Most of the energies for these sequential steps are exothermic, but not for the B(12)H(12)(2)(-) to B(13)H(13)(2)(-) and the B(14)H(14)(2)(-) to B(15)H(15)(2)(-) stages. The cumulative total energies (DeltaH(add)) of these BH group additions, based on B(5)H(5)(2)(-) as the reference zero, tend to increase with increasing cluster size. DeltaH(add) indicates that the larger unknown closo-boranes B(13)H(13)(2)(-) to B(17)H(17)(2)(-) are more stable than B(9)H(9)(2)(-), B(10)H(10)(2)(-), and B(11)H(11)(2)(-); this agrees with E/n and with Lipscomb's earlier conclusion based on the PRDDO average energies. B(13)H(13)(2)(-), B(14)H(14)(2)(-), and B(15)H(15)(2)(-) are less stable than B(12)H(12)(2)(-), which has the lowest average energy on a per vertex basis among the closo-borane dianions. However, the total DeltaH(add) treatment indicates the larger B(16)H(16)(2)(-) and B(17)H(17)(2)(-) to be favorable relative to B(12)H(12)(2)(-), because of the larger number of vertexes. The formation of B(13)H(13)(2)(-) from B(12)H(12)(2)(-) is especially unfavorable. The further formation of B(14)H(14)(2)(-) and B(15)H(15)(2)(-) via BH transfer also is endothermic. These are not the only thermodynamic difficulties in building up large closo-borane dianions beyond B(12)H(12)(2)(-). The highly exothermic disproportionation of larger and smaller closo-borane dianions, e.g., B(12+)(n)()H(12+)(n)()(2)(-) + B(12)(-)(n)()H(12)(-)(n)()(2)(-) --> 2B(12)H(12)(2)(-) (n = 1-5), also indicate possible synthetic problems in preparing larger closo-boranes with more than 12 vertexes under condition where smaller boranes are present. All the larger closo-B(n)()H(n)()(2)(-) (n = 13-17) cluster exhibit "three-dimensional aromaticity", judging from the computed Nucleus Independent Chemical Shifts (NICS), which range from -30.9 to -36.5 ppm. The trends in NICS values are similar to the variations in the bond length alternations, Deltar. Thus, the qualitative relationships between geometric and magnetic criteria of aromaticity found earlier for the smaller clusters extends to the larger closo-borane dianions, B(n)()H(n)()(2)(-) (n = 13-17).