Essential reactive intermediates in nucleoside chemistry: cyclonucleoside cations

DFT-based modeling as well as experimental examination of model keto nucleosides have revealed that high susceptibility of these compounds to acids is due to formation of intermediate cyclonucleoside cations of low energy. Theoretically established chemical structures of these previously overlooked intermediates explain the reaction courses for a cluster of nucleoside reactions.     

Theoretical study of the bonding in Fe---M dimers

The electronic structures of Fe₂, FeMn, FeCo, FeCu and FeNi have been calculated using Gaussian-76 SCF techniques. Gaussian basis sets contracted to [4s, 2p, 1d] functions are used on each atom resulting in sets of near double zeta accuracy in the valence region. The calculated UHF electronic ground state configurations for these Fe---M dimers are comparable with those experimentally determined. By examining the Mulliken atomic overlap population analysis, a correlation is found between the Mössbauer spectrum and calculated binding strengths in these dimers. Our calculations, fixed at r_e of 2.3 Å, show that the binding strengths decrease from FeCu, FeMn, Fe₂, FeCo, FeNi.     

Front Propagation Dynamics with Exponentially-Distributed Hopping

We study reaction-diffusion systems where diffusion is by jumps whose sizes are distributed exponentially. We first study the Fisher-like problem of propagation of a front into an unstable state, as typified by the A+B → 2A reaction. We find that the effect of fluctuations is especially pronounced at small hopping rates. Fluctuations are treated heuristically via a density cutoff in the reaction rate. We then consider the case of propagating up a reaction rate gradient. The effect of fluctuations here is pronounced, with the front velocity increasing without limit with increasing bulk particle density. The rate of increase is faster than in the case of a reaction-gradient with nearest-neighbor hopping. We derive analytic expressions for the front velocity dependence on bulk particle density. Computer simulations are performed to confirm the analytical results.     

Fluctuation-regularized front propagation dynamics in reaction-diffusion systems

We introduce and study a new class of fronts in finite particle-number reaction-diffusion systems, corresponding to propagating up a reaction-rate gradient. We show that these systems have no traditional mean-field limit, as the nature of the long-time front solution in the stochastic process differs essentially from that obtained by solving the mean-field deterministic reaction-diffusion equations. Instead, one can incorporate some aspects of the fluctuations via introducing a density cutoff. Using this method, we derive analytic expressions for the front velocity dependence on bulk particle density and show self-consistently why this cutoff approach can get the correct leading-order physics.     

Pericyclic organometallic reactions. Cycloaddition reactions of (η-cycloheptatriene)Ru(CO)3. Crystal structure of tricarbonyl[(2,3,4,9-η)-bicyclo[4.2.1]non-2-ene-4,9-diyl-7,7,8,8-tetracarbonitrile]ruthenium

(η⁴-Cycloheptatriene)Ru(CO)₃ reacts with tetracyanoethylene (TCNE), 4-phenyltriazoline-3,5-dione (PTAD) and (carbomethoxy)maleic anhydride (CMA) to give stable 3 + 2 σ,π-allylic adducts. The 3 + 2 adduct with TCNE equilibrates via a [4,4]-sigmahaptotropic rearrangement with the less stable 6 + 2 adduct, which decomposes under the reaction conditions to the demetallated 6 + 2 adduct. It is concluded that σ,π-allylic adducts are in general more stable than their isomeric η⁴-π counterparts. The structure of the 3 + 2 TCNE adduct was determined by a single-crystal X-ray diffraction study.     

Ab initio study of the ground and excited states of HCP and its isomer HPC

The potential energy surface of HCP converting to HPC in its ground electronic state has been investigated with ab initio methods at levels up to MP2/6-311G**//MP4/6-311G** as well as TZV + + ** CASSCF. All geometries are fully optimized and compare favorably to previous theoretical and experimental values. The HCP molecule is predicted to be 85.4 kcal/mol lower in energy than its linear isomer at the-MP2/6-31G*//MP2/6-31G* level. The energy barrier for hydrogen rearrangement is found to be merely 2.3 kcal from the HPC end. CASSCF studies were initiated to clarify the low barrier and lent support to a flat surface as HPC converts to stable, linear HCP at the TZV + + ** level. CASSCF also predicts that HPC is unstable with respect to bending. Harmonic vibrational frequencies for HCP results in 5% accuracy or better. A bent triplet is found to be the lowest excited state using the CASSCF method. © 1993 John Wiley & Sons, Inc.     

Peptide conjugation: unexpected ring opening of azacrown ether nucleophiles in the oxazolone-based coupling

Unexpected cleavage of the macrocylic ring of secondary azacrown ethers when interacting with the Aib8 (Aib = alpha-aminoisobutyric acid) oxazolone indicates the possibility for a new mechanism of peptide racemization due to transformations of the oxazolones formed from the N-derivatives of alpha-amino acids in peptide synthesis.     

Synthesis and characterization of new thorium and uranium phenolate complexes

The reaction between the chelating amino bisphenole ligand (ONOO)H₂ (1) and (ONNO)H₂ (2) with an excess of NaH gives the corresponding bis-sodium salts 3 and 4 quantitatively.The salts were reacted with thorium tetrachloride at room temperature to obtain the corresponding (ONOO)ThCl₂ (5) and (ONNO)ThCl₂ (6) complexes.However, ThCl₄ and UCl₄ react with (3) at higher temperatures to give the corresponding isomorphous homoleptic complexes (ONOO)₂Th (7) and (ONOO)₂U (8).We have also synthesized and characterized a thorium salicylaldiminato complex L₃ThCl (11) , in order to study the effect of the bridged ligand on the molecular structure.     

Recombination dramatically speeds up evolution of finite populations

We study the role of recombination, in the form of bacterial transformation, in speeding up Darwinian evolution. This is done by adding a new process to a previously studied Markov model of evolution on a smooth fitness landscape; this new process allows alleles to be exchanged with those in the surrounding medium. Our results, both numerical and analytic, indicate that, for a wide range of intermediate population sizes, recombination dramatically speeds up the rate of evolutionary advance.