Computer simulation in template-directed oligonucleotide synthesis.

A computer simulation (KINSIM) modeling up to 33 competing reactions was used in order to investigate the product distribution in a template-directed oligonucleotide synthesis as a function of time and concentration of the reactants. The study is focused on the poly(C)-directed elongation reaction of an oligoguanylate (a 7-mer is chosen) with guanosine 5'-monophosphate-2-methyl-imidazolide (2-MeImpG), the activated monomer. It is known that the elongation of oligoguanylates to form oligomeric products such as 8-mer, 9-mer, 10-mer, etc., is in competition with (1) the dimerization and further oligomerization reaction of 2-MeImpG that leads to the formation of dimers and short oligomers, and (2) the hydrolysis of 2-MeImpG that forms inactive guanosine 5'-monophosphate, 5'-GMP. Experimentally determined rate constants for the above three processes at 37 degrees C and pH 7.95 were used in the simulation; the initial concentrations of 2-MeImpG, [M]o, and of the oligoguanylate primer, [7-mer]o, were varied, and KINSIM calculated the distribution of products as a function of time until equilibration was reached, i.e., when all the activated monomer has been consumed. In order to sort out how strongly the elongation reaction may be affected by the competing hydrolysis and dimerization, we also simulated the idealized situation in which these competing reactions do not occur.(ABSTRACT TRUNCATED AT 250 WORDS)

Carbon-to-carbon identity proton transfers from propyne, acetimide, thioacetaldehyde, and nitrosomethane to their respective conjugate anions in the gas phase. An ab initio study.

Gas-phase acidities of CH3Y (Y: NO, C identical to CH, CH=NH, and CH=S), barriers to the identity proton-transfer CH3Y + CH2=Y- reversible CH2=Y- + CH3Y, as well as geometries and charge distributions of CH3Y, CH2=Y- and the transition states of the proton transfers were determined by ab initio methods at the MP2/6-311 + G(d,p)//MP2/6-311 + G(d,p), B3LYP/6-311 + G(d,p), and BPW-91/6-311 + G-(d,p) levels of theory. The acidities were also calculated at the CCSD(T)/6-311 + G(2df,2p) level. To make more meaningful comparisons, the same quantities for previously studied systems (Y: H, CH=CH2, CH=O, CN, NO2) were recalculated at the levels used in the present work. The geometric parameters as well as the group charges indicate that the transition states for all the reactions are imbalanced, although there is no correlation between the degree of imbalance and the pi-acceptor strength of the Y group. Based on multi-parameter correlations with the field (sigma F), resonance (sigma R), and polarizability effect (sigma alpha) substituent constants, the contributions of each of these effects to the acidities and barriers were evaluated. For the Y groups whose sigma F, sigma R, and sigma alpha are unknown (CH=NH, CH=S, C identical to CH), a method for estimating these substituent constants is proposed. The barriers for the CH3Y/CH2=Y- systems are all lower than for the CH4/CH3- system; this contrasts with the situation in solution where the Y groups lead to an increase in the barrier. The reasons for this reversal are analyzed. We also make an attempt to clarify the issue as to why the transition states of these reactions are imbalanced, a question which continues to draw attention in the literature.

Physical organic chemistry of transition metal carbene complexes. 23. Kinetic and thermodynamic acidities of cationic benzothienyl- and selenylcarbene complexes of rhenium in aqueous acetonitrile.

The pK(a) values of a cationic selenyl- (5H(+)) and a benzothienylcarbene complex (6H(+)) and rate constants for the reversible deprotonation of these complexes by water, carboxylate ions, primary aliphatic amines, secondary alicyclic amines (5H(+) only), and OH(-) (5H(+) only) were determined in 50% MeCN-50% water (v/v) at 25 degrees C. In comparison with neutral Fischer-type carbene complexes such as 1H, the cationic complexes 5H(+) and 6H(+) are much more acidic, and the intrinsic barriers to proton transfer are substantially higher. This paper discusses a variety of factors that contribute to these differences, with the most important ones being that 5H(+) and 6H(+) are cationic, which makes the C(5)H(5)(NO)(PPh(3))Re moiety a stronger pi-acceptor than the (CO)(5)M moieties, coupled with the fact that the deprotonated forms of 5H(+) and 6H(+ )are aromatic molecules.

Carbon-to-carbon identity proton transfer from allene, ketene, ketenimine, and thioketene to their respective conjugate anions in the gas phase. An ab initio study.

Gas-phase acidities of CH2=C=X (X = CH2, NH, O, and S) and barriers for the identity proton transfers (X=C=CH2 + HC triple bond C-X- right harpoon over left harpoon -X-C triple bond CH + CH2=C=X) as well as geometries and charge distributions of CH2=C=X, HC triple bond C-X- and the transition states of the proton transfer were determined by ab initio methods at the MP2/6-311+G(d,p)//MP2/6-311+G(d,p) and B3LYP/6-311+G(d,p) levels of theory. The acidities were also calculated at the CCSD(T)/6-311+G(2df,p) level. A major objective of this study was to examine how the enhanced unsaturation of CH2=C=X compared to that of CH3CH=X may affect acidities, transition state imbalances, and intrinsic barriers of the identity proton transfer. The results show that the acidities are all higher while the barriers are lower than for the corresponding CH3CH=X series. The transition states are all imbalanced but less so than for the reactions of CH3CH=X.

Magnesium ion catalyzed P-N bond hydrolysis in imidazolide-activated nucleotides. Relevance to template-directed synthesis of polynucleotides.

Magnesium, an ion necessary in enzymatic as well as in nonenzymatic template-directed polynucleotide-synthesizing reactions, has been found to catalyze the hydroxide ion attack on the P-N bond of selected 5'-monophosphate imidazolide derivatives of nucleotides, such as guanosine 5'-monophosphate 2-methylimidazolide (2-MeImpG), guanosine 5'-monophosphate imidazolide (ImpG), and adenosine 5-monophosphate 2-methylimidazolide (2-MeImpA). Calcium ion behaves similarly, but quantitatively the effects are smaller. Pseudo-first-order rate constants of 2-MeImpG and ImpG hydrolysis as a function of Mg2+ concentration have been obtained in the range 6 < or = pH < or = 10 at 37 degrees C. Mg2+ catalysis is particularly effective around pH 10 where a 0.02 M concentration leads to 15-fold acceleration and a 0.2 M concentration to a 115-fold acceleration of the rate. At other pH values Mg2+ catalysis is less dramatic, mainly because the noncatalyzed reaction is faster. Mg2+ catalysis is attributed to the reaction of the zwitterionic form of the substrate (SH+/-, imidazolide moiety protonated) with OH- rather than reaction of the anionic form (S-, imidazolide moiety deprotonated) with water. This conclusion is based on a study of the N-methylated substrates N-MeImpG and 1,2-diMeImpg, respectively, which were generated in situ by the equilibrium reaction of ImpG with N-methylimidazole and 2-MeImpG with 1,2-dimethylimidazole, respectively. In contrast, the absence of Mg2+ the reaction of S- with water competes with the reaction of SH+/- with OH-. The present study bears on the mechanism of the Mg2(+)-catalyzed template-directed synthesis of oligo-and polynucleotides derived from 2-MeImpG and on the competition between oligonucleotide synthesis and hydrolysis of 2-MeImpG.

Kinetic dissection of individual steps in the poly(C)-directed oligoguanylate synthesis from guanosine 5'-monophosphate 2-methylimidazolide.

A kinetic study of oligoguanylate synthesis on a polycytidylate template, poly(C), as a function of the concentration of the activated monomer, guanosine 5'-monophosphate 2-methylimidazolide, 2-MeImpG, is reported. Reactions were run with 0.005-0.045 M 2-MeImpG in the presence of 0.05 M poly(C) at 23 degrees C. The kinetic results are consistent with a reaction scheme (eq 1) that consists of a series of consecutive steps, each step representing the addition of one molecule of 2-MeImpG to the growing oligomer. This scheme allows the calculation of second-order rate constants for every step by analyzing the time-dependent growth of each oligomer. Computer simulations of the course of reaction based on the determined rate constants and eq 1 are in excellent agreement with the product distributions seen in the HPLC profiles. In accord with an earlier study (Fakhrai, H.; Inoue, T.; Orgel, L. E. Tetrahedron 1984, 40, 39), rate constants, ki, for the formation of the tetramer and longer oligomers up to the 16-mer were found to be independent of length and somewhat higher than k3 (formation of trimer), which in turn is much higher than k2 (formation of dimer). The ki (i > or = 4), k3, and k2 values are not true second-order rate constants but vary with monomer concentration. Mechanistic models for the dimerization (Scheme I) and elongation reactions (Scheme II) are proposed that are consistent with our results. These models take into account that the monomer associates with the template in a cooperative manner. Our kinetic analysis allowed the determination of rate constants for the elementary processes of covalent bond formation between two monomers (dimerization) and between an oligomer and a monomer (elongation) on the template. A major conclusion from our study is that bond formation between two monomer units or between a primer and a monomer is assisted by the presence of additional next-neighbor monomer units. This is consistent with recent findings with hairpin oligonucleotides (Wu, T.; Orgel, L. E. J. Am. Chem. Soc. 1992, 114, 317). Our study is the first of its kind that shows the feasibility of a thorough kinetic analysis of a template-directed oligomerization and provides a detailed mechanistic model of these reactions.

Unraveling structure-reactivity relationships in SNV reactions: kinetics of the reactions of methoxybenzylidenemalononitrile, 2-(methylthiobenzylidene)-1,3-indandione, 2-(benzylthiobenzylidene)-1,3-indandione, and methyl beta-methylthio-alpha-nitrocinnamate with OH- and thiolate ions in aqueous DMSO.

The kinetics of the title reactions were determined in 50% DMSO-50% water (v/v) at 20 degrees C; n-BuS-, HOCH2CH2S-, and MeO2CCH2S- were used as thiolate ions. The reactions with the thiolate ions gave rise to two separate kinetic processes. The first refers to rapid, reversible attachment of RS- to the substrate leading to a tetrahedral intermediate (k1RS), k(-1)RS, the second to the conversion of the intermediate to products (k2RS). In most cases all of the rate constants (k1RS, k(-1)RS and k2RS could be determined. In combination with results from previous studies, a detailed discussion regarding the effects of activating substituents and leaving groups on rate and equilibrium constants as well as on intrinsic rate constants is presented. The reaction with OH- only allowed a determination of k1OH for nucleophilic attack on the substrate; in this case the tetrahedral intermediate remains at steady-state levels under all conditions.