DFT mechanistic studies of boron-silicon exchange reactions between silyl-substituted arenes and boron bromides.

C-B bond forming reactions are important methodologies in modern synthetic chemistry, since many borylated organic substrates, ranging from alkanes and alkenes to arenes and heteroarenes, are useful intermediates for the synthesis of natural products, pharmaceuticals, and organic π-conjugated materials. Among numerous borylation methods, C-Si/B-Br exchange reactions have attracted increasing attention in recent years. While experimental exploration has been continually carried out for more than two decades, mechanistic insights into this type of reaction have not yet been clearly established. To address this deficiency of knowledge, we performed density functional theory (DFT) calculations to map out the reaction pathways for a range of boron-silicon exchange reactions between boron tribromide (BBr3) and trimethylsilyl-substituted arenes (TMSAr). Our computational analyses have disclosed the energetic, structural, and electronic properties for key stationary points on the potential energy surfaces (PES) in both the gas and solution (CH2Cl2) phases.

Computational Mechanistic Analysis of Intramolecular Cycloadditions of the 1,3-Dithiolium Cation with Adjacent Alkene and Allene Functional Groups.

In this work, the molecular mechanisms for the intramolecular cycloaddition reactions of the 1,3-dithiolium cation with adjacent alkenyl and allenyl groups were investigated by density functional theory calculations. Transition states for the mechanistic steps were searched, and their connections to corresponding reactive intermediates were validated by the intrinsic reaction coordinate method. Our studies demonstrate that both the alkenyl and allenyl groups can readily react with a neighboring 1,3-dithiolium cation first through a one-step asynchronous [3 + 2] cycloaddition path, with moderate activation energy barriers (ca. 20-30 kcal/mol) to overcome. Subsequent to the intramolecular dithiolium-alkene/allene cycloadditions, the resulting intermediates continue to undergo a series of reactions, including rearrangement, ring opening, and deprotonation to eventually yield the thermodynamically favored products, which carry a fused tricyclic molecular skeleton, 3,8-dihydro-2H-indeno[2,1-b]thiophene. Detailed geometric and energetic properties for all of the stationary points (transition states and intermediates) on the reaction potential surfaces have been calculated and examined. Key transition states and reactive intermediates were subjected to quantum theory of atoms in molecules and natural bonding orbital calculations to elucidate their bonding features and the stabilizing effects arising from orbital interactions. Finally, a comparative study using the continuum solvation model based on the charge density was conducted to evaluate the solvent effects on the intramolecular dithiolium-alkene/allene cycloadditions, which are the rate-limiting steps of the overall reactions. The results show that different organic solvents (polar and nonpolar) do not lead to much variations in the heights of activation energy barriers and hence indicate that solvent effects are actually insignificant on the reactions.

Mechanisms for the deamination reaction of cytosine with H2O/OH(-) and 2H2O/OH(-): a computational study.

Mechanisms for the deamination reaction of cytosine with H 2O/OH (-) and 2H 2O/OH (-) to produce uracil were investigated using ab initio calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at MP2 and B3LYP using the 6-31G(d) basis set and at B3LYP/6-31+G(d) levels of theory. Single point energies were also determined at MP2/G3MP2Large and G3MP2 levels of theory. Thermodynamic properties (Delta E, Delta H, and Delta G), activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway investigated. Intrinsic reaction coordinate (IRC) analysis was performed to characterize the transition states on the potential energy surface. Seven pathways for the deamination reaction were found. All pathways produce an initial tetrahedral intermediate followed by several conformational changes. The final intermediate for all pathways dissociates to product via a 1-3 proton shift. The activation energy for the rate-determining step, the formation of the tetrahedral intermediate for pathway D, the only pathway that can lead to uracil, is 115.3 kJ mol (-1) at the G3MP2 level of theory, in excellent agreement with the experimental value (117 +/- 4 kJ mol (-1)).

Computational study of the deamination reaction of cytosine with H2O and OH-.

The mechanism for the deamination reaction of cytosine with H(2)O and OH(-) to produce uracil was investigated using ab initio calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at RHF/6-31G(d), MP2/6-31G(d), and B3LYP/6-31G(d) levels and for anions at the B3LYP/6-31+G(d) level. Single-point energies were also determined at B3LYP/6-31+G(d), MP2/GTMP2Large, and G3MP2 levels of theory. Thermodynamic properties (DeltaE, DeltaH, and DeltaG), activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway that was investigated. Intrinsic reaction coordinate analysis was performed to characterize the transition states on the potential energy surface. Two pathways for deamination with H(2)O were found, a five-step mechanism (pathway A) and a two-step mechanism (pathway B). The activation energy for the rate-determining steps, the formation of the tetrahedral intermediate for pathway A and the formation of the uracil tautomer for pathway B, are 221.3 and 260.3 kJ/mol, respectively, at the G3MP2 level of theory. The deamination reaction by either pathway is therefore unlikely because of the high barriers that are involved. Two pathways for deamination with OH(-) were also found, and both of them are five-step mechanisms. Pathways C and D produce an initial tetrahedral intermediate by adding H(2)O to deprotonated cytosine which then undergoes three conformational changes. The final intermediate dissociates to product via a 1-3 proton shift. Deamination with OH(-), through pathway C, resulted in the lowest activation energy, 148.0 kJ/mol, at the G3MP2 level of theory.