A numerical study is reported concerning the first and second singlet excited-states of 5-benzyluracil using the multireference self-consistent field (state-averaged CASSCF) method. The vertical excitation energies of low-lying excited-states were characterized using the SA-CASSCF method, as well as using higher-level methods, such as CASPT2, MRCI and EOM-CCSD. The local minima and conical intersections found on the potential energy surfaces (PESs) were characterized in terms of molecular geometry and natural population analysis. Different relaxation pathways on the PESs are identified and discussed by comparing with the similar pathways found for the individual monomers of uracil and benzene. The molecule can be thought of as a model system for the study of crosslink reaction between DNA and proteins induced by UV light.

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The individual steps of a model Pd-catalyzed Negishi coupling between vinyl bromide and MeZnClS 2 (S = THF), using Pd(PMe 3 ) 2 as catalyst, have been examined with the aid of DFT computations in THF solution with the B97D functional to gain further insight into the role of Pd−Zn interactions on the oxidative addition and reductive elimination steps. Comparisons between such processes taking place on monometallic Pd complexes and on bimetallic Pd−Zn complexes reveal a detrimental effect of Pd−Zn interactions in oxidative addition, whereas reductive elimination is favored by Pd−Zn cooperativity. Additionally, a cis transmetalation pathway has been characterized that complements previous studies involving trans complexes.

Pathways for the rearrangement of the E and Z isomers of allyl- and methyl-substituted vinyl allene oxides to stereodefined cyclopentenones have been studied by DFT computations. Regardless of the reactant geometry, cis-configured cyclopentenones are found to be formed in a stepwise cascade comprising as key steps the ring opening of the oxirane to give an oxidopentadienyl diradical, its isomerization, and electrocyclization. An allyl substituent at the C atom of the starting vinyl allene oxide induces opposite effects on the activation energies for ring opening: a decrease owing to assistance by homoconjugation for the out motion and an increase due to the stereoelectronic stabilization of the reactant. As a result, allyl- and methyl-substituted vinyl allene oxides exhibit comparable activation energies. Only model systems with crotyl substituents afford lower activation energies than the methyl counterparts due to the additional stabilization of the forming charge deficiency at a secondary carbon by homoconjugation. Moreover, upon homoconjugative interaction reactants of Z geometry are predicted to undergo cyclization more readily than the E isomers. The results with Z-crotyl substituent are congruent with the spontaneous rearrangement of natural vinyl allene oxide derived from α-linolenic acid to a racemic cis-cyclopentenone (12-oxo-PDA).

The three competing paths for the rearrangement of 1 (involving 1,2- and 1,3-ester migration with alkyne or oxirane activation) evidence the multifaceted character of gold as a catalyst. The most favorable mechanism for this useful synthetic transformation involves a cascade of more than eight steps. All the functional groups in the substrate play a crucial and synergistic role, and sequential gold coordination to both the pi-system and the lone pairs of oxygen is needed. Exploration of these three paths suggests the use of a nonalkynophilic Lewis acid (BF(3)) as a possible synthetic alternative for this transformation.