Non-Adiabatic Chemical Reaction Triggered by Electron Photodetachment: An ab initio Quantum Dynamical Study

Dynamics following electron photodetachment in a complex of a chloride anion with ammonia is explored by a combination of electronic structure and quantum dynamical methods. This system serves as a prototype for investigating a hithertho unexplored class of chemical reactions - non-adiabatic proton transfer triggered by a detachment of an electron. All the reactive and non-reactive channels of this process are characterized and the respective quantum yields are presented

Photochemical Steps in the Prebiotic Synthesis of Purine Precursors from HCN

So much excitement: The mechanism for the photoconversion of the HCN tetramer into a precursor of purine nucleobases and nucleotides has been revealed by computational methods. Dissipation of the photoenergy in less than 2 ps eliminates the possibility of hot-ground-state reactions. Instead, a series of photoexcitations followed by internal conversion (IC) drives the reaction via an excited azetene

Theoretical study of the ground and excited states of 7-methyl guanine and 9-methyl guanine: comparison with experiment

The keto–enol tautomerization of 7-methyl-guanine and 9-methyl-guanine in the excited state was investigated using the time-dependent DFT (TDDFT) method. For both species, the potential energy surfaces of the ground state and two lowest singlet excited states (due to p - p* and n - p* transitions) have been investigated and their features discussed in terms of consequences on the excited state dynamics. The findings suggest that, for both species, the state due to the n - p* transition, suspected to be an intermediate in the excited state deactivation, exhibits two minima with the second minimum characterized by an elongated N1–H distance. This structure, intermediate between enol and keto tautomers, might play a role in the excited state relaxation. The existence of this second well, however, is observed in both 7- and 9-methyl guanine, which suggests that it cannot account alone for the different photophysical behavior of these species

Does Stacking Restrain the Photodynamics of Individual Nucleobases?

Nonadiabatic photodynamical simulations of 4-aminopyrimidine (4-APy) used as a model for adenine were performed by embedding it between two stacking methyl-guanine (mGua) molecules to determine the effect of spatial restrictions on the ultrafast photodeactivation mechanism of this nucleobase. A hybrid multiconfigurational ab initio/molecular mechanical approach in combination with surface hopping was used. During the dynamics the formation of a significant fraction of intrastrand hydrogen bonding from 4-APy to mGua above and below is observed. These findings show that this type of hydrogen bond may play an important role for the photodynamics within one DNA strand and that it should be of interest even in irregular segments of double stranded nucleic acids structures. The relaxation mechanism of internal conversion to the ground state is dominated by ring puckering, and an overall elongation of the lifetime of the embedded system by approximately 20% as compared to the isolated 4-APy is computed

Strikingly Different Effects of Hydrogen Bonding on the Photodynamics of Individual Nucleobases in DNA: Comparison of Guanine and Cytosine

Ab initio surface hopping dynamics calculations were performed to study the photophysical behavior of cytosine and guanine embedded in DNA using a quantum mechanical/molecular mechanics (QM/MM) approach. It was found that the decay rates of photo excited cytosine and guanine were affected in a completely different way by the hydrogen bonding to the DNA environment. In case of cytosine, the geometrical restrictions exerted by the hydrogen bonds did not influence the relaxation time of cytosine significantly due to the generally small cytosine ring puckering required to access the crossing region between excited and ground state. On the contrary, the presence of hydrogen bonds significantly altered the photodynamics of guanine. The analysis of the dynamics indicates that the major contribution to the lifetime changes comes from the interstrand hydrogen bonds. These bonds considerably restricted the out-of-plane motions of the NH(2) group of guanine which are necessary for the ultrafast decay to the ground state. As a result, only a negligible amount of trajectories decayed into the ground state for guanine embedded in DNA within the simulation time of 0.5 ps, while for comparison, the isolated guanine relaxed to the ground state with a lifetime of about 0.22 ps. These examples show that, in addition to phenomena related to electronic interactions between nucleobases, there also exist relatively simple mechanisms in DNA by which the lifetime of a nucleobase is significantly enhanced as compared to the gas phase

Resonant Infrared Multiple Photon Dissociation Spectroscopy of Anionic Nucleotide Monophosphate Clusters

We report mid-infrared spectra and potential energy surfaces of four anionic, 2'-deoxynucleotide-5'-monophosphates (dNMPs) and the ionic DNA pairs [dGMP-dCMP-H](1-), [dAMP-dTMP-H](1-) with a total charge of the complex equal to -1. We recorded IR action Spectra by resonant IR multiple-photon dissociation (IRMPD) using the FELIX free electron laser. The potential energy surface study employed an on-the-fly molecular dynamics quenching method (MD/Q), using a semiempirical AM1 method, followed by an optimization of the most stable structures using density functional theory. By employing infrared multiple-photon dissociation (IRMPD) spectroscopy in combination with high-level computational methods, we aim at a better understanding of the hydrogen bonding competition between the phosphate, moieties and the nucleobases. We find that, unlike in multimer double stranded DNA structures, the hydrogen bonds in these isolated nucleotide pairs are predominantly formed between the phosphate groups. This intermolecular interaction appears to exceed the stabilization energy resulting from base pairing and directs the overall cluster structure and alignment