A hitherto unknown stability of DNA basepairs

Direct capture of a low-energy free-electron into delocalized σ* orbitals for enabling state- and bond-selective reactions

Chemically activating a bond by capturing a low-energy free-electron directly and resonantly into its σ* orbital is conceptually simple and yet the most fascinating possibility for achieving state-specific and bond-specific chemical control. But this direct approach has not been explored experimentally due to the very low resonant electron capture cross-section of electrons into the σ* orbital. Here we report defunctionalization and dehydrogenation reactions that are bond-selectively enabled by the direct capture of a low-energy electron into the σ* orbital. The remarkable efficiency of these reactions can be attributed to superpositions of the σ* orbital with its vicinal or conjugatedσ CH * orbitals. The ubiquity of such quantum superpositions in molecules opens unprecedented experimental possibilities in the aspiration to control chemical reactions using low-energy free-electrons.

Electron Attachment to the Nucleobase Uracil in Diethylene Glycol: The Signature of a Doorway

The cellular environment plays a significant role in low energy electron-mediated radiation damage to genetic materials. In this study, we have modeled the effect of the bulk medium on electron attachment to nucleobases in diethylene glycol (DEG) using uracil as a test case, in accordance with recent experimental work on the observation of dissociative quasi-free electron attachment to nucleoside via excited anion radical in solution (in DEG). Our EOM-CCSD-based quantum mechanical/molecular mechanical (QM/MM) simulations indicate that the electron scavenging by uracil in DEG is much slower than that observed in the aqueous medium due to its viscosity. This work also establishes that a doorway mechanism exists in uracil microsolvated and bulk solvated with DEG, with the dipole-bound state and solvent-bound state acting as doorway states, respectively.

Prebiotic chemical origin of biomolecular complementarity

The early Earth, devoid of the protective stratospheric ozone layer, must have sustained an ambient prebiotic physicochemical medium intensified by the co-existence of shortwave UV photons and very low energy electrons (vLEEs). Consequently, only intrinsically stable molecules against these two co-existing molecular destructors must have proliferated and thereby chemically evolved into the advanced molecules of life. Based on this view, we examined the stability inherent in nucleobases and their complementary pairs as resistance to the molecular damaging effects of shortwave UV photons and vLEEs. This leads to the conclusion that nucleobases could only proliferated as their complementary pairs under the unfavorable prebiotic conditions on early Earth. The complementary base pairing not only enhances but consolidates the intrinsic stability of nucleobases against short-range UV photons, vLEEs, and possibly many as-yet-unknown deleterious agents co-existed in the prebiotic conditions of the early Earth. In short, complementary base pairing is a manifestation of chemical evolution in the unfavorable prebiotic medium created by the absence of the stratospheric ozone layer.

Intramolecular Proton Transfer in the Radical Anion of Cytidine Monophosphate Sheds Light on the Sensitivities of Dry vs Wet DNA to Electron Attachment-Induced Damage

Single-strand breaks (SSBs) induced via electron attachment were previously observed in dry DNA under ultrahigh vacuum (UHV), while hydrated electrons were found not able to induce this DNA damage in an aqueous solution. To explain these findings, crossed electron-molecular beam (CEMB) and anion photoelectron spectroscopy (aPES) experiments coupled to density functional theory (DFT) modeling were used to demonstrate the fundamental importance of proton transfer (PT) in radical anions formed via electron attachment. Three molecular systems were investigated: 5'-monophosphate of 2'-deoxycytidine (dCMPH), where PT in the electron adduct is feasible, and two ethylated derivatives, 5'-diethylphosphate and 3',5'-tetraethyldiphosphate of 2'-deoxycytidine, where PT is blocked due to substitution of labile protons with the ethyl residues. CEMB and aPES experiments confirmed the cleavage of the C3'/C5'-O bond as the main dissociation channel related to electron attachment in the ethylated derivatives. In the case of dCMPH, however, electron attachment (in the aPES experiments) yielded its parent (intact) radical anion, dCMPH^-, suggesting that its dissociation was inhibited. The aPES-measured vertical detachment energy of the dCMPH^- was found to be 3.27 eV, which agreed with its B3LYP/6-31++G(d,p)-calculated value and implied that electron-induced proton transfer (EIPT) had occurred during electron attachment to the dCMPH model nucleotide. In other words, EIPT, subduing dissociation, appeared to be somewhat protective against SSB. While EIPT is facilitated in solution compared to the dry environment, the above findings are consistent with the stability of DNA against hydrated electron-induced SSB in solution versus free electron-induced SSB formation in dry DNA.

Low-Energy Electron Damage to Plasmid DNA in Thin Films: Dependence on Substrates, Surface Density, Charging, Environment, and Uniformity

The interaction of low-energy electrons (LEEs) with DNA plays a significant role in the mechanisms leading to biological damage induced by ionizing radiation, particularly in radiotherapy, and its sensitization by chemotherapeutic drugs and nanoparticles. Plasmids constitute the form of DNA found in mitochondria and appear as a suitable model of genomic DNA. In a search for the best LEE targets, damage was induced to plasmids, in thin films in vacuum, by 6, 10, and 100 eV electrons under single collision conditions. The yields of single- and double-strand breaks, other cluster damage, isolated base lesions, and crosslinks were measured by electrophoresis and enzyme treatment. The films were deposited on oriented graphite or polycrystalline tantalum, with or without DNA autoassembly via diaminopropane (Dap) intercalation. Yields were correlated with the influence of vacuum, film uniformity, surface density, substrates, and the DNA environment. Aided by surface potential measurements and scanning electron microscopy and atomic force microscopy images, the lyophilized Dap-DNA films were found to be the most practical high-quality targets. These studies pave the way to the fabrication of LEE target-films composed of plasmids intercalated with biomolecules that could mimic the cellular environment; for example, as a first step, by replacing Dap with an amino acid.

Origin of resonant character in the electron impact two-body neutral-fragmentation of methane

The observation of peaks in the threshold region of two-body neutral fragmentation of methane molecule, i.e.,  CH 4   ->  CH 3 + H, by low energy electron (LEE) impact has been an enigma. The prevailing explanation that this resonant behavior is due to excitation energy transfer is unsatisfactory since this process is not expected to show peaks in the cross-sections unless there is the involvement of electron-molecule resonances. Our first-principles calculations now reveal that the observed peaks could be explained as due to the formation of negative ion resonances, which dominantly dissociate into two neutral fragments and a free-electron. This case of methane is a pointer to the possibility that such reactions contribute significantly to neutral radical production from molecules by LEE impact in comparison to dissociative electron attachment, and in general could play a significant role in electron-based chemical control.