Hongfang Yang

Multi-zinc-expanded graphene patches: Tetraradical versus diradical character

Three classes of multi‐Zn‐expanded graphene patches in different shapes are computationally designed through introducing a Zn chain into the corresponding middle benzenoid chain. Both density functional theory and complete active space self‐consistent field calculations predict that molecules of nnn‐quasi‐linear and nnn‐slightly bent series have the open‐shell broken‐symmetry (BS) singlet diradical ground states, whereas those of n(n+1)n species possess quintet tetraradical as their ground state and become open‐shell BS singlet tetraradicals when they are in a higher energy state. These results offer the first theoretical attempt to introduce multi‐Zn into the small graphene patches to form Zn‐expanded graphene patches, leading them to polyradical structures. This work provides an executable strategy to yield molecules which have stable polyradicaloid character and enhanced electronic properties of multi‐Zn‐expanded graphene patches.

Reduced graphene oxide-stabilized copper nanocrystals with enhanced catalytic activity and SERS properties

Well-defined Cu/reduced graphene oxide (rGO) hybrid materials are successfully synthesized by controlling the amount of ascorbic acid and maintaining an appropriate pH value. We found that graphene oxide (GO) served not only as the precursor for graphene, but also as an effective surfactant to hamper the aggregation of copper nanoparticles, resulting in a small size of the copper nanoparticles. Furthermore, the as-prepared copper composites can serve as an effective catalyst for 4-nitrophenol in aqueous conditions and exhibit surface enhanced Raman scattering in the detection of crystal violet (CV). Notably, the obtained copper nanoparticle hybrids with rGO have extremely high air stability after exposure to air. Density functional theory calculations firstly reveal that rGO can effectively prevent Cu nanoparticles from spontaneous oxidation due to its slightly lower ionization potential than that of Cu nanoparticles. We expect the as-prepared rGO-stabilized copper nanocrystals with small size to meet the increasing demands of industrial applications at reduced costs.

Computational design of the magnetism-tunable oligobenzylic carbanion complexes

Unrestricted density functional theory calculations in combination with the broken symmetry approach have been employed to study several benzylic carbanions. As a free anion, 2-(3,5-dinitrophenyl)-1,3-dithiane carbanion has near-degenerate singlet and triplet states and appears to be a promising magnetism-tunable species. In this work, we computationally design some of its derivatives in two ways: expanding the π-conjugated structures and introducing Lewis acids (Li+, Na+, and K+, and polar molecules are considered here) with different acidities. Calculations reveal that ring expansion does not change its open-shell broken symmetry singlet diradical ground state and antiferromagnetic character, but decreases its magnetism, whereas introduction of Lewis acids can lead to different ground states (triplet vs. singlet) and different magnetism, depending on the binding sites of the Lewis acid. That is, they show closed-shell singlet ground states without magnetism when a cation locates near the anionic center of the 1,3-dithiane ring, but convert to triplet as their ground states with ferromagnetic character when the cation moves to one nitro group of the 3,5-dinitrophenyl-based π-conjugation-expanded fragment. These findings regarding modulation through ring expansion and Lewis acid-binding ways make the magnetisms of 2-(3,5-dinitrophenyl)-1,3-dithiane-based carbanions tunable, and thus provide prospects of a new extension of the results from the previous study for designing magnetism-tunable building blocks for novel electromagnetic materials.

310-Helical Peptide Acting as a Dual Relay for Charge-Hopping Transfer in Proteins

We present a density functional calculational study to clarify that a 3(10)-helix peptide can serve as a novel dual-relay element to mediate long-range charge migrations via its C- and N-termini in proteins. The ionization potential of the 3(10)-helix C-terminus correlates inversely with the helix length, HOMO energy, and dipole moment. In particular, it decreases considerably with the increase in the number of peptide units, even to a smaller value than that of the easily oxidized amino acid residue, which implies the possibility of releasing an electron and forming a hole at the 3(10)-helical C-terminus. On the other hand, the electron affinity of the 3(10)-helical N-terminus correlates positively with the helix length and dipole moment but inversely with the LUMO energy. Clearly, the increasing positive electron-binding energy with the increase in the number of peptide units implies that the 3(10)-helical N-terminus can capture an excess electron and play an electron-relaying role. The relaying ability of the 3(10)-helical C-terminus and N-terminus not only depends on the helix length but also varies subject to the capping effect, the collaboration and competition of proximal groups, and solvent environments. In contrast to the known hole relays such as the side chains of Tyr and Trp and electron relays such as the side chains of protonated Lys and Arg, either the hole relay (the 3(10)-helix C-terminus) or the electron relay (the 3(10)-helix N-terminus) is property-tunable and could apply to different proteins in assisting or mediating long-range charge migrations.

Rational Design for Building Blocks of DNA-Based Conductive Nanowires through Multi-Copper Incorporation into Mismatched Base Pairs

Metal-modified DNA base pairs, which possess potential electrical conductivity and can serve as conductive nanomaterials, have recently attracted much attention. Inspired by our recent finding that multicopper incorporation into natural DNA base pairs could improve the electronic properties of base pairs, herein, we designed two novel multi-copper-mediated mismatched base pairs (G(3Cu)T and A(2Cu)C), and examined their structural and electronic properties by means of density functional theory calculations. The results reveal that these multi-Cu-mediated mismatched base pairs still have planar geometries that are thermodynamically favorable to stability, and their binding energies are close to those of multi-Cu-mediated normal base pairs (G(3Cu)C and A(2Cu)T). Their HOMO-LUMO gaps and ionization potentials decrease significantly compared to the corresponding natural base pairs. As evidenced by the charge transfer excitation transitions, transverse electronic communication of G(3Cu)T and A(2Cu)C is remarkably enhanced, suggesting that they facilitate electron migration along the DNA wires upon incorporation. Further examinations also clarify the possibility to build promising DNA helices using the G(3Cu)T and/or A(2Cu) C base pairs. The calculated electronic properties of the three-layer-stacked multi-Cu-mediated mismatched base pairs illustrate that the Cu(m)-DNA have better conductivity. This work provides perspectives for the development and application of DNA nanowires.

Magnetism‐Tunable Oligoacene Dioxide Diradicals: Promising Magnetic Oligoacene‐Like Molecules

Graphene oxide has attracted intense research interest recently because the graphene oxide synthesis route, as a promising alternative for cost-effective mass production of graphene, has been explored. To further study the oxidation process and possible mechanism and to explore applicability of the oxidized products, we have performed a computational study on three series of oligoacene dioxides, focusing on their structures and electronic properties. Taking 1,5-dioxidized naphthalene as a starting point, three series of oligoacene dioxides are considered as follows: 1) middle insertion by 1-2 benzene rings; 2) single-side expansion using 1-2 benzene rings; 3) double-side expansion using two benzene rings. On the basis of density functional theory and complete active space self-consistent field (CASSCF) calculations, we reveal that oligoacene dioxides in the middle insertion series have a triplet ground state, whereas those in the single-side expansion series and the double-side expansion series have open-shell broken-symmetry singlet diradical ground states except for their common origin naphthalene-1,5-dioxide whose ground state is triplet and which is also viewed as the origin of the middle insertion series. Magnetic coupling interactions of these oligoacene dioxides are also determined. This work should help people toward an atomistic understanding of the electronic structures and properties of possible intermediates or products and even the oxidation mechanism of graphene sheets, and provides a reasonable strategy of designing novel graphene-oxide-based magnetic materials.

Computational insights into the charge relaying properties of β-turn peptides in protein charge transfers.

Density functional theory calculations suggest that β-turn peptide segments can act as a novel dual-relay elements to facilitate long-range charge hopping transport in proteins, with the N terminus relaying electron hopping transfer and the C terminus relaying hole hopping migration. The electron- or hole-binding ability of such a β-turn is subject to the conformations of oligopeptides and lengths of its linking strands. On the one hand, strand extension at the C-terminal end of a β-turn considerably enhances the electron-binding of the β-turn N terminus, due to its unique electropositivity in the macro-dipole, but does not enhance hole-forming of the β-turn C terminus because of competition from other sites within the β-strand. On the other hand, strand extension at the N terminal end of the β-turn greatly enhances hole-binding of the β-turn C terminus, due to its distinct electronegativity in the macro-dipole, but does not considerably enhance electron-binding ability of the N terminus because of the shared responsibility of other sites in the β-strand. Thus, in the β-hairpin structures, electron- or hole-binding abilities of both termini of the β-turn motif degenerate compared with those of the two hook structures, due to the decreased macro-dipole polarity caused by the extending the two terminal strands. In general, the high polarity of a macro-dipole always plays a principal role in determining charge-relay properties through modifying the components and energies of the highest occupied and lowest unoccupied molecular orbitals of the β-turn motif, whereas local dipoles with low polarity only play a cooperative assisting role. Further exploration is needed to identify other factors that influence relay properties in these protein motifs.

Hydrated Electron Transfer to Nucleobases in Aqueous Solutions Revealed by Ab Initio Molecular Dynamics Simulations.

We present an ab initio molecular dynamics (AIMD) simulation study into the transfer dynamics of an excess electron from its cavity-shaped hydrated electron state to a hydrated nucleobase (NB)-bound state. In contrast to the traditional view that electron localization at NBs (G/A/C/T), which is the first step for electron-induced DNA damage, is related only to dry or prehydrated electrons, and a fully hydrated electron no longer transfers to NBs, our AIMD simulations indicate that a fully hydrated electron can still transfer to NBs. We monitored the transfer dynamics of fully hydrated electrons towards hydrated NBs in aqueous solutions by using AIMD simulations and found that due to solution-structure fluctuation and attraction of NBs, a fully hydrated electron can transfer to a NB gradually over time. Concurrently, the hydrated electron cavity gradually reorganizes, distorts, and even breaks. The transfer could be completed in about 120-200 fs in four aqueous NB solutions, depending on the electron-binding ability of hydrated NBs and the structural fluctuation of the solution. The transferring electron resides in the π*-type lowest unoccupied molecular orbital of the NB, which leads to a hydrated NB anion. Clearly, the observed transfer of hydrated electrons can be attributed to the strong electron-binding ability of hydrated NBs over the hydrated electron cavity, which is the driving force, and the transfer dynamics is structure-fluctuation controlled. This work provides new insights into the evolution dynamics of hydrated electrons and provides some helpful information for understanding the DNA-damage mechanism in solution.

Radical–Radical Interactions among Oxidized Guanine Bases Including Guanine Radical Cation and Dehydrogenated Guanine Radicals

We present here a theoretical investigation of the structural and electronic properties of di-ionized GG base pairs (G(•+)G(•+),G(-H1)(•)G(•+), and G(-H1)(•)G(-H1)(•)) consisting of the guanine cation radical (G(•+)) and/or dehydrogenated guanine radical (G(-H1)(•)) using density functional theory calculations. Different coupling modes (Watson-Crick/WC, Hoogsteen/Hoog, and minor groove/min hydrogen bonding, and π-π stacking modes) are considered. We infer that a series of G(•+)G(•+) complexes can be formed by the high-energy radiation. On the basis of density functional theory and complete active space self-consistent (CASSCF) calculations, we reveal that in the H-bonded and N-N cross-linked modes, (G(•+)G(•+))WC, (G(-H1)(•)G(-H1)(•))WC, (G(-H1)(•)G(-H1)(•))minI, and (G(-H1)(•)G(-H1)(•))minIII have the triplet ground states; (G(•+)G(•+))HoogI, (G(-H1)(•)G(•+))WC, (G(-H1)(•)G(•+))HoogI, (G(-H1)(•)G(•+))minI, (G(-H1)(•)G(•+))minII, and (G(-H1)(•)G(-H1)(•))minII possess open-shell broken-symmetry diradical-characterized singlet ground states; and (G(•+)G(•+))HoogII, (G(•+)G(•+))minI, (G(•+)G(•+))minII, (G(•+)G(•+))minIII, (G(•+)G(•+))HoHo, (G(-H1)(•)G(•+))minIII, (G(-H1)(•)G(•+))HoHo, and (G(-H1)(•)G(-H1)(•))HoHo are the closed-shell systems. For these H-bonded diradical complexes, the magnetic interactions are weak, especially in the diradical G(•+)G(•+) series and G(-H1)(•)G(-H1)(•) series. The magnetic coupling interactions of the diradical systems are controlled by intermolecular interactions (H-bond, electrostatic repulsion, and radical coupling). The radical-radical interaction in the π-π stacked di-ionized GG base pairs ((G(•+)G(•+))ππ, (G(-H1)(•)G(•+))ππ, and (G(-H1)(•)G(-H1)(•))ππ) are also considered, and the magnetic coupling interactions in these π-π stacked base pairs are large. This is the first theoretical prediction that some di-ionized GG base pairs possess diradical characters with variable degrees of ferromagnetic and antiferromagnetic characteristics, depending on the dehydrogenation characters of the bases and their interaction modes. Hopefully, this work provides some helpful information for the understanding of different structures and properties of the di-ionized GG base pairs.

Interactions of amino acids with oxidized guanine in the gas phase associated with the protection of damaged DNA.

Density functional theory calculations were employed to study the stabilization process of the guanine radical cation through amino acid interactions as well as to understand the protection mechanisms. On the basis of our calculations, several protection mechanisms are proposed in this work subject to the type of the amino acid. Our results indicate that a series of three-electron bonds can be formed between the amino acids and the guanine radical cation which may serve as relay stations supporting hole transport. In the three-electron-bonded, π-π-stacked, and H-bonded modes, amino acids can protect guanine from oxidation or radiation damage by sharing the hole, while amino acids with reducing properties can repair the guanine radical cation through proton-coupled electron transfer or electron transfer. Another important finding is that positively charged amino acids (ArgH(+), LysH(+), and HisH(+)) can inhibit ionization of guanine through raising its ionization potential. In this situation, a negative dissociation energy for hydrogen bonds in the hole-trapped and positively charged amino acid-Guanine dimer is observed, which explains the low hole-trapping efficiency. We hope that this work provides valuable information on how to protect DNA from oxidation- or radiation-induced damages in biological systems.