Yuxiang Bu

Shandong University, Chi-nan-shih, Shandong Sheng, China

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Publications (191)522.09 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: The structural, electronic and optical properties of hexagonal ferrites MFe12O19 (M = Sr, Ba, Pb, Sr0.5Ba0.5, Sr0.5Pb0.5 and Ba0.5Pb0.5) are calculated by plane-wave pseudopotential density functional theory with general gradient approximation (GGA) and GGA+U. The calculated lattice constants and band gaps are in good agreement with the available experimental and theoretical values. Lattice constants change corresponding to the cation radii at M-sites. The electronic structure shows that all the six hexaferrites are narrow gap semiconductors and Sr2+ and Ba2+ at M-sites have little contribution to the DOS at the vicinity of Fermi level due to the ionic bond interaction nature between M2+ and O2−. It should be noted that for Pb2+, comparing with the narrow localized s-states of Sr2+ and Ba2+, there is a significant broadening of its s-states from −7 eV to the Fermi level, indicating its minority donation to the valence band near Ef. The six MFOs (FO refers Fe12O19) could be classified into two categories: Pb-containing hexaferrites (PFO, SPFO and BPFO) and others (SFO, BFO and SBFO). The former has larger static dielectric constants. This study will serve as the base for the investigation of the correlation among factors such as site preferences, properties and substitution strategies for MFOs.
    Computational Materials Science 07/2015; 105. DOI:10.1016/j.commatsci.2015.04.021 · 1.88 Impact Factor
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    ABSTRACT: 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. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    ChemPhysChem 05/2015; DOI:10.1002/cphc.201500040 · 3.36 Impact Factor
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    ABSTRACT: We unravel intriguing dynamical diradical behavior governed by structural fluctuation in pentacene using ab initio molecular dynamics simulation. In contrast to static equilibrium configuration of pentacene with a closed-shell ground state without diradical character, due to structural fluctuation, some of its dynamical snapshot configurations exhibit an open-shell broken-symmetry singlet ground state with diradical character, and such diradical character presents irregular pulsing behavior in time evolution. Not all structural changes can lead to diradical character, only those involving the shortening of cross-linking C-C bonds and variations of the C-C bonds in polyacetylene chains are the main contributors. This scenario about diradicalization is distinctly different from that in long acenes. The essence is that structural distortion cooperatively raises the HOMO and lowers the LUMO, efficiently reducing the HOMO-LUMO and singlet-triplet energy gaps, which facilitate the formation of a broken-symmetry open-shell singlet state. The irregular pulsing behavior originates from the mixing of normal vibrations in pentacene. This fascinating behavior suggests the potential application of pentacene as a suitable building block in the design of new electronic devices due to its magnetism-controllability through energy induction. This work provides new insight into inherent electronic property fluctuation in acenes.
    Physical Chemistry Chemical Physics 05/2015; 17(21). DOI:10.1039/c5cp00902b · 4.20 Impact Factor
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    ABSTRACT: In this paper, a density functional theory method benchmark study has been conducted on the adsorption energy of hydrogen. The effects of different density functionals, dispersion, and the size of basis sets have been explored on the prediction of adsorption energy. The results show that the adsorp-tion energies predicted by different density functionals varies considerably; the dispersion term cannot be ignored; the basis set and model have minor contributions for the final result; larger models are more independent on the basis set, and large basis set can make up the deficiency of smaller model. We expect that the method selection strategy proposed in this study could provide valuable clues for relevant studies.
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    ABSTRACT: Ternary spherical Ag–Cu2O/reduced graphene oxide (rGO) nanohybrids with excellent hierarchical structures are developed through a simple one-pot, two-stage reduction synthetic route at room temperature without any surfactant. In the resultant complex heterostructures, both Ag and rGO are in direct contact with Cu2O, and Ag nanocrystals are mainly deposited on the surface of Cu2O spheres. The resultant ternary spherical Ag–Cu2O/rGO composite exhibits excellent photocatalytic activity in photocatalytic degradation of methyl orange (MO) under visible light irradiation, which is much higher than that of either the single component (Cu2O) or two component systems (spherical Cu2O/rGO and Ag–Cu2O). In particular, the resultant ternary composites possess excellent stability and extend the light absorption range. The PL spectrum results have demonstrated that not only Ag but also rGO could capture the photogenerated electrons from Cu2O, thus leading to effective separation of electrons and holes. In particular, it is found that the direct junction and interaction between Ag and Cu2O in the ternary composites are more beneficial for charge transportation than the direct contact between Ag and rGO (labeled as sample Ag-rGO-Cu2O), and thereby the resultant Ag–Cu2O/rGO composites with such complex heterostructures exhibit a better photoactivity than the sample Ag-rGO-Cu2O. This work provides an insight into designing and synthesizing new Cu2O-based hybrid materials for effectively improving the photocatalytic performance.
    03/2015; 3(11). DOI:10.1039/C4TA06772J
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    ABSTRACT: We present a theoretical investigation of the structural and electronic properties of double-electron oxidized adenine–thymine base pair as well as its deprotonated Watson–Crick derivatives. Double-electron oxidation can destabilize the AT unit, leading to a barrier-hindered metastable A+T+ state with a dissociation channel featuring negative dissociation energy. This unusual energetic phenomenon originates from the competition of electrostatic repulsion and attractively hydrogen-bonding interaction co-existing between A+ and T+. The associated double-proton-transfer process is also explored, suggesting a possible two-step mechanism. Magnetic coupling interactions of various diradical structures are controlled by both intra- and inter-molecular interactions.
    Chemical Physics Letters 01/2015; 619. DOI:10.1016/j.cplett.2014.11.027 · 1.99 Impact Factor
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    ABSTRACT: 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.
    ChemPhysChem 11/2014; 16(2). DOI:10.1002/cphc.201402657 · 3.36 Impact Factor
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    ABSTRACT: Ab initio molecular dynamics simulations reveal that an excess electron (EE) can be more efficiently localized as a cavity-shaped state in aqueous glucose solution (AGS) than in water. Compared with that (similar to 1.5 ps) in water, the localization time is shortened by similar to 0.7-1.2 ps in three AGSs (0.56, 1.12, and 2.87 M). Although the radii of gyration of the solvated EEs are all close to 2.6 angstrom in the four solutions, the solvated EE cavities in the AGSs become more compact and can localize similar to 80% of an EE, which is considerably larger than that (similar to 40-60% and occasionally similar to 80%) in water. These observations are attributed to a modification of the hydrogen-bonded network by the introduction of glucose molecules into water. The water acts as a promoter and stabilizer, by forming voids around glucose molecules and, in this fashion, favoring the localization of an EE with high efficiency. This study provides important information about EEs in physiological AGSs and suggests a new strategy to efficiently localize an EE in a stable cavity for further exploration of biological function.
    Journal of Chemical Theory and Computation 10/2014; 10(10):4189-4197. DOI:10.1021/ct500238k · 5.31 Impact Factor
  • Xiaohua Chen, Yuxiang Bu
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    ABSTRACT: Amino fragments (-NH2) are well-known to exist widely in biological systems and their protonated forms are inclined to trap electrons and form Rydberg radicals (-NH3 center dot) in the electron-excess systems. Taking CH3-NH3+ as a mimicking group of the protonated alkylamine side-chain of lysine, ab initio calculations indicate that the proton/electron cooperatively transfer from CH3NH3 to CH3NH2 via a single-proton-coupled Rydberg-state electron transfer (ET) mechanism with an Rydberg-orbital channel for ET outside the -NHn hydrogens and a N-H+ -> N proton migrating pathway. Besides, in big amine clusters, CH3NH3 center dot(NH3)(n)center dot NH2CH3 (n = 1-3), the proton/electron transfer along an amine wire is stepwise and every step takes place via the similar single-proton-coupled Rydberg-state ET mechanism with low energy barrier (<4.0 kcal/mol). When a water chain, (H2O)(n) (n = 1-3), lies between CH3NH3 and NH2CH3 as a bridge, the energy barriers (8.5-15.0 kcal/mol) of proton/electron cooperatively transfer between CH3NH3 and NH2CH3 are raised significantly as compared to these of the pure amine wires (<4.0 kcal/mol). We attribute this fact to the combined effects of the proton binding energies and electron affinities of CH3NH2 and H2O. Interestingly, different from the amine-wire case, movement of the solvated electron along the water-wire can promote two or three protons synchronously moving at the same direction. This process can be described in terms of a multi-proton-coupled solvated-ET mechanism.
    The Journal of Physical Chemistry C 08/2014; 118(33):18861-18867. DOI:10.1021/jp504041n · 4.84 Impact Factor
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    ABSTRACT: Due to the fact that natural DNA may lack sufficient conductance for direct application in molecular electronics, a novel design of outer-expanded purine analogues was proposed by incorporating an aromatic ring at the N7-C8 site into natural G and A bases from the outside. The effect of the outer-expansion modification on electronic properties of DNA was investigated by density functional theory and molecular dynamics. The analyses revealed that these purine analogues not only preserve the same sizes of natural purine bases, thus avoiding distortions of DNA skeleton induced by the normal ring-inner-expansion modification, but also keep the selectivity of pairing with their natural counterpart C and T bases. More importantly, their electronic properties are enhanced, indicated by the narrowed HOMO–LUMO gaps, the lowered ionization potentials and the improved ultraviolet absorption spectra. This work may provide helpful information for designing of artificial bases as promising building blocks of biomolecular nanowires. © 2014 Wiley Periodicals, Inc.
    International Journal of Quantum Chemistry 07/2014; 114(14). DOI:10.1002/qua.24690 · 1.17 Impact Factor
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    ABSTRACT: We present an ab initio molecular dynamics simulation study of a CH3CN-(H2O)40 cluster with an excess electron (EE) injected vertically in this work. Instead of surface bound or internally solvated electron, a hydrated CH3CN- is firstly formed as the CN transient after geometrical relaxation. The driving forces for the formation of CH3CN- are bending vibration of <CCN angle which initiates transfer of an extra charge to the CH3CN LUMO and hydration effect of the immediate water molecules which plays a stabilizing role. Solvent thermal fluctuation can lead to different resonances (the quasi-C2-resonance versus quasi-N-resonance) from the CN transient and further cause the hydrated CH3CN- system to evolve via two distinctly different pathways featuring spontaneous proton transfer to the central C and N sites, producing two different protonation products, respectively. The solvent thermal fluctuation induced formation of hydrogen bonding with the corresponding sites (C2 versus N) are responsible for the quasi-resonances and interconversion between three resonant structures and further proton transfers featuring spontaneous transfer of a proton to C2 or to N from its a interacting water molecule. The duration of CH3CN- for either of the two proton transfer processes is less than 200 fs. On the basis of experimental ESR results in which only the CH3CHN radical was found and present theoretical calculations, it is suggested that the trans-CH3CNH radical can be further converted to the CH3CHN radical via a water-mediated hydrogen atom transfer path.
    The Journal of Physical Chemistry A 05/2014; 118(39). DOI:10.1021/jp5030284 · 2.78 Impact Factor
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    ABSTRACT: 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.
    Theoretical Chemistry Accounts 04/2014; 133(4). DOI:10.1007/s00214-014-1460-2 · 2.14 Impact Factor
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    ABSTRACT: The proton/electron transfer reactions between cysteine residue (Cys) and tyrosinyl radical (Tyr(•)) are an important step for many enzyme-catalyzed processes. Based on the statistical analysis of protein data bank, we designed three representative models to explore the possible proton/electron transfer mechanisms from Cys to Tyr(•) in proteins. Our ab initio calculations on simplified models and quantum mechanical/molecular mechanical (QM/MM) calculations on real protein environment reveal that the direct electron transfer between Cys and Tyr(•) is difficult to occur, but an inserted water molecule can greatly promote the proton/electron transfer reactions by a double-proton-coupled electron transfer (dPCET) mechanism. The inserted H2O plays two assistant roles in these reactions. The first one is to bridge the side chains of Tyr(•) and Cys via two hydrogen bonds which acts as the proton pathway, and the other one is to enhance the electron overlap between the lone-pair orbital of sulphur atom and the π-orbital of phenol moiety, and to function as electron transfer pathway. This water-mediated dPCET mechanism may offer great help for us to understand the detailed electron transfer processes between Tyr and Cys residues in proteins, such as the electron transfer from Cys439 to Tyr730(•) in the class I ribonucleotide reductase.
    Journal of the American Chemical Society 03/2014; 136(12). DOI:10.1021/ja406340z · 11.44 Impact Factor
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    ABSTRACT: In this article we present density functional theory (DFT) calculations on the iron(IV)-oxo catalyzed methane C-H activation reactions for complexes in which the FeIV=O core is surrounded by five negatively charged ligands. We found that it follows a hybrid pathway that mixes features of the classical σ and π pathways in quintet surfaces. These calculations show that, the Fe-O-H arrangement in this hybrid pathway is bent, in sharp contrast to the collinear character as observed for the classical quintet σ pathways before. The calculations have also shown that it is the equatorial ligands that play key roles in tuning the reactivity of FeIV=O complexes. The strong π-donating equatorial ligands employed in the current study cause a weak π(FeO) bond and thereby shift the electronic accepting orbitals (EAO) from the vertically orientated O pz orbital to the horizontally orientated O px. In addition, all the equatorial ligands are small in size and would therefore be expected have small steric effects upon substrate horizontal approaching. Therefore, for the small and strong π-donating equatorial ligands, the collinear Fe-O-H arrangement is not the best choice for the quintet reactivity. This study adds new element to iron(IV)-oxo catalyzed C-H bond activation reactions.
    The Journal of Physical Chemistry B 01/2014; 118(6). DOI:10.1021/jp410727r · 3.38 Impact Factor
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    ABSTRACT: In view of the important implications of excess electrons (EEs) interacting with CO2-H2O clusters in many fields, using ab initio molecular dynamics simulation technique, we reveal the structures and dynamics of an EE associated with its localization and subsequent time evolution in heterogeneous CO2-H2O mixed media. Our results indicate that although hydration can increase the electron-binding ability of a CO2 molecule, it only plays an assisting role. Instead, it is the bending vibrations that play the major role in localizing the EE. Due to enhanced attraction of CO2, an EE can stably reside in the empty, low-lying π* orbital of a CO2 molecule via a localization process arising from its initial binding state. The localization is completed within a few tens of femtoseconds. After EE trapping, the ∠OCO angle of the core CO2- oscillates in the range of 127°̃142°, with an oscillation period of about 48 fs. The corresponding vertical detachment energy of the EE is about 4.0 eV, which indicates extreme stability of such a CO2-bound solvated EE in [CO2(H2O)n]- systems. Interestingly, hydration occurs not only on the O atoms of the core CO2- through formation of O⋯H-O H-bond(s), but also on the C atom, through formation of a C⋯H-O H-bond. In the latter binding mode, the EE cloud exhibits considerable penetration to the solvent water molecules, and its IR characteristic peak is relatively red-shifted compared with the former. Hydration on the C site can increase the EE distribution at the C atom and thus reduce the C⋯H distance in the C⋯H-O H-bonds, and vice versa. The number of water molecules associated with the CO2- anion in the first hydration shell is about 4̃7. No dimer-core (C2O4-) and core-switching were observed in the double CO2 aqueous media. This work provides molecular dynamics insights into the localization and time evolution dynamics of an EE in heterogeneous CO2-H2O media.
    The Journal of Chemical Physics 12/2013; 140(4). DOI:10.1063/1.4863343 · 3.12 Impact Factor
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    ABSTRACT: We report an ab initio molecular dynamics simulation study of the solvation and dynamics of an excess electron in liquid acetonitrile (ACN). Four families of states are observed: a diffusely solvated state and three ACN core-localized states with monomer core, quasi-dimer (π*-Rydberg mode) core, and dual-core/dimer core (a coupled dual-core). These core localized states cannot be simply described as the corresponding anions because only a part of the excess electron resides in the core molecule(s). The quasi-dimer core state actually is a mixture that features cooperative excess electron capture by the π* and Rydberg orbitals of two ACNs. Well-defined dimer anion and solvated electron cavity were not observed in the 5–10 ps simulations, which may be attributed to slow dynamics of the formation of the dimer anion and difficulty of the formation of a cavity in such a fluxional medium. All of the above observed states have near-IR absorptions and thus can be regarded as the solvated electron states but with different structures, which can interpret the experimentally observed IR band. These states undergo continuous conversions via a combination of long-lasting breathing oscillation and core switching, characterized by highly cooperative oscillations of the electron cloud volume and vertical detachment energy. The quasi-dimer core and diffusely solvated states dominate the time evolution, with the monomer core and dual-core/dimer core states occurring occasionally during the breathing and core switching processes, respectively. All these oscillations and core switchings are governed by a combination of the electron-impacted bending vibration of the core ACN molecule(s) and thermal fluctuations.
    Journal of Chemical Theory and Computation 10/2013; 9(11):4727–4734. DOI:10.1021/ct4002174 · 5.31 Impact Factor
  • Mei Wang, Jing Zhao, Yuxiang Bu
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    ABSTRACT: We present a computational study of the double-electron oxidized guanine-cytosine base pair as well as its deprotonated derivatives, focusing on their structural and electronic properties. Some novel electromagnetic characteristics are found. A hydrazine-like (N-N) cross-linked structure between the G and C radical moieties is the lowest-energy one for the [GC](2+) complexes. Double-electron oxidation can considerably destabilize the GC unit and leads to a barrier-hindered dissociation channel with negative dissociation energy. This channel is governed by a balance between electrostatic repulsion and attractive hydrogen-bonding interaction co-existing between G˙(+) and C˙(+). The proton/electron transfer reactions in the double-electron oxidized Watson-Crick base pair occur through a proton transfer induced charge migration mechanism. For the deprotonated [GC](2+) derivative, the [G(-H(+))C](+) series prefers to accompany by transfer of an electron from the G to C moiety when the G(+) is deprotonated, and its highest-doubly occupied molecular orbital mainly localizes over the C moiety with a π-bonding character. For the diradical G˙(+)C(-H)˙ series in which the C moiety is deprotonated, the two unpaired electrons reside one on each moiety in the π system. The diradical base pairs possess open-shell broken symmetry singlet states, and their magnetic coupling interactions are controlled by both intra- and inter-molecular interactions. The double-electron oxidized Watson-Crick base pair shows strong antiferromagnetic coupling, whereas the magnetic interactions of other diradical derivatives are relatively weak. This study highlights the crucial role of H-bonding in determining the magnetic interactions.
    Physical Chemistry Chemical Physics 09/2013; 15(42). DOI:10.1039/c3cp52745j · 4.20 Impact Factor
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    ABSTRACT: We present here a theoretical investigation of the structural and electronic properties of the 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 - 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•+)minII, (G(-H1)•G•+)minIII, (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, 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•+)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.
    The Journal of Physical Chemistry B 08/2013; 117(37). DOI:10.1021/jp4042149 · 3.38 Impact Factor
  • Lianwen Zhou, Yuxiang Bu
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    ABSTRACT: An excess electron in condensed phase models of hydrated protonated histidine residue (HisH+) in proteins has been investigated using ab initio calculations and molecular dynamics simulations, which focuses on electron-binding mode and evolution mechanism of the captured electron in the HisH+ side chain hydrated clusters. Results indicate that distribution of an excess electron is highly associated with the number of water molecules and the geometric configurations of the hydrated clusters. An electron can stably localize in three cases depending on the size of the hydrated clusters. First, an excess electron always occupies the π* orbital of the imidazole ring not only after vertical binding but also in relaxation process. Second, an excess electron firstly vertically localizes in a Rydberg-like orbital, and then relaxes to reside in the π* LUMO localizing in the imidazole ring. Third, an electron always occupies the Rydberg-like orbital both after vertical binding and after relaxation. Furthermore, molecular dynamics simulations reveal that the captured excess electron prefers to localize around HisH+ no mater how it distributes at the initially bound states (localized versus delocalized), and the evolution time for the solvated electron from the initially bound state to the finally localized state at HisH+ is about 220 fs, as demonstrated from an excess electron-bound HisH+(H2O)40 model cluster.
    Computational and Theoretical Chemistry 07/2013; 1016:54–61. DOI:10.1016/j.comptc.2013.04.014 · 1.37 Impact Factor
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    ABSTRACT: We present a density functional theory calculational study for clarifying that a 310-helix peptide can serve as a novel dual relay element to mediate long-range charge migrations via its C- and N-terminus in proteins. The ionization potential of the 310-helix C-terminus correlates inversely with the helix length, HOMO energy, and dipole moment. In particular, it decreases considerably with the increase 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 310-helical C-terminus. On the other hand, the electron affinity of the 310-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 of peptide units implies that the 310-helical N-terminus can capture an excess electron and play an electron-relaying role. The relaying ability of the 310-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, etc. In contrast with the known hole relays such as the side-chains of Tyr, Trp and electron relays such as the side-chains of protonated Lys and Arg, etc., either the hole relay (the 310-helix C-terminus) or the electron relay (the 310-helix N-terminus) is property-tunable and could apply to different proteins for assisting or mediating charge long-rang migrations.
    The Journal of Physical Chemistry B 05/2013; 117(21). DOI:10.1021/jp4012526 · 3.38 Impact Factor

Publication Stats

1k Citations
522.09 Total Impact Points

Institutions

  • 1996–2015
    • Shandong University
      • • Department of Chemical Engineering
      • • Institute of Theoretical Chemistry
      • • Key Laboratory for Colloid and Interface Chemistry
      • • State Key Laboratory for Crystal Materials
      Chi-nan-shih, Shandong Sheng, China
  • 1994–2015
    • Qufu Normal University
      Küfow, Shandong Sheng, China
  • 2007–2009
    • University of Jinan (Jinan, China)
      Chi-nan-shih, Shandong Sheng, China
  • 2004–2006
    • Michigan State University
      • Department of Chemistry
      East Lansing, MI, United States
  • 2000
    • The University of Hong Kong
      Hong Kong, Hong Kong