Yuxiang Bu

Shandong University, Jinan, Shandong Sheng, China

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Publications (168)339.94 Total impact

  • [show abstract] [hide abstract]
    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; · 10.68 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; · 3.61 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; · 3.83 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; · 3.61 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; · 3.61 Impact Factor
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    ABSTRACT: We report an ab initio molecular dynamics simulation study on the accommodation of a dielectron in a pyridinium ionic liquid in both the singlet and triplet state. In contrast to water and liquid ammonia, a dielectron does not prefer to reside in cavity-shaped structures in the ionic liquid. Instead, it prefers to be distributed over more cations, with long-lived diffuse and short-lived localized distributions, and with a triplet ground state and a low-lying, open-shell singlet excited state. The two electrons evolve nonsynchronously in both states via a diffuse-versus-localized interconversion mechanism that features a dynamic bipolaron with a modest mobility, slightly lower than a hydrated electron. This work presents the first detailed study on the structures and dynamics of a dielectron in ionic liquids.
    Physical Review Letters 03/2013; 110(10):107602. · 7.94 Impact Factor
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    ABSTRACT: 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.
    ChemPhysChem 02/2013; · 3.35 Impact Factor
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    ABSTRACT: We present a combined M06 functional calculation and ab initio molecular dynamics simulation study of an excess electron (EE) in a microhydrated aromatic complex (modeled by benzene (Bz)-water binary clusters, Bz(H(2)O)(n)). Calculated results illustrate that Bz ring and water clusters are indeed linked through the π⋯HO interactions in the neutral Bz(H(2)O)(n) (n = 1-8) clusters, and the size of the water cluster does not influence the nature of its interaction with the π system for the oligo-hydrated complexes. The states and the dynamics of an EE trapped in such Bz-water clusters were also determined. All of possible localized states for the EE can be roughly classified into two types: (i) single, ring-localized states (the Bz-centered valence anions) in which an EE occupies the LUMO of the complexes originating from the LUMO (π∗) of the Bz ring, and the π⋯HO interactions are enhanced for increase of electron density of the Bz ring. In this mode, the carbon skeleton of the Bz part is significantly deformed due to increase of electron density and nonsymmetric distribution of electron density induced by the interacting H-O bonds; (ii) solvated states, in which an EE is trapped directly as a surface state by the dangling hydrogen atoms of water molecules or as a solvated state in a mixed cavity formed by Bz and water cluster. In the latter case, Bz may also participate in capturing an EE using its C-H bonds in the side edge of the aromatic ring as a part of the cavity. In general, a small water cluster is favorable to the Bz-centered valence anion state, while a large one prefers a solvated electron state. Fluctuations and rearrangement of water molecules can sufficiently modify the relative energies of the EE states to permit facile conversion from the Bz-centered to the water cluster-centered state. This indicates that aromatic Bz can be identified as a stepping stone in electron transfer and the weak π⋯HO interaction plays an important role as the driving force in conversion of the two states.
    The Journal of Chemical Physics 01/2013; 138(1):014310. · 3.16 Impact Factor
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    ABSTRACT: 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.
    ChemPhysChem 11/2012; · 3.35 Impact Factor
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    ABSTRACT: This work presents a density functional theory calculational study for clarifying that peptide loops (-[peptide](n)-) including the N-terminal and the C-terminal oligopeptides and the α-helix N-terminal can serve as an intriguing kind of relay elements, as an addition to the known relay stations served by aromatic amino acids for electron hopping migration. For these protein motifs, an excess electron generally prefers to reside at the -NH(3)(+) group in a Rydberg state for the N-terminal peptides, or at the -COOH group in a dipole-bound state for the C-terminal peptides, and at the N-terminal in a dipole-bound π*-orbital state for the peptide loops and α-helices. The electron binding ability can be effectively enhanced by elongation for the α-helix N-terminal, and by bending, twisting, and even β-turning for the peptide chains. The relay property is determined by the local dipole instead of the total dipole of the peptide chains. Although no direct experiment supports this hypothesis, a series of recent studies regarding charge hopping migration associated with the peptide chains and helices could be viewed as strong evidence. But, further studies are still needed by considering the effects from relative redox potential between the donor and acceptor sites, protein environment, and structure water molecules.
    Physical Chemistry Chemical Physics 10/2012; · 3.83 Impact Factor
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    ABSTRACT: 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.
    ChemPhysChem 07/2012; 13(14):3293-302. · 3.35 Impact Factor
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    ABSTRACT: 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.
    Journal of Computational Chemistry 05/2012; 33(21):1773-80. · 3.84 Impact Factor
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    ABSTRACT: We present an ab initio molecular dynamics simulation of the dynamics of an excess electron solvated in supercritical CO2. The excess electron can exist in three types of states: CO2-core localized, dual-core localized, and diffuse states. All these states undergo continuous state conversions via a combination of long lasting breathing oscillations and core switching, as also characterized by highly cooperative oscillations of the excess electron volume and vertical detachment energy. All of these oscillations exhibit a strong correlation with the electron-impacted bending vibration of the core CO2, and the core-switching is controlled by thermal fluctuations.
    Physical Review Letters 05/2012; 108(20). · 7.94 Impact Factor
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    ABSTRACT: We present a combined first-principles calculation and molecular dynamics simulation study of an excess electron (EE) in condensed phase of a microhydrated protonated amino group in proteins in this work. The protonated amino group, -NH(3)(+), is modeled by a CH(3)NH(3)(+) and an amount of water molecules are included to form various microhydrated CH(3)NH(3)(+) clusters, and the states and the dynamics of the trapped EE are analyzed. In addition to the localized and delocalized states observed, the N-H/O-H bond cleavage phenomena followed by escape of a H atom are also observed for some hydrated clusters in which the -NH(3)(+) group exposes on the surface of the cluster and directly participates in binding an EE. The state-to-state conversion is controlled by thermal motion of molecules in the clusters, and the cleavage of the N-H or the O-H bond and the H escape are determined by the binding modes of the EE. The H-escape nature could be attributed to the dissociation of the N-H or O-H bond induced by the trapped EE which transfers to their antibonding orbitals. This work provides a microscopical picture of the EE trapping at a microhydrated hydrophilic group in proteins, long-range electron migration, and the H-evolving mechanisms relevant for the lesions or damages of proteins or DNA. This is the first step in considering increasingly larger peptide fragments for further investigation of the detailed lesion/damage or charge migration mechanisms. Further work about this topic is underway.
    The Journal of Chemical Physics 03/2012; 136(10):105101. · 3.16 Impact Factor
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    Wenming Sun, Yuxiang Bu, Yixuan Wang
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    ABSTRACT: To discuss the protection mechanism of DNA from radiation as well as assess the performance of PM6-DH2 on noncovalent interactions, the interaction of four nucleic acid bases (NABs) such as adenine (A), cytosine (C), guanine (G), and thymine (T), with Li@C(60) was extensively investigated with the-state-of-art theoretical methods describing noncovalent systems, like M06-2x, PBE-D, and PM6-DH2 methods. In the gas phase, the binding strength of NABs to Li@C(60) from M06-2x decreases in the sequence, G>C>A>T. As dispersion was explicitly included, PBE-D relatively enhances the binding of A and T and corrects the sequence to, G>A>C∼T. PM6-DH2 predicted similar binding energies to those from PBE-D within 0.5 kcal/mol and the same binding sequence, suggesting that the PM6-DH2 method is promising for nano-scale systems. In the aqueous solution, binding of NABs-Li@C(60) is considerably decreased, and the M06-2X and PM6-D methods yield a different sequence from the gas phase, G>A>T>C. The encapsulation of Li atom results in a lower IP for Li@C(60) than those of NABs, and the dominant localization of single-occupied molecular orbital on Li@C(60) moiety of the complexes NABs-Li@C(60) further indicates that an electron would be ejected from Li@C(60) upon radiation and Li@C(60) is therefore able to protect DNA bases from radiation. In addition, it was revealed that Li prefers coordination with the hexagonal ring at Li@C(60) , which clarifies the existing controversy in this respect. Finally, Yang's reduced density gradient approach clearly shows that the weak and strong noncovalent interaction regions in the complexes, NABs-Li@C(60) and (NABs-Li@C(60) )(+).
    Journal of Computational Chemistry 12/2011; 33(5):490-501. · 3.84 Impact Factor
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    ABSTRACT: The effect of double proton transfer (DPT) on charge migration of DNA was investigated by the nonequilibrium Green's function method combined with density functional theory. The results revealed that DPT not only lowers ionization potentials, but also improves the delocalization of the localized π-orbitals at each base moiety through adjusting energy levels and spatial distributions of their molecular orbitals. Furthermore, DPT leads to both the strengthening of the second-order interactions of the Watson-Crick H-bond zones, and the promotion of the charge transfer transitions between two pairing bases in the UV absorption spectra. Electronic transport calculations indicated that DPT can improve the charge migration along the DNA duplex for specific sequences through enhancing transverse base-to-base electronic communication. This work will provide a new insight into the understanding of DNA charge conduction which can be electronically promoted or regulated by DPT.
    The Journal of Chemical Physics 10/2011; 135(13):134315. · 3.16 Impact Factor
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    ABSTRACT: Internucleotide (2h)J(NN) spin-spin couplings and chemical shifts (δ((1)H) and Δδ((15)N)) of N-H···N H-bond units in the natural and radiation-damaged G-C base pairs were predicted using the appropriate density functional theory calculations with a large basis set. Four possible series of the damaged G-C pairs (viz., dehydrogenated and deprotonated G-C pairs, GC(•-) and GC(•+) radicals) were discussed carefully in this work. Computational NMR results show that radicalization and anionization of the base pairs can yield strong effect on their (2h)J(NN) spin scalar coupling constants and the corresponding chemical shifts. Thus, variations of the NMR parameters associated with the N-H···N H-bonds may be taken as an important criterion for prejudging whether the natural G-C pair is radiation-damaged or not. Analysis shows that (2h)J(NN) couplings are strongly interrelated with the energy gaps (ΔE(LP→σ*)) and the second-order interaction energies (E(2)) between the donor N lone-pair (LP(N)) and the acceptor σ*(N-H) localized NBO orbitals, and also are sensitive to the electron density distributions over the σ*(N-H) orbital, indicating that (2h)J(NN) couplings across the N-H···N H-bonds are charge-transfer-controlled. This is well supported by variation of the electrostatic potential surfaces and corresponding charge transfer amount between G and C moieties. It should be noted that although the NMR spectra for the damaged G-C pair radicals are unavailable now and the states of the radicals are usually detected by the electron spin resonance, this study provides a correlation of the properties of the damaged DNA species with some of the electronic parameters associated with the NMR spectra for the understanding of the different state character of the damaged DNA bases.
    Journal of Computational Chemistry 04/2011; 32(6):1159-69. · 3.84 Impact Factor
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    Wenming Sun, Yuxiang Bu, Yixuan Wang
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    ABSTRACT: The major objective of this paper is to address a controversial binding sequence between nucleic acid bases (NABs) and C(60) by investigating adsorptions of NABs and their cations on C(60) fullerene with a variety of density functional theories including two novel hybrid meta-GGA functionals, M05-2x and M06-2x, as well as a dispersion-corrected density functional, PBE-D. The M05-2x/6-311++G** provides the same binding sequence as previously reported, guanine(G) > cytosine(C) > adenine (A) > thymine (T); however, M06-2x switches the binding strengths of A and C, and PBE-D eventually results in the following sequence, G>A>T>C, which is the same as the widely accepted hierarchy for the stacking of NABs on other carbon nanomaterials such as single-walled carbon nanotube and graphite. The results indicate that the questionable relative binding strength is due to insufficient electron correlation treatment with the M05-2x or even the M06-2x method. The binding energy of G@C(60) obtained with the M06-2x/6-311++G(d,p) and the PBE-D/cc-pVDZ is -7.10 and -8.07 kcal/mol, respectively, and the latter is only slightly weaker than that predicted by the MP2/6-31G(d,p) (-8.10kca/mol). Thus, the PDE-D performs better than the M06-2x for the observed NAB@C(60) π-stacked complexes. To discuss whether C(60) could prevent NABs from radiation-induced damage, ionization potentials of NABs and C(60), and frontier molecular orbitals of the complexes NABs@C(60) and (NABs@C(60))(+) are also extensively investigated. These results revealed that when an electron escapes from the complexes, a hole was preferentially created in C(60) for T and C complexes, while for G and A the hole delocalizes over the entire complex, rather than a localization on the C(60) moiety. The interesting finding might open a new strategy for protecting DNA from radiation-induced damage and offer a new idea for designing C(60)-based antiradiation drugs.
    The Journal of Physical Chemistry C 03/2011; 115(8):3220-3228. · 4.81 Impact Factor
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    ABSTRACT: To better understand the potential role of sulfuric acid aerosols in the atmosphere, the electron capture properties of the H(2)SO(4)...HOO˙ complex have been systematically investigated by employing the MP2 and B3LYP methods in combination with the atoms in molecules (AIM) theory, energy decomposition analysis (EDA), and ab initio molecular dynamics. It was found that the electron capture process is a favorable reaction thermodynamically and kinetically. The excess electron can be captured by the HOO˙ fragment initially, and then the proton of the H(2)SO(4) fragment associated with the intermolecular H-bonds is transferred to the HOO˙ fragment without any activation barriers, resulting in the formation of the HOOH species directly. Therefore, the electron capture process of the H(2)SO(4)...HOO˙ complex provides an alternative source of HOOH in the atmosphere. The nature of the coupling interactions in the electron capture products are clarified, and the most stable anionic complex is also determined. Additionally, the influences of the adjacent water molecules on the electron capture properties are investigated, as well as the distinct IR features of the most stable electron capture product.
    Physical Chemistry Chemical Physics 02/2011; 13(13):5931-9. · 3.83 Impact Factor
  • Li Han, Yuxiang Bu
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    ABSTRACT: Motivated by a promising expansion of the genetic alphabet and a successful design of conductive DNA bases justified from the hetero-ring-expanded purine base (G and A) analogs, we extend our hetero-ring expansion scheme to the pyrimidine bases (C and T) to examine the ring-expansion effects on various properties of these single-ring bases with a comparison with those in the double-ring purine case. Four kinds of the hetero-rings are considered to expand C and T, forming the C and T analogs (nC and nT), respectively. The relevant structures and properties were investigated by means of quantum calculations and molecular dynamics simulations. The results reveal that all the modified bases can form base pairs specifically with their natural counterparts and assemble duplex helices which have comparable stability to native ones. The HOMO-LUMO gaps of G-nC and A-nT are smaller than those of the natural pairs, and the assembled duplex helices ((G-nC)(12) and (A-nT)(12)) are diameter-enlarged but with smaller rise and twist, both of which favor DNA-conduction, as confirmed by ionization potentials and spin density distributions. In addition, the hetero-ring expansion can lower the activation barriers and reduce the reaction heats of the inter-base double proton transfers. In particular, as evidenced by NMR parameters and the excited states, the hetero-ring expansion leads to an enhancement of the transverse electronic communication between two pairing bases, clearly facilitating the conduction along the helices. Furthermore, the hetero-ring expansion effect on the pyrimidine bases is larger than that on the purine bases. In summary, this work presents clear theoretical evidence for the possibility of hetero-ring expanded pyrimidine bases as promising candidates for the motifs of the genetic alphabet and DNA nanowires.
    Physical Chemistry Chemical Physics 02/2011; 13(13):5906-14. · 3.83 Impact Factor

Publication Stats

233 Citations
10 Downloads
339.94 Total Impact Points

Institutions

  • 1996–2013
    • Shandong University
      • • Institute of Theoretical Chemistry
      • • Key Laboratory for Colloid and Interface Chemistry
      Jinan, Shandong Sheng, China
  • 1994–2011
    • Qufu Normal University
      Küfow, Shandong Sheng, China
  • 2005–2009
    • Michigan State University
      • Department of Chemistry
      East Lansing, MI, United States
  • 2007
    • Albany State University
      • Department of Natural Sciences
      Albany, GA, United States
  • 2001–2005
    • University of Jinan (Jinan, China)
      Chi-nan-shih, Shandong Sheng, China
  • 2000
    • The University of Hong Kong
      Hong Kong, Hong Kong