Yun-Xiang Lu

Zhejiang University, Hangzhou, Zhejiang Sheng, China

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Publications (19)21.03 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Ab initio calculations on the complexes formed between unsaturated hydrocarbon(R) and dihalogen molecules(XY), R⋯(XY)n (n = 1–2), have been performed at MP2/aug-cc-PVDZ level of theory. Geometrical structures, interaction energies and topological parameters derived from the theory of atoms in molecules (AIM) developed by Bader have been studied systematically to characterize the halogen⋯π interactions. The present theoretical investigation indicates that such interactions in all trimolecular complexes R⋯(XY)2 are significantly stronger than those in the corresponding bimolecular series R⋯(XY), demonstrating the existence of cooperativity effect. This may provide a theoretical basis for our understanding the reaction mechanism of the electrophilic addition of halogen to the unsaturated hydrocarbons.
    Journal of Molecular Structure THEOCHEM 03/2009; 897:12-16. · 1.37 Impact Factor
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    ABSTRACT: A systematic theoretical investigation on a series of dimeric complexes formed between some halocarbon molecules and electron donors has been carried out by employing both ab initio and density functional methods. Full geometry optimizations are performed at the Moller-Plesset second-order perturbation (MP2) level of theory with the Dunning's correlation-consistent basis set, aug-cc-pVDZ. Binding energies are extrapolated to the complete basis set (CBS) limit by means of two most commonly used extrapolation methods and the aug-cc-pVXZ (X = D, T, Q) basis sets series. The coupled cluster with single, double, and noniterative triple excitations [CCSD(T)] correction term, determined as a difference between CCSD(T) and MP2 binding energies, is estimated with the aug-cc-pVDZ basis set. In general, the inclusion of higher-order electron correlation effects leads to a repulsive correction with respect to those predicted at the MP2 level. The calculations described herein have shown that the CCSD(T) CBS limits yield binding energies with a range of -0.89 to -4.38 kcal/mol for the halogen-bonded complexes under study. The performance of several density functional theory (DFT) methods has been evaluated comparing the results with those obtained from MP2 and CCSD(T). It is shown that PBEKCIS, B97-1, and MPWLYP functionals provide accuracies close to the computationally very expensive ab initio methods.
    Journal of Computational Chemistry 09/2008; 30(5):725-32. · 3.84 Impact Factor
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    ABSTRACT: Bidentate charge-assisted halogen bonds between halo-perfluorocarbons and halide ions play crucial roles in determining the formation of double-helix systems that display an ample phase behavior. This paper presents an ab initio investigation of several trimeric complexes of halo-perfluorocarbons and halo-hydrocarbons with halide anions. In all cases, the intermolecular distances are shown to be much less than the sums of van der Waals radii of involved atoms and the interactions are essentially linear. Bifurcated halogen bonding energies, calculated at the MP2/lanl2DZ∗ level, vary over a range from −1.91 to −30.07kcal/mol. The interactions are comparable to, or even prevail over, conventional hydrogen bonds. Computations described herein also unveil that halo-perfluorocarbons form significantly stronger halogen bonds with anions relative to corresponding halo-hydrocarbons. These results agree with those of the quantum theory of atoms in molecules, since bond critical points are found for these halogen bonds. Finally, natural bond orbital analysis has been applied to provide more insights into the nature of bidentate charge-assisted halogen bonds.
    Journal of Molecular Structure THEOCHEM 03/2008; 853(1):39-44. · 1.37 Impact Factor
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    ABSTRACT: Short interfluorine contacts (FF) are ubiquitous in crystal structures. This article presents a theoretical study of five dimeric complexes formed between fluorine-containing molecules and hydrogen fluorine at the MP2 computational levels. The results derived from ab initio calculations show that in all cases, the intermolecular distances are less than the sum of van der Waals radii. Difluorine bond energies, computed at the MP2/aug-cc-pVTZ level of theory, span over a range from −0.71 to −3.77 kJ/mol, thus indicating that interfluorine interactions are relatively very weak but non-negligible. The electrostatic force contributes dominantly to the stability of the systems under investigation, and as such the dispersion interaction makes energetic contributions to binding. As an NBO analysis suggested, the charge-transfer force plays a minor role in the formation of the complexes. Finally, to gain more insights into the nature of interfluorine interactions, topological analysis of the electron density distribution and properties of bond critical points are determined by means of the quantum theory of atoms in molecules. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
    International Journal of Quantum Chemistry 01/2008; 108(6):1083 - 1089. · 1.17 Impact Factor
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    ABSTRACT: Halogen bonding, a specific intermolecular noncovalent interaction, plays crucial roles in fields as diverse as molecular recognition, crystal engineering, and biological systems. This paper presents an ab initio investigation of a series of dimeric complexes formed between bromobenzene and several electron donors. Such small model systems are selected to mimic halogen bonding interactions found within crystal structures as well as within biological molecules. In all cases, the intermolecular distances are shown to be equal to or below sums of van der Waals radii of the atoms involved. Halogen bonding energies, calculated at the MP2/aug-cc-pVDZ level, span over a wide range, from -1.52 to -15.53 kcal/mol. The interactions become comparable to, or even prevail over, classical hydrogen bonding. For charge-assisted halogen bonds, calculations have shown that the strength decreases in the order OH- > F- > HCO2- > Cl- > Br-, while for neutral systems, their relative strengths attenuate in the order H2CS > H2CO > NH3 > H2S > H2O. These results agree with those of the quantum theory of atoms in molecules (QTAIM) since bond critical points (BCPs) are identified for these halogen bonds. The QTAIM analysis also suggests that strong halogen bonds are more covalent in nature, while weak ones are mostly electrostatic interactions. The electron densities at the BCPs are recommended as a good measure of the halogen bond strength. Finally, natural bond orbital (NBO) analysis has been applied to gain more insights into the origin of halogen bonding interactions.
    The Journal of Physical Chemistry A 10/2007; 111(42):10781-8. · 2.77 Impact Factor
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    ABSTRACT: A series of dimeric complexes formed between bromocarbon molecules and two anions (Br− and CN−) have been investigated by using MP2 method. The quantum theory of atoms in molecules (QTAIM) and the second-order perturbation natural bond orbital (NBO) approaches were applied to analyze the electron density distributions of these complexes and to explore the nature of charge-assisted halogen bonding interactions. As anticipated, these interactions are significantly stronger relative to the corresponding neutral ones. The results derived from ab initio calculations described herein reveal a major contribution from the electrostatic interaction on the stability of the systems considered. Beside the electrostatic interaction, the charge-transfer force and the second-order orbital interaction also play an important role in the formation of the complexes, as a NBO analysis suggested. The presence of halogen bonds in the complexes has been identified in terms of the QTAIM methodology, and several linear relationships have been established to provide more insight into charge-assisted halogen bonding interactions. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
    International Journal of Quantum Chemistry 05/2007; 108(1):90 - 99. · 1.17 Impact Factor
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    ABSTRACT: In this work, ab initio calculations have been carried out to investigate the interactions between the π face of benzene and several halocarbon molecules. The results derived from these calculations reveal the predominant noncovalent C–X/π interactions in all cases. The calculated interaction energies for the halocarbon–benzene complexes span over a reasonably narrow range, from −1.29 to −3.16 kcal/mol, indicating that the C–X/π interactions are comparable in strength to the well-documented C–H/π interactions. The significant gain of the attraction by electron correlation illustrates that the systems considered should be primarily stabilized by the dispersion interaction. As a charge density analysis has suggested, the charge-transfer force plays a minor role in the C–X/π interactions. The halogen-bonding nature of the C–X/π interactions has been identified in terms of the bond critical point analysis within the theory of atoms in molecules (AIM).
    Chemical Physics 04/2007; · 1.96 Impact Factor
  • Yan-hua Wang, Li Li, Yun-xiang Lu, Jian-wei Zou
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    ABSTRACT: Ab initio and density functional calculations were employed to investigate the bonding patterns in the adenine-5-bromouracil (AT+) complexes. It is shown that the Br atom in 5-bromouracil (T+) is involved in bonding both with the hydrogen atom of the amino group of adenine (A) and with N7(A) (or N1(A)). With this motif, the Br atom interacts with a nucleophile (H) in a ``head-on" fashion and an electrophile(N) in a ``side-on" fashion, forming both hydrogen and halogen bonds. Electrostatic attraction between the Br atom in T+ and N7 (or N1) of adenine was found via the electrostatic potential analysis. The existence of the Br. . .N interactions in the pairs was further confirmed by means of Bader's atoms in molecules theory. A bond critical point is identified for the halogen bonds and the topological parameters at the bond critical point indicate the typical closed-shell interactions in the pairs. Natural bond orbital analysis suggests that the charge transfer from the lone pair of the nitrogen atom of adenine is mainly directed to the C-Br antibonding orbital. Finally, halogen bonds in the T+AT+A tetrads were also explored. Bibtex entry for this abstract Preferred format for this abstract (see Preferences) Find Similar Abstracts: Use: Authors Title Abstract Text Return: Query Results Return items starting with number Query Form Database: Astronomy Physics arXiv e-prints
    Chinese Journal of Chemical Physics - CHIN J CHEM PHYS. 01/2007; 20(5):531-536.
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    ABSTRACT: This Letter presents an ab initio investigation on several dimeric complexes of fluorine-containing molecules with ammonia. Fluorine bond energies, computed at the MP2/aug-cc-pVTZ level of theory, vary in a range from −0.13 to −9.30kcal/mol, thus indicating that fluorine bonding interactions are comparable in strength to traditional halogen bonds. The quantum theory of atoms in molecules and the second-order perturbation natural bond orbital analyses are also applied to explore the nature of fluorine bonding.
    Chemical Physics Letters - CHEM PHYS LETT. 01/2007; 449(1):6-10.
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    ABSTRACT: Noncovalent halogen/π interactions of FCl with substituted benzenes have been investigated using ab initio calculations. It was shown that the predicted maximum interaction energy gap between the substituted and unsubstituted systems amounts to 1.14 kcal/mol, and therefore substituents on benzene have a pronounced effect on the strength of halogen/π interactions. While the presence of electron-donating groups (NH2, CH3, and OH) on benzene enhances the interaction energy appreciably, an opposite effect is observed for electron-accepting groups (NO2, CN, Br, Cl, and F). The large gain of the attraction by electron correlation illustrates that the stabilities of the systems considered arise primarily from the dispersion interaction. Beside the dispersion interaction, the charge-transfer interaction also plays an important role in halogen/π interactions, as a charge density analysis suggested. To provide more insight into the nature of halogen/π interactions, topological analysis of the electron density distribution and properties of bond critical points were determined in terms of the atoms in molecules (AIM) theory. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
    International Journal of Quantum Chemistry 12/2006; 107(6):1479 - 1486. · 1.17 Impact Factor
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    ABSTRACT: A series of complexes formed between halogen-containing molecules and ammonia have been investigated by means of the atoms in molecules (AIM) approach to gain a deeper insight into halogen bonding. The existence of the halogen bond critical points (XBCP) and the values of the electron density (ρb) and Laplacian of electron density (Δ2ρb) at the XBCP reveal the closed-shell interactions in these complexes. Integrated atomic properties such as charge, energy, polarization moment, volume of the halogen bond donor atoms, and the corresponding changes (Δ) upon complexation have been calculated. The present calculations have demonstrated that the halogen bond represents different AIM properties as compared to the well-documented hydrogen bond. Both the electron density and the Laplacian of electron density at the XBCP have been shown to correlate well with the interaction energy, which indicates that the topological parameters at the XBCP can be treated as a good measure of the halogen bond strength. In addition, an excellent linear relationship between the interatomic distance d(X···N) and the logarithm of ρb has been established.
    Chinese Journal of Chemistry 12/2006; 24(12):1709 - 1715. · 0.92 Impact Factor
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    ABSTRACT: Ab initio calculations have been performed on single-electron halogen bonds between methyl radical and bromine-containing molecules to gain a deeper insight into the nature of such noncovalent interactions. Bader's atoms in molecules (AIM) theory have also been applied to the analysis of the linking of the single-electron halogen bond. Various characteristics of the RBr…CH3 interaction, i.e., binding energies, geometrical parameters and topological properties of the electron density have been determined. The presence of the bond critical points (BCPs) between the bromine atom and methyl radical and the values of electron density and Laplacian of electron density at these BCPs indicate the closed-shell interactions in the complexes. The single-electron halogen bonds, which are significantly weaker than the normal halogen bonds, exhibit equally bond strength as compared to the single-electron hydrogen bond. It has been also found that plotting of the binding energies versus topological properties of the electron density at the BCPs gives two straight lines. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
    International Journal of Quantum Chemistry 09/2006; 107(2):501 - 506. · 1.17 Impact Factor
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    ABSTRACT: Density functional theory calculations at the B3LYP/6-31+G(d,p) level of theory have been performed to explore proton exchanges between phenols and ammonia or amines, which can be used to account for previous NMR experiments. For the parent phenol-NH(3) system, a transition state with a symmetric phenolate-NH(4)(+)-like structure, which lies about 35 kcal mol(-1) in energy above the hydrogen-bonded complex, has been successfully located. An intrinsic reaction coordinate (IRC) analysis indicates that the proton exchange is a concerted process, which can be roughly divided into four continuous subprocesses. A series of para-substituted phenol-NH(3) systems have been considered to investigate the substituent effect. Whereas introduction of an electron-withdrawing group on the phenol appreciably reduces the barrier, an opposite effect is observed for an electron-donating group. Moreover, it has been disclosed that there exists a good linear correlation between the activation barriers and the interaction energies between the phenols and NH(3), indicating the important role of proton transfer (or hydrogen bonding) in determining the proton exchange. Also considered are the proton exchanges between phenol and amines and those for some sterically hindered systems. The results show that the phenol tends to exchange hydrogen with the amines, preferably the secondary amines, and that the steric effect is favorable for the proton exchange, which imply that, as the IRC analysis suggested, besides the proton transfer, the flip of the ammonium-like moiety may play a significant role in the course of proton exchange. For all of these systems, we investigated the solvent effects and found that the barrier heights of proton exchange decrease remarkably as compared to those in a vacuum due to the ion pair feature of the transition state. Finally, we explored the phenol radical cation-NH(3) system; the barrierless proton transfer and remarkably low barrier (5.2 kcal mol(-1)) of proton exchange provide further evidence for the importance of proton transfer in the proton exchange.
    The Journal of Physical Chemistry A 08/2006; 110(29):9261-6. · 2.77 Impact Factor
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    ABSTRACT: Ab initio calculations at the MP2(full)/aug-cc-pvdz level of theory have been performed to explore the nature of bifurcated or three-center halogen bonds. It has been shown that the three-center interactions in the chlorine-containing complexes are very weak, whereas the interactions in the bromine-containing complexes are relatively stronger. Bifurcated halogen bonds, where single intermolecular contacts are much longer than those of the two-center halogen bonds, exhibit weaker bond strength as compared to the two-center ones. The topological parameters obtained by means of Bader's atoms in molecules (AIM) theory have also been applied for the analysis of these interactions.
    Journal of Molecular Structure THEOCHEM 08/2006; 767:139-142. · 1.37 Impact Factor
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    ABSTRACT: A series of complexes formed between bromine-containing molecules RBr and HF have been investigated at the MP2(full)/aug-cc-pvdz level of theory. This, together with a previous work [J.W. Zou, Y.J. Jiang, M. Guo, G.X. Hu, B. Zhang, H.C. Liu, Q.S. Yu, Chem. Eur. J. 11 (2005) 740] on the halogen-bonded RBr⋯NH3 complexes, offers a quantitative insight into the nucleophile ‘head on’ and electrophile ‘side on’ interactions of halogens. It has been shown that the stronger electron-withdrawing ability of the moiety bound to the bromine is, the weaker is the Br⋯H interaction to which it gives rise, which is contrary to the trend probed in the RBr⋯NH3 complexes. Several linear relationships have been established to provide further understanding of the ‘amphiphilicity’ of covalently-bonded halogens. The topological parameters obtained in terms of Bader's atoms in molecules (AIM) theory have also been applied for the analysis of these Br⋯H interactions.
    Journal of Molecular Structure-theochem - J MOL STRUC-THEOCHEM. 01/2006; 766(2):119-124.
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    ABSTRACT: Ab initio calculations at the MP2/aug-cc-PVDZ level of theory have been carried out to investigate a large number of complexes formed between halogen-containing molecules and several electron donors. It is shown that the strength of certain halogen bonds turns out to be greater than that of well-studied hydrogen bonds. Bader’s atoms in molecules (AIM) theory has also been applied, and it is found that the electron densities at the halogen bond critical points correlate with the interaction energies, which indicates that the electron density can serve as a convenient measure of the strength of the different types of halogen bonding. Similar to hydrogen bonds, halogen bonds can be classified in a range from weak bonds, which are regarded as electrostatic interactions, to strong bonds, which have some degree of covalent character.
    Journal of Molecular Structure-theochem - J MOL STRUC-THEOCHEM. 01/2006; 776(1):83-87.
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    ABSTRACT: The Myers–Saito (C2–C7) cyclization and the alternative Schmittel (C2–C6) cyclization of enyne-1,2,3-triene 1R and its hetero analogues 2R–5R were investigated by using pure density functional theory method (BPW91) in connection with the 6-311G(d, p) basis set. It has been shown that heteroatom-containing reactants lower significantly reaction barriers for both cyclization modes and reduce the difference between the barrier of the C2–C7 cyclization mode and that of the C2–C6 one. The Myers–Saito cyclization of 4R is associated with the smallest reaction barrier and the highest exothermicity. Whereas the Schmittel cyclization of 4R is exothermic, all the others are predicted to be endothermic.
    Journal of Molecular Structure-theochem - J MOL STRUC-THEOCHEM. 01/2005; 732(1):233-238.
  • Yun-Xiang Lu, Qing-Sen Yu, Jian-Wei Zou
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    ABSTRACT: The effects of several substituents X on the intramolecular dehydro Diels–Alder reactions of conjugated enynes (1R–9R) were investigated at the B3LYP/6-311G(d,p) level of theory. Geometry optimizations and harmonic frequency calculations were performed for all reactants, transition structures, as well as products. It has shown that all transition structures are asynchronous, with forming C4C8 bond length being shorter than C1C9 distance except for 9TS. 7R with the protonated amino (X=NH2+) function displays a lower barrier than 6R with the amino (X=NH) function. The intramolecular [4+2] cycloaddition with X=O has the lowest reaction barrier and the highest exothermicity.
    Journal of Molecular Structure-theochem - J MOL STRUC-THEOCHEM. 01/2005; 731(1):207-211.
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    ABSTRACT: The effect of substituents on the enone–dienol tautomerism of but-2-enal by [1,5]-H shift has been investigated systematically. All stationary point structures and energies of substituted but-2-enal are obtained at the levels of B3LYP/6-31G* and B3LYP/6-311++G(d,p). It is shown that the substituents in the 2-substituted series exert more significant effects on the relative energies of dienol with respect to enone and the energy barriers for enolization than those in the 3- or 4-substituted series. In general, the relative energies and energy barriers could be reduced by the electron-withdrawing substituents BH2, CN, NO, since the structure of dienol and the corresponding transition state could be stabilized more than those of enone, but increased by the electron-donating substituents in the order NH2
    Journal of Molecular Structure-theochem - J MOL STRUC-THEOCHEM. 01/2005; 755(1):31-37.