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Tu, Yaoquan
Publications (10 of 17) Show all publications
Gao, L., Tu, Y., Wegman [Palmebäck-Wegman], P., Wingren, S. & Eriksson, L. A. (2011). A mechanistic hypothesis for the cytochrome P450-catalyzed cis-trans isomerization of 4-hydroxytamoxifen: an unusual redox reaction. Journal of Chemical Information and Modeling, 51(9), 2293-2301
Open this publication in new window or tab >>A mechanistic hypothesis for the cytochrome P450-catalyzed cis-trans isomerization of 4-hydroxytamoxifen: an unusual redox reaction
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2011 (English)In: Journal of Chemical Information and Modeling, ISSN 1549-9596, E-ISSN 1549-960X, Vol. 51, no 9, p. 2293-2301Article in journal (Refereed) Published
Abstract [en]

We provide a detailed description of the cis-trans isomerization of 4-hydroxytamoxifen/endoxifen catalyzed by several isoforms from the cytochrome P450 (CYP) superfamily, including CYP1B1, CYP2B6, and CYP2C19. We show that the reactions mainly involve redox processes catalyzed by CYP, DFT calculation results strongly suggest that the isomerization occurs via a cationic intermediate. The cationic cis-isomer is more than 3 kcal/mol more stable than the trans form, resulting in an easier conversion from trans-to-cis than cis-to-trans. The cis-trans isomerization is a rarely reported CYP reaction and is ascribed to the lack of a second abstractable proton on the ethenyl group of the triarylvinyl class of substrates. The cationic intermediates thus formed instead of the stable dehydrogenation products allow for isomerization to occur. As a comparison, the reactions for the tamoxifen derivatives are compared to those of other substrates, 4-hydroxyacetanilide and raloxifene, for which the stable dehydrogenation products are formed.

National Category
Chemical Sciences Biomedical Laboratory Science/Technology
Research subject
Chemistry; Biomedicine
Identifiers
urn:nbn:se:oru:diva-20857 (URN)10.1021/ci2001082 (DOI)000295114700026 ()
Available from: 2012-01-11 Created: 2012-01-11 Last updated: 2018-02-14Bibliographically approved
Zhang, Q., Bulone, V., Ågren, H. & Tu, Y. (2011). A molecular dynamics study of the thermal response of crystalline cellulose I beta. Cellulose (London), 18(2), 207-221
Open this publication in new window or tab >>A molecular dynamics study of the thermal response of crystalline cellulose I beta
2011 (English)In: Cellulose (London), ISSN 0969-0239, E-ISSN 1572-882X, Vol. 18, no 2, p. 207-221Article in journal (Refereed) Published
Abstract [en]

Molecular dynamics simulations were performed to better understand the atomic details of thermal induced transitions in cellulose I beta. The latest version of the GLYCAM force field series (GLYCAM06) was used for the simulations. The unit cell parameters, density, torsion angles and hydrogen-bonding network of the crystalline polymer were carefully analyzed. The simulated data were validated against the experimental results obtained by X-ray diffraction for the crystal structure of cellulose I beta at room and high temperatures, as well as against the temperature-dependent IR measurements describing the variation of hydrogen bonding patterns. Distinct low and high temperature structures were identified, with a phase transition temperature of 475-500 K. In the high-temperature structure, all the origin chains rotated around the helix axis by about 30A degrees and the conformation of all hydroxymethyl groups changed from tg to either gt on origin chains or gg on center chains. The hydrogen-bonding network was reorganized along with the phase transition. Compared to the previously employed GROMOS 45a4 force field, GLYCAM06 yields data in much better agreement with experimental observations, which reflects that a cautious parameterization of the nonbonded interaction terms in a force field is critical for the correct prediction of the thermal response in cellulose crystals.

Place, publisher, year, edition, pages
Springer, 2011
Keywords
Cellulose I beta, Molecular dynamics, GLYCAM06, Thermal response
National Category
Chemical Sciences
Research subject
Chemistry
Identifiers
urn:nbn:se:oru:diva-17101 (URN)10.1007/s10570-010-9491-x (DOI)000288253000002 ()2-s2.0-79952533565 (Scopus ID)
Available from: 2011-09-05 Created: 2011-09-02 Last updated: 2017-12-08Bibliographically approved
Gao, L., Tu, Y., Wegman [Palmebäck-Wegman], P., Wingren, S. & Eriksson, L. A. (2011). Conformational enantiomerization and estrogen receptor alpha binding of anti-cancer drug tamoxifen and its derivatives. Journal of Chemical Information and Modeling, 51(2), 306-314
Open this publication in new window or tab >>Conformational enantiomerization and estrogen receptor alpha binding of anti-cancer drug tamoxifen and its derivatives
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2011 (English)In: Journal of Chemical Information and Modeling, ISSN 1549-9596, E-ISSN 1549-960X, Vol. 51, no 2, p. 306-314Article in journal (Refereed) Published
Abstract [en]

The anticancer drug tamoxifen (TAM) displays two chiral vinyl propeller structures, which interconvert so rapidly that the process is undetectable on the NMR time scale. In the present work, the enantiomerization processes were investigated with molecular modeling techniques. The threshold mechanisms probed at the different rings were shown to be identical, i.e., involving a synchronous three-ring flip, with a correlated rotation of the rings. In order to reveal the pharmacological profiles of the two chiral forms, we performed structural studies on the ligand binding domain of estrogen receptor alpha. (ER alpha LBD) and associated ligands. The enantiomers, with opposite torsional twist, were found to be discriminated by ER alpha. For TAM and its main metabolites, the effects of the stereoselectivity of ER alpha are overcome by the low energy cost for helical inversion between the two torsional enantiomers, estimated to be similar to 3 kcal/mol.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2011
National Category
Medical and Health Sciences
Research subject
Medicine
Identifiers
urn:nbn:se:oru:diva-17124 (URN)10.1021/ci100401t (DOI)000287685700012 ()21194224 (PubMedID)2-s2.0-79952139350 (Scopus ID)
Available from: 2011-09-05 Created: 2011-09-02 Last updated: 2017-12-08Bibliographically approved
Li, X., Hede, T., Tu, Y., Leck, C. & Ågren, H. (2011). Glycine in aerosol water droplets: a critical assessment of Kohler theory by predicting surface tension from molecular dynamics simulations. Atmospheric Chemistry And Physics, 11(2), 519-527
Open this publication in new window or tab >>Glycine in aerosol water droplets: a critical assessment of Kohler theory by predicting surface tension from molecular dynamics simulations
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2011 (English)In: Atmospheric Chemistry And Physics, ISSN 1680-7316, E-ISSN 1680-7324, Vol. 11, no 2, p. 519-527Article in journal (Refereed) Published
Abstract [en]

Aerosol particles in the atmosphere are important participants in the formation of cloud droplets and have significant impact on cloud albedo and global climate. According to the Kohler theory which describes the nucleation and the equilibrium growth of cloud droplets, the surface tension of an aerosol droplet is one of the most important factors that determine the critical supersaturation of droplet activation. In this paper, with specific interest to remote marine aerosol, we predict the surface tension of aerosol droplets by performing molecular dynamics simulations on two model systems, the pure water droplets and glycine in water droplets. The curvature dependence of the surface tension is interpolated by a quadratic polynomial over the nano-sized droplets and the limiting case of a planar interface, so that the so-called Aitken mode particles which are critical for droplet formation could be covered and the Kohler equation could be improved by incorporating surface tension corrections.

Place, publisher, year, edition, pages
Copernicus GmbH, 2011
National Category
Chemical Sciences
Research subject
Chemistry
Identifiers
urn:nbn:se:oru:diva-17158 (URN)10.5194/acp-11-519-2011 (DOI)000286722300008 ()2-s2.0-78751504505 (Scopus ID)
Available from: 2011-09-05 Created: 2011-09-02 Last updated: 2017-12-08Bibliographically approved
Li, X., Tu, Y., Tian, H. & Ågren, H. (2010). Computer simulations of aqua metal ions for accurate reproduction of hydration free energies and structures. Journal of Chemical Physics, 132(10), Article ID 104505.
Open this publication in new window or tab >>Computer simulations of aqua metal ions for accurate reproduction of hydration free energies and structures
2010 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 132, no 10, article id 104505Article in journal (Refereed) Published
Abstract [en]

Metal ions play essential roles in biological processes and have attracted much attention in both experimental and theoretical fields. By using the molecular dynamics simulation technology, we here present a fitting-refining procedure for deriving Lennard-Jones parameters of aqua metal ions toward the ultimate goal of accurately reproducing the experimentally observed hydration free energies and structures. The polarizable SWM4-DP water model {proposed by Lamoureux et al. [J. Chem. Phys. 119, 5185 (2003)] } is used to properly describe the polarization effects of water molecules that interact with the ions. The Lennard-Jones parameters of the metal ions are first obtained by fitting the quantum mechanical potential energies of the hexahydrated complex and are subsequently refined through comparison between the calculated and experimentally measured hydration free energies and structures. In general, the derived Lennard-Jones parameters for the metal ions are found to reproduce hydration free energies accurately and to predict hydration structures that are in good agreement with experimental observations. Dynamical properties are also well reproduced by the derived Lennard-Jones parameters.

Place, publisher, year, edition, pages
Melville, USA: American Institute of Physics (AIP), 2010
Keywords
Free energy, Lennard-Jones potential, molecular dynamics method, polarisability, solvation, water
National Category
Chemical Sciences
Research subject
Chemistry
Identifiers
urn:nbn:se:oru:diva-12582 (URN)10.1063/1.3352567 (DOI)000275589700030 ()20232969 (PubMedID)2-s2.0-77949643950 (Scopus ID)
Available from: 2010-11-25 Created: 2010-11-25 Last updated: 2018-09-06Bibliographically approved
Lu, H., Tu, Y., Lin, X., Fang, B., Luo, D. & Laaksonen, A. (2010). Effects of laser irradiation on the structure and optical properties of ZnO thin films. Materials letters (General ed.), 64(19), 2072-2075
Open this publication in new window or tab >>Effects of laser irradiation on the structure and optical properties of ZnO thin films
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2010 (English)In: Materials letters (General ed.), ISSN 0167-577X, E-ISSN 1873-4979, Vol. 64, no 19, p. 2072-2075Article in journal (Refereed) Published
Abstract [en]

The effects of laser irradiation on the surface microstructure and optical properties of ZnO films deposited on glass substrates were investigated experimentally and compared with those of thermal annealing. X-ray diffraction (XRD) and atomic force microscopy (AFM) measurements showed that the irradiation treatment with an Ar+ laser of 514 nm for 5 min improves the crystalline quality of ZnO thin films through increasing the grain size and enhancing the c-axis orientation, with the effects similar to those of the thermal annealing at 500 °C for 1 h. Laser irradiation was found to be more effective both for the relaxation of the residual compressive stress in the as-grown films and for the modification of the surface morphology. A significant increase in the UV absorption and a widening in the optical band-gap of the films were also observed after laser irradiation.

Place, publisher, year, edition, pages
Amsterdam, Netherlands: Elsevier, 2010
Keywords
Thin films, Semiconductors, Laser treatment, Annealing, Microstructure, Optical properties
National Category
Chemical Sciences
Research subject
Chemistry
Identifiers
urn:nbn:se:oru:diva-12633 (URN)10.1016/j.matlet.2010.06.022 (DOI)000281595100012 ()
Available from: 2010-12-01 Created: 2010-12-01 Last updated: 2018-04-19Bibliographically approved
Tian, B., Tu, Y., Strid, Å. & Eriksson, L. A. (2010). Hydroxylation and ring-opening mechanism of an unusual flavoprotein monooxygenase, 2-Methyl-3-hydroxypyridine-5-carboxylic Acid Oxygenase: a theoretical study. Chemistry - A European Journal, 16(8), pp. 2557-2566
Open this publication in new window or tab >>Hydroxylation and ring-opening mechanism of an unusual flavoprotein monooxygenase, 2-Methyl-3-hydroxypyridine-5-carboxylic Acid Oxygenase: a theoretical study
2010 (English)In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 16, no 8, p. 2557-2566Article in journal, News item (Refereed) Published
Abstract [en]

Hybrid meta-GGA density functional theory MPWB1K functional is used to study the hydroxylation and ring-opening mechanism of 2-methyl-3-hydroxypyridine- 5-carboxylic acid oxygenase (MHPCO). This enzyme catalyzes the conversion of 2-methyl-3-hydroxypyridine-5-carboxylic acid (MHPC) to α-(N-acetylamino- methylene) succinic acid (AAMS), which is the essential ring-opening step in the bacterial degradation of Vitamin B6. MHPCO belongs to the flavin-containing aromatic hydroxylases. However, MHPCO is capable of catalyzing a subsequent aromatic ring cleavage reaction to yield acyclic products rather than hydroxylated aromatic ones. Our calculations show that the rearomatization of the hydroxylated intermediate occurs spontaneously in aqueous solution, implying that the ring-opening process occurs inside the enzyme active site with limited water around. The instability of the hydroxylated intermediate of MHPCO is the main reason that the acyclic products are formed. Previously proposed mechanisms for the ring-opening step are studied, and are shown to be less likely to occur (ΔΔG≠298 >35 kcal/mol). Two new pathways with reasonable barrier heights (ΔΔG≠298 <15 kcal/mol) are reported herein, which are in accordance with all experimental information present to date.

Place, publisher, year, edition, pages
Weinheim: Wiley-VCH-Verl., 2010
National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry
Identifiers
urn:nbn:se:oru:diva-8661 (URN)10.1002/chem.200902253 (DOI)000275685800028 ()2-s2.0-77149131524 (Scopus ID)
Available from: 2012-08-06 Created: 2009-11-28 Last updated: 2017-10-02Bibliographically approved
Tu, Y. & Laaksonen, A. (2010). Implementing Quantum Mechanics into Molecular Mechanics: Combined QM/MM Modeling Methods. In: John R. Sabin and Erkki Brändas (Ed.), Combining Quantum Mechanics and Molecular Mechanics:  Some Recent Progresses in QM/MM Methods (pp. 1-15). San Diego, USA: Elsevier
Open this publication in new window or tab >>Implementing Quantum Mechanics into Molecular Mechanics: Combined QM/MM Modeling Methods
2010 (English)In: Combining Quantum Mechanics and Molecular Mechanics:  Some Recent Progresses in QM/MM Methods / [ed] John R. Sabin and Erkki Brändas, San Diego, USA: Elsevier, 2010, p. 1-15Chapter in book (Other academic)
Place, publisher, year, edition, pages
San Diego, USA: Elsevier, 2010
Series
Advances in Quantum Chemistry, ISSN 0065-3276 ; 59
National Category
Chemical Sciences
Research subject
Chemistry
Identifiers
urn:nbn:se:oru:diva-8732 (URN)10.1016/S0065-3276(10)59001-4 (DOI)000277623400001 ()978-0-12-380898-1 (ISBN)
Available from: 2009-12-10 Created: 2009-12-10 Last updated: 2018-04-18Bibliographically approved
Li, X., Zhang, Q., Tu, Y., Ågren, H. & Tian, H. (2010). Modulation of Iridium(III) phosphorescence via photochromic ligands: a density functional theory study. Physical Chemistry, Chemical Physics - PCCP, 12(41), 13730-13736
Open this publication in new window or tab >>Modulation of Iridium(III) phosphorescence via photochromic ligands: a density functional theory study
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2010 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 12, no 41, p. 13730-13736Article in journal (Refereed) Published
Abstract [en]

The photochromic iridium(iii) complex (Py-BTE)(2)Ir(acac) synthesized by Tan et al. [W. Tan et al., Org. Lett. 2009, 11, 161-164] has shown distinct photo-reactivity and photo-controllable phosphorescence. We here present a density functional theory study on the (Py-BTE)(2)Ir(acac) complex to explore the mechanism at the molecular level and to help further design of photochromic iridium(iii) complexes with the desirable properties. The hybrid functional PBE0, with 25% Hartree-Fock exchange, is found to give an optimal structure compared with X-ray crystallographic data. The absorption bands are well reproduced by using time-dependent density functional theory calculations, lending the possibility to assign the metal-to-ligand and intra-ligand charge transfer transitions. The radiative and nonradiative deactivation rate constants, k(r) and k(nr), are rationalized for both the open-ring and closed-ring forms of the complex. The very large k(nr) and small k(r) make the closed-ring form of the complex non-emissive. The triplet reactivity of the Py-BTE ligand is also studied by performing density functional theory calculations on the potential energy surfaces of the ground state and the lowest triplet state

Place, publisher, year, edition, pages
Stockholm, Sweden: KTH Royal Institute of Technology, 2010
National Category
Chemical Sciences
Research subject
Chemistry
Identifiers
urn:nbn:se:oru:diva-12635 (URN)10.1039/c0cp00564a (DOI)000282972400042 ()20877839 (PubMedID)2-s2.0-77958101710 (Scopus ID)
Available from: 2010-12-01 Created: 2010-12-01 Last updated: 2018-04-19Bibliographically approved
Kang, Y., Li, X., Tu, Y., Wang, Q. & Ågren, H. (2010). On the mechanism of protein adsorption onto hydroxylated and nonhydroxylated TiO2 surfaces. The Journal of Physical Chemistry C, 114(34), 14496-14502
Open this publication in new window or tab >>On the mechanism of protein adsorption onto hydroxylated and nonhydroxylated TiO2 surfaces
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2010 (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 114, no 34, p. 14496-14502Article in journal (Refereed) Published
Abstract [en]

Protein adsorption onto implant surfaces is of great importance for the regulation of implant bioactivity. Surface modification of implants is a promising way in the molecular design of biocompatible materials against nonspecific adsorption of proteins. On the basis of these fundamental facts, we focus in this work on the different behavior of protein adsorption on hydroxylated and nonhydroxylated rutile TiO2 (110) surfaces through molecular dynamics simulations. Our investigation indicates that the distribution of the water molecules at the interface induced by the surface modification plays an important role in the protein adsorption. The surface with modified hydroxyl groups was observed to have much greater affinity to the protein, as reflected by the larger protein−surface electrostatic interaction and by the larger amount of adsorbed residues. The highly ordered structure of the modified hydroxyl groups on the hydroxylated surface diminishes the possibility of hydrogen bond formation between the surface and the water molecules above it, which in turn makes it easier for the protein to move closer to the surface with hydroxyl modification.

Place, publisher, year, edition, pages
Washington DC, USA: American Chemical Society (ACS), 2010
National Category
Chemical Sciences
Research subject
Chemistry
Identifiers
urn:nbn:se:oru:diva-12634 (URN)10.1021/jp1037156 (DOI)000281129100026 ()2-s2.0-77956149715 (Scopus ID)
Available from: 2010-12-01 Created: 2010-12-01 Last updated: 2018-04-19Bibliographically approved
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