| Year |
Citation |
Score |
| 2020 |
Mu X, Xu D. QM/MM investigation of substrate binding of subclass B3 metallo-β-lactamase SMB-1 from Serratia marcescents: insights into catalytic mechanism. Journal of Molecular Modeling. 26: 71. PMID 32146530 DOI: 10.1007/S00894-020-4330-Y |
0.401 |
|
| 2020 |
Zhang J, Qin C, Zhong Y, Wang X, Wang W, Hu D, Liu X, Xue C, Zhou R, Shen L, Song Y, Xu D, Lin Z, Guo J, Su H, et al. Atomically precise metal-chalcogenide semiconductor molecular nanoclusters with high dispersibility: Designed synthesis and intracluster photocarrier dynamics Nano Research. 13: 2828-2836. DOI: 10.1007/S12274-020-2936-0 |
0.328 |
|
| 2019 |
Wang R, Xu D. Molecular dynamics investigations of oligosaccharides recognized by family 16 and 22 carbohydrate binding modules. Physical Chemistry Chemical Physics : Pccp. PMID 31535114 DOI: 10.1039/C9Cp04673A |
0.361 |
|
| 2019 |
Shi M, Xu D. Molecular Dynamics Investigations Suggest a Non-specific Recognition Strategy of 14-3-3σ Protein by Tweezer: Implication for the Inhibition Mechanism. Frontiers in Chemistry. 7: 237. PMID 31058132 DOI: 10.3389/Fchem.2019.00237 |
0.327 |
|
| 2019 |
Yang Z, Wei T, Huang H, Yang H, Zhou Y, Xu D. Insights into the biotransformation of 2,4,6-trinitrotoluene by the old yellow enzyme family of flavoproteins. A computational study. Physical Chemistry Chemical Physics : Pccp. PMID 30801593 DOI: 10.1039/C8Cp07873D |
0.373 |
|
| 2018 |
Shi M, Xu D, Zeng J. GPU Accelerated Quantum Virtual Screening: Application for the Natural Inhibitors of New Dehli Metalloprotein (NDM-1) Frontiers in Chemistry. 6: 564. PMID 30515379 DOI: 10.3389/Fchem.2018.00564 |
0.324 |
|
| 2018 |
Xiong J, Zhang C, Xu D. Catalytic mechanism of type C sialidase from Streptococcus pneumoniae: from covalent intermediate to final product. Journal of Molecular Modeling. 24: 297. PMID 30259133 DOI: 10.1007/S00894-018-3822-5 |
0.372 |
|
| 2018 |
Mu X, Xu D. QM/MM Molecular Dynamics Investigations of the Substrate Binding of Leucotriene A4 Hydrolase: Implication for the Catalytic Mechanism. The Journal of Physical Chemistry. B. PMID 29965770 DOI: 10.1021/Acs.Jpcb.8B04203 |
0.405 |
|
| 2018 |
Yang Z, Chen J, Zhou Y, Huang H, Xu D, Zhang C. Understanding the hydrogen transfer mechanism for the biodegradation of 2,4,6-trinitrotoluene catalyzed by pentaerythritol tetranitrate reductase: molecular dynamics simulations. Physical Chemistry Chemical Physics : Pccp. PMID 29683158 DOI: 10.1039/C8Cp00345A |
0.386 |
|
| 2018 |
Li P, Zhang C, Xu D. Molecular dynamics investigations of cello-oligosaccharide recognition by Cel9G-CBM3c from Clostridium cellulovorans. Physical Chemistry Chemical Physics : Pccp. PMID 29399685 DOI: 10.1039/C7Cp07175B |
0.349 |
|
| 2018 |
Liu Q, Dong X, Zou G, Xu D, Lin Z. An inorganic-organic hybrid solid with B5O7(OH)3 clusters bridged and decorated by zinc–amine complexes Inorganic Chemistry Communications. 96: 97-100. DOI: 10.1016/J.Inoche.2018.08.013 |
0.313 |
|
| 2017 |
Xiong J, Xu D. Insights into Catalytic Mechanism of Unsaturated Glucuronyl Hydrolase of Bacillus sp. GL1. The Journal of Physical Chemistry. B. PMID 28071912 DOI: 10.1021/Acs.Jpcb.6B10501 |
0.382 |
|
| 2015 |
Wang K, Li J, Xu D, Luo D, Lin Z. Open-framework beryllium phosphates with a zeolitic CrB4 topology and their structural analogues containing 12-ring channels Crystengcomm. 17: 2162-2167. DOI: 10.1039/C4Ce02226B |
0.306 |
|
| 2015 |
Wang K, Yang N, Xu D, Luo D, Lin Z. New open-framework beryllium phosphates with hcb, sql, and bnn topologies Inorganic Chemistry Communications. 58: 95-98. DOI: 10.1016/J.Inoche.2015.06.020 |
0.334 |
|
| 2014 |
Wang K, Luo D, Xu D, Guo F, Liu L, Lin Z. New open-framework cobalt sulfate-oxalates based on molecular and chain-like building blocks. Dalton Transactions (Cambridge, England : 2003). 43: 13476-9. PMID 25110964 DOI: 10.1039/C4Dt01503G |
0.32 |
|
| 2014 |
Xu D, Cui Q, Guo H. Quantum mechanical/molecular mechanical studies of zinc hydrolases International Reviews in Physical Chemistry. 33: 1-41. DOI: 10.1080/0144235X.2014.889378 |
0.372 |
|
| 2014 |
Shi M, Zhang C, Xie Y, Xu D. Stereoselective inclusion mechanism of ketoprofen into β-cyclodextrin: insights from molecular dynamics simulations and free energy calculations Theoretical Chemistry Accounts. 133. DOI: 10.1007/S00214-014-1556-8 |
0.352 |
|
| 2014 |
Wang K, Luo D, Xu D, Liu L, Lin Z. Open-Framework Beryllium Hydrogen Phosphates with (3,4)-Connected Networks European Journal of Inorganic Chemistry. 2014: 2025-2028. DOI: 10.1002/Ejic.201400113 |
0.308 |
|
| 2013 |
Zheng M, Xu D. New Delhi metallo-β-lactamase I: substrate binding and catalytic mechanism. The Journal of Physical Chemistry. B. 117: 11596-607. PMID 24025144 DOI: 10.1021/jp4065906 |
0.326 |
|
| 2013 |
Liu J, Zheng M, Zhang C, Xu D. "Amide resonance" in the catalysis of 1,2-α-L-fucosidase from Bifidobacterium bifidum. The Journal of Physical Chemistry. B. 117: 10080-92. PMID 23952813 DOI: 10.1021/Jp402110J |
0.381 |
|
| 2013 |
Zheng M, Xu D. Catalytic mechanism of hyaluronate lyase from Streptococcus pneumonia [corrected] : quantum mechanical/molecular mechanical and density functional theory studies. The Journal of Physical Chemistry. B. 117: 10161-72. PMID 23944739 DOI: 10.1021/jp406206s |
0.311 |
|
| 2013 |
Zhang C, Wu S, Xu D. Catalytic mechanism of angiotensin-converting enzyme and effects of the chloride ion. The Journal of Physical Chemistry. B. 117: 6635-45. PMID 23672666 DOI: 10.1021/Jp400974N |
0.383 |
|
| 2013 |
Liu T, Luo D, Xu D, Zeng H, Lin Z. Solvent induced structural variation in magnesium carboxylate frameworks Inorganic Chemistry Communications. 29: 110-113. DOI: 10.1016/J.Inoche.2012.12.017 |
0.313 |
|
| 2012 |
Zheng M, Zhang H, Xu D. Initial events in the degradation of hyaluronan catalyzed by hyaluronate lyase from Streptococcus [corrected] pneumoniae: QM/MM simulation. The Journal of Physical Chemistry. B. 116: 11166-72. PMID 22916709 DOI: 10.1021/jp306754a |
0.311 |
|
| 2011 |
Thomas PW, Zheng M, Wu S, Guo H, Liu D, Xu D, Fast W. Characterization of purified New Delhi metallo-β-lactamase-1. Biochemistry. 50: 10102-13. PMID 22029287 DOI: 10.1021/Bi201449R |
0.33 |
|
| 2011 |
Wu S, Zhang C, Cao R, Xu D, Guo H. pH-Dependent reactivity for glycyl-L-tyrosine in carboxypeptidase-A-catalyzed hydrolysis. The Journal of Physical Chemistry. B. 115: 10360-7. PMID 21732684 DOI: 10.1021/Jp2046504 |
0.366 |
|
| 2011 |
Wang X, Wu S, Xu D, Xie D, Guo H. Inhibitor and substrate binding by angiotensin-converting enzyme: quantum mechanical/molecular mechanical molecular dynamics studies. Journal of Chemical Information and Modeling. 51: 1074-82. PMID 21520937 DOI: 10.1021/Ci200083F |
0.353 |
|
| 2011 |
Smith CR, Smith GK, Yang Z, Xu D, Guo H. Quantum mechanical/molecular mechanical study of anthrax lethal factor catalysis Theoretical Chemistry Accounts. 128: 83-90. DOI: 10.1007/S00214-010-0765-Z |
0.375 |
|
| 2010 |
Wu S, Xu D, Guo H. QM/MM studies of monozinc β-lactamase CphA suggest that the crystal structure of an enzyme-intermediate complex represents a minor pathway. Journal of the American Chemical Society. 132: 17986-8. PMID 21138257 DOI: 10.1021/Ja104241G |
0.323 |
|
| 2010 |
Wu S, Zhang C, Xu D, Guo H. Catalysis of carboxypeptidase A: promoted-water versus nucleophilic pathways. The Journal of Physical Chemistry. B. 114: 9259-67. PMID 20583802 DOI: 10.1021/Jp101448J |
0.397 |
|
| 2009 |
Smith GK, Ke Z, Hengge AC, Xu D, Xie D, Guo H. Active-site dynamics of SpvC virulence factor from Salmonella typhimurium and density functional theory study of phosphothreonine lyase catalysis. The Journal of Physical Chemistry. B. 113: 15327-33. PMID 19715325 DOI: 10.1021/Jp9052677 |
0.369 |
|
| 2009 |
Xu D, Guo H. Quantum mechanical/molecular mechanical and density functional theory studies of a prototypical zinc peptidase (carboxypeptidase A) suggest a general acid-general base mechanism. Journal of the American Chemical Society. 131: 9780-8. PMID 19552427 DOI: 10.1021/Ja9027988 |
0.433 |
|
| 2008 |
Li L, Li Z, Wang C, Xu D, Mariano PS, Guo H, Dunaway-Mariano D. The electrostatic driving force for nucleophilic catalysis in L-arginine deiminase: a combined experimental and theoretical study. Biochemistry. 47: 4721-32. PMID 18366187 DOI: 10.1021/Bi7023496 |
0.38 |
|
| 2008 |
Xu D, Guo H. Ab initio QM/MM studies of the phosphoryl transfer reaction catalyzed by PEP mutase suggest a dissociative metaphosphate transition state. The Journal of Physical Chemistry. B. 112: 4102-8. PMID 18331021 DOI: 10.1021/Jp0776816 |
0.38 |
|
| 2008 |
Zhou S, Xie D, Xu D, Guo H, Field RW. Theoretical emission spectra of HNC(over(A, ̃)1 A″) on a new ab initio potential energy surface Chemical Physics Letters. 455: 145-150. DOI: 10.1016/J.Cplett.2008.02.064 |
0.317 |
|
| 2007 |
Xu D, Guo H, Cui Q. Antibiotic deactivation by a dizinc beta-lactamase: mechanistic insights from QM/MM and DFT studies. Journal of the American Chemical Society. 129: 10814-22. PMID 17691780 DOI: 10.1021/Ja072532M |
0.42 |
|
| 2007 |
Zhang L, Xie D, Xu D, Guo H. Supermolecule density functional calculations suggest a key role for solvent in alkaline hydrolysis of p-nitrophenyl phosphate. Chemical Communications (Cambridge, England). 1638-40. PMID 17530085 DOI: 10.1039/B617946K |
0.326 |
|
| 2007 |
Wang C, Xu D, Zhang L, Xie D, Guo H. Molecular dynamics and density functional studies of substrate binding and catalysis of arginine deiminase. The Journal of Physical Chemistry. B. 111: 3267-73. PMID 17388453 DOI: 10.1021/Jp067541G |
0.363 |
|
| 2007 |
Xu D, Guo H, Cui Q. Antibiotic binding to dizinc beta-lactamase L1 from Stenotrophomonas maltophilia: SCC-DFTB/CHARMM and DFT studies. The Journal of Physical Chemistry. A. 111: 5630-6. PMID 17388313 DOI: 10.1021/Jp068746S |
0.373 |
|
| 2006 |
Riccardi D, Schaefer P, Yang Y, Yu H, Ghosh N, Prat-Resina X, König P, Li G, Xu D, Guo H, Elstner M, Cui Q. Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes. The Journal of Physical Chemistry. B. 110: 6458-69. PMID 16570942 DOI: 10.1021/Jp056361O |
0.358 |
|
| 2006 |
Xu D, Xie D, Guo H. Catalytic mechanism of class B2 metallo-beta-lactamase. The Journal of Biological Chemistry. 281: 8740-7. PMID 16423823 DOI: 10.1074/Jbc.M512517200 |
0.407 |
|
| 2006 |
Wu J, Xu D, Lu X, Wang C, Guo H, Dunaway-Mariano D. Contributions of long-range electrostatic interactions to 4-chlorobenzoyl-CoA dehalogenase catalysis: a combined theoretical and experimental study. Biochemistry. 45: 102-12. PMID 16388585 DOI: 10.1021/Bi051477W |
0.391 |
|
| 2005 |
Xie D, Xu D, Zhang L, Guo H. Theoretical study of general base-catalyzed hydrolysis of aryl esters and implications for enzymatic reactions. The Journal of Physical Chemistry. B. 109: 5259-66. PMID 16863192 DOI: 10.1021/Jp0506181 |
0.404 |
|
| 2005 |
Xu D, Guo H, Liu Y, York DM. Theoretical studies of dissociative phosphoryl transfer in interconversion of phosphoenolpyruvate to phosphonopyruvate: solvent effects, thio effects, and implications for enzymatic reactions. The Journal of Physical Chemistry. B. 109: 13827-34. PMID 16852731 DOI: 10.1021/Jp051042I |
0.373 |
|
| 2005 |
Zhang L, Xie D, Xu D, Guo H. Reactivity of metaphosphate and thiometaphosphate in water: a DFT study. The Journal of Physical Chemistry. A. 109: 11295-303. PMID 16331914 DOI: 10.1021/Jp054430T |
0.323 |
|
| 2005 |
Xu D, Zhou Y, Xie D, Guo H. Antibiotic binding to monozinc CphA beta-lactamase from Aeromonas hydropila: quantum mechanical/molecular mechanical and density functional theory studies. Journal of Medicinal Chemistry. 48: 6679-89. PMID 16220984 DOI: 10.1021/Jm0505112 |
0.401 |
|
| 2005 |
Xu D, Guo H. Electrostatic influence of active-site waters on the nucleophilic aromatic substitution catalyzed by 4-chlorobenzoyl-CoA dehalogenase. Febs Letters. 579: 4249-53. PMID 16051230 DOI: 10.1016/J.Febslet.2005.06.056 |
0.354 |
|
| 2005 |
Wang J, Li H, Mei Y, Lou B, Xu D, Xie D, Guo H, Wang W. Direct, facile aldehyde and ketone alpha-selenenylation reactions promoted by L-prolinamide and pyrrolidine sulfonamide organocatalysts. The Journal of Organic Chemistry. 70: 5678-87. PMID 15989353 DOI: 10.1021/Jo0506940 |
0.319 |
|
| 2004 |
Xu D, Wei Y, Wu J, Dunaway-Mariano D, Guo H, Cui Q, Gao J. QM/MM studies of the enzyme-catalyzed dechlorination of 4-chlorobenzoyl-CoA provide insight into reaction energetics. Journal of the American Chemical Society. 126: 13649-58. PMID 15493922 DOI: 10.1021/Ja0460211 |
0.401 |
|
| 2004 |
Yuan L, Feng W, Yamato K, Sanford AR, Xu D, Guo H, Gong B. Highly efficient, one-step macrocyclizations assisted by the folding and preorganization of precursor oligomers. Journal of the American Chemical Society. 126: 11120-1. PMID 15355071 DOI: 10.1021/Ja0474547 |
0.325 |
|
| 2004 |
Xu D, Guo H, Gao J, Cui Q. A QM/MM study of a nucleophilic aromatic substitution reaction catalyzed by 4-chlorobenzoyl-CoA dehalogenase. Chemical Communications (Cambridge, England). 892-3. PMID 15045116 DOI: 10.1039/B401159G |
0.348 |
|
| 2003 |
XU D, GUO H, XIE D. THEORETICAL STUDIES OF $\tilde{A}{}^1
A^{\prime\prime}\to\tilde{X}{}^1 A^\prime$ RESONANCE EMISSION SPECTRA OF HCN/DCN USING SINGLE LANCZOS PROPAGATION METHOD Journal of Theoretical and Computational Chemistry. 2: 639-648. DOI: 10.1142/S0219633603000707 |
0.302 |
|
| 2003 |
Xu D, Guo H, Zou S, Bowman J. A scaled ab initio potential energy surface for acetylene and vinylidene Chemical Physics Letters. 377: 582-588. DOI: 10.1016/S0009-2614(03)01184-9 |
0.324 |
|
| 2002 |
Xu D, Xie D, Guo H. Theoretical study of predissociation dynamics of HCN/DCN in their first absorption bands The Journal of Chemical Physics. 116: 10626-10635. DOI: 10.1063/1.1480874 |
0.314 |
|
| 2002 |
Xu D, Xie D, Guo H. Predissociation of HCN/DCN in Two Lowest-Lying Singlet Excited States: Effect of Fermi Resonances on Spectra and Dynamics The Journal of Physical Chemistry A. 106: 10174-10183. DOI: 10.1021/Jp021442V |
0.309 |
|
| 2002 |
Xu D, Li G, Xie D, Guo H. Full-dimensional quantum calculations of vibrational energy levels of acetylene (HCCH) up to 13,000 cm−1 Chemical Physics Letters. 365: 480-486. DOI: 10.1016/S0009-2614(02)01503-8 |
0.311 |
|
| 2001 |
Xu D, Xie D, Guo H. A new ab initio potential energy surface of HCN(11A″) and the predissociative resonances of HCN and DCN Chemical Physics Letters. 345: 517-524. DOI: 10.1016/S0009-2614(01)00924-1 |
0.309 |
|
| 2000 |
Xue Y, Xu D, Xie D, Yan G. Density functional theory studies on tautomeric stability and infrared spectra of 2-chloroadenine. Spectrochimica Acta Part a: Molecular and Biomolecular Spectroscopy. 56: 1929-1938. PMID 10989885 DOI: 10.1016/S1386-1425(00)00252-3 |
0.304 |
|
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