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    de Jong, Wibe

    TitleComputational Sr Sci/Engr
    SchoolLawrence Berkeley National Lab
    DepartmentComputational Research
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/486-4589
    vCardDownload vCard

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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Takeshita TY, de Jong W, Neuhauser D, Baer R, Rabani E. Stochastic Formulation of the Resolution of Identity: Application to Second Order Møller-Plesset Perturbation Theory. J Chem Theory Comput. 2017 Sep 15. PMID: 28914534.
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      2. Deblonde GJ, Sturzbecher-Hoehne M, Rupert PB, An DD, Illy MC, Ralston CY, Brabec J, de Jong W, Strong RK, Abergel RJ. Chelation and stabilization of berkelium in oxidation state +IV. Nat Chem. 2017 Sep; 9(9):843-849. PMID: 28837177.
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      3. de Jong W, Dau PD, Wilson RE, Marçalo J, Van Stipdonk MJ, Corcovilos TA, Berden G, Martens J, Oomens J, Gibson JK. Revealing Disparate Chemistries of Protactinium and Uranium. Synthesis of the Molecular Uranium Tetroxide Anion, UO4. Inorg Chem. 2017 Mar 20; 56(6):3686-3694. PMID: 28276685.
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      4. Atta-Fynn R, Bylaska EJ, de Jong W. Strengthening of the Coordination Shell by Counter Ions in Aqueous Th4+ Solutions. J Phys Chem A. 2016 Dec 29; 120(51):10216-10222. PMID: 27977185.
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      5. Brown DM, Cho H, de Jong W. Bridging experiment and theory: a template for unifying NMR data and electronic structure calculations. J Cheminform. 2016; 8:8. PMID: 26865863; PMCID: PMC4748447.
      6. Cox RM, Armentrout PB, de Jong W. Reactions of Th(+) + H2, D2, and HD Studied by Guided Ion Beam Tandem Mass Spectrometry and Quantum Chemical Calculations. J Phys Chem B. 2016 Mar 03; 120(8):1601-14. PMID: 26414691.
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      7. Gong Y, de Jong W, Gibson JK. Gas phase uranyl activation: formation of a uranium nitrosyl complex from uranyl azide. J Am Chem Soc. 2015 May 13; 137(18):5911-5. PMID: 25906363.
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      8. Cox RM, Armentrout PB, de Jong W. Activation of CH4 by Th(+) as studied by guided ion beam mass spectrometry and quantum chemistry. Inorg Chem. 2015 Apr 06; 54(7):3584-99. PMID: 25768128.
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      9. Odoh SO, Bylaska EJ, de Jong W. Coordination and hydrolysis of plutonium ions in aqueous solution using Car-Parrinello molecular dynamics free energy simulations. J Phys Chem A. 2013 Nov 27; 117(47):12256-67. PMID: 24168210.
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      10. Odoh SO, Govind N, Schreckenbach G, de Jong W. Cation-cation interactions in [(UO2)2(OH)n](4-n) complexes. Inorg Chem. 2013 Oct 07; 52(19):11269-79. PMID: 24024761.
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      11. van Dam HJ, Vishnu A, de Jong W. A Case for Soft Error Detection and Correction in Computational Chemistry. J Chem Theory Comput. 2013 Sep 10; 9(9):3995-4005. PMID: 26592395.
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      12. Tecmer P, Govind N, Kowalski K, de Jong W, Visscher L. Reliable modeling of the electronic spectra of realistic uranium complexes. J Chem Phys. 2013 Jul 21; 139(3):034301. PMID: 23883021.
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      13. Johnson DF, Bhaskaran-Nair K, Bylaska EJ, de Jong W. Thermodynamics of tetravalent thorium and uranium complexes from first-principles calculations. J Phys Chem A. 2013 Jun 13; 117(23):4988-95. PMID: 23675905.
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      14. de Jong W, Walker AM, Hanwell MD. From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language. J Cheminform. 2013 May 24; 5(1):25. PMID: 23705910; PMCID: PMC3764975.
      15. Mikosch J, Zhang J, Trippel S, Eichhorn C, Otto R, Sun R, de Jong W, Weidemüller M, Hase WL, Wester R. Indirect dynamics in a highly exoergic substitution reaction. J Am Chem Soc. 2013 Mar 20; 135(11):4250-9. PMID: 23324058.
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      16. Rios D, Schoendorff G, Van Stipdonk MJ, Gordon MS, Windus TL, Gibson JK, de Jong W. Roles of acetone and diacetone alcohol in coordination and dissociation reactions of uranyl complexes. Inorg Chem. 2012 Dec 03; 51(23):12768-75. PMID: 23146003.
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      17. Sun R, Park K, de Jong W, Lischka H, Windus TL, Hase WL. Direct dynamics simulation of dioxetane formation and decomposition via the singlet ·O-O-CH2-CH2· biradical: non-RRKM dynamics. J Chem Phys. 2012 Jul 28; 137(4):044305. PMID: 22852616.
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      18. Atta-Fynn R, Johnson DF, Bylaska EJ, Ilton ES, Schenter GK, de Jong W. Structure and hydrolysis of the U(IV), U(V), and U(VI) aqua ions from ab initio molecular simulations. Inorg Chem. 2012 Mar 05; 51(5):3016-24. PMID: 22339109.
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      19. Srebro M, Govind N, de Jong W, Autschbach J. Optical rotation calculated with time-dependent density functional theory: the OR45 benchmark. J Phys Chem A. 2011 Oct 13; 115(40):10930-49. PMID: 21827151.
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      20. Schoendorff G, de Jong W, Van Stipdonk MJ, Gibson JK, Rios D, Gordon MS, Windus TL. On the formation of "hypercoordinated" uranyl complexes. Inorg Chem. 2011 Sep 05; 50(17):8490-3. PMID: 21823574.
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      21. Atta-Fynn R, Bylaska EJ, Schenter GK, de Jong W. Hydration shell structure and dynamics of curium(III) in aqueous solution: first principles and empirical studies. J Phys Chem A. 2011 May 12; 115(18):4665-77. PMID: 21500828.
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      22. van Dam HJ, Vishnu A, de Jong W. Designing a Scalable Fault Tolerance Model for High Performance Computational Chemistry: A Case Study with Coupled Cluster Perturbative Triples. J Chem Theory Comput. 2011 Jan 11; 7(1):66-75. PMID: 26606219.
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      23. Cho H, de Jong W, Sattelberger AP, Poineau F, Czerwinski KR. Comprehensive solid-state NMR characterization of electronic structure in ditechnetium heptoxide. J Am Chem Soc. 2010 Sep 29; 132(38):13138-40. PMID: 20806889.
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      24. Schoendorff G, de Jong W, Gordon MS, Windus TL. Gas phase computational studies on the competition between nitrile and water ligands in uranyl complexes. J Phys Chem A. 2010 Aug 26; 114(33):8902-12. PMID: 20608719.
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      25. de Jong W, Bylaska E, Govind N, Janssen CL, Kowalski K, Müller T, Nielsen IM, van Dam HJ, Veryazov V, Lindh R. Utilizing high performance computing for chemistry: parallel computational chemistry. Phys Chem Chem Phys. 2010 Jul 14; 12(26):6896-920. PMID: 20532308.
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      26. Cho H, de Jong W, Soderquist CZ. Publisher's note: "Probing the oxygen environment in UO(2)(2+) by solid-state 17O nuclear magnetic resonance spectroscopy and relativistic density functional calculations" [J. Chem. Phys. 132, 084501 (2010)]. J Chem Phys. 2010 Mar 14; 132(10):109901. PMID: 20232988.
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      27. Cho H, de Jong W, Soderquist CZ. Probing the oxygen environment in UO(2)(2+) by solid-state 17O nuclear magnetic resonance spectroscopy and relativistic density functional calculations. J Chem Phys. 2010 Feb 28; 132(8):084501. PMID: 20192301.
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      28. Groenewold GS, de Jong W, Oomens J, Van Stipdonk MJ. Variable denticity in carboxylate binding to the uranyl coordination complexes. J Am Soc Mass Spectrom. 2010 May; 21(5):719-27. PMID: 20188585.
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      29. Schoendorff G, Windus TL, de Jong W. Density functional studies on the complexation and spectroscopy of uranyl ligated with acetonitrile and acetone derivatives. J Phys Chem A. 2009 Nov 12; 113(45):12525-31. PMID: 19572680.
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      30. Lipton AS, Heck RW, de Jong W, Gao AR, Wu X, Roehrich A, Harbison GS, Ellis PD. Low temperature 65Cu NMR spectroscopy of the Cu+ site in azurin. J Am Chem Soc. 2009 Oct 07; 131(39):13992-9. PMID: 19746904; PMCID: PMC2782662.
      31. Aubriet F, Gaumet JJ, de Jong W, Groenewold GS, Gianotto AK, McIlwain ME, Van Stipdonk MJ, Leavitt CM. Cerium oxyhydroxide clusters: formation, structure, and reactivity. J Phys Chem A. 2009 Jun 04; 113(22):6239-52. PMID: 19432463.
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      32. Leavitt CM, Bryantsev VS, de Jong W, Diallo MS, Goddard WA, Groenewold GS, Van Stipdonk MJ. Addition of H2O and O2 to acetone and dimethylsulfoxide ligated uranyl(V) dioxocations. J Phys Chem A. 2009 Mar 19; 113(11):2350-8. PMID: 19216506.
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      33. Zhang J, Lourderaj U, Addepalli SV, de Jong W, Hase WL. Quantum chemical calculations of the Cl- + CH3I --> CH3Cl + I- potential energy surface. J Phys Chem A. 2009 Mar 12; 113(10):1976-84. PMID: 19115824.
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      34. Nichols P, Govind N, Bylaska EJ, de Jong W. Gaussian Basis Set and Planewave Relativistic Spin-Orbit Methods in NWChem. J Chem Theory Comput. 2009 Mar 10; 5(3):491-9. PMID: 26610216.
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      35. Kowalski K, Hammond JR, de Jong W, Sadlej AJ. Coupled cluster calculations for static and dynamic polarizabilities of C60. J Chem Phys. 2008 Dec 14; 129(22):226101. PMID: 19071950.
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      36. Groenewold GS, Van Stipdonk MJ, de Jong W, Oomens J, Gresham GL, McIlwain ME, Gao D, Siboulet B, Visscher L, Kullman M, Polfer N. Infrared spectroscopy of dioxouranium(V) complexes with solvent molecules: effect of reduction. Chemphyschem. 2008 Jun 23; 9(9):1278-85. PMID: 18478514.
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      37. Hammond JR, de Jong W, Kowalski K. Coupled-cluster dynamic polarizabilities including triple excitations. J Chem Phys. 2008 Jun 14; 128(22):224102. PMID: 18554001.
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      38. Bryantsev VS, de Jong W, Cossel KC, Diallo MS, Goddard WA, Groenewold GS, Chien W, Van Stipdonk MJ. Two-electron three-centered bond in side-on (eta2) uranyl(V) superoxo complexes. J Phys Chem A. 2008 Jul 03; 112(26):5777-80. PMID: 18540589.
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      39. Lipton AS, Heck RW, Staeheli GR, Valiev M, De Jong WA, Ellis PD. A QM/MM approach to interpreting 67Zn solid-state NMR data in zinc proteins. J Am Chem Soc. 2008 May 14; 130(19):6224-30. PMID: 18410102.
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      40. Nichols P, Bylaska EJ, Schenter GK, de Jong W. Equatorial and apical solvent shells of the UO2 2+ ion. J Chem Phys. 2008 Mar 28; 128(12):124507. PMID: 18376943.
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      41. Jackson VE, Craciun R, Dixon DA, Peterson KA, de Jong W. Prediction of vibrational frequencies of UO2(2+) at the CCSD(T) level. J Phys Chem A. 2008 May 01; 112(17):4095-9. PMID: 18348547.
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      42. de Macedo LG, de Jong W. Fully relativistic calculations on the potential energy surfaces of the lowest 23 states of molecular chlorine. J Chem Phys. 2008 Jan 28; 128(4):041101. PMID: 18247920.
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      43. Groenewold GS, Oomens J, de Jong W, Gresham GL, McIlwain ME, Van Stipdonk MJ. Vibrational spectroscopy of anionic nitrate complexes of UO22+ and Eu3+ isolated in the gas phase. Phys Chem Chem Phys. 2008 Feb 28; 10(8):1192-202. PMID: 18270621.
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      44. Kowalski K, Hammond JR, de Jong W. Linear response coupled cluster singles and doubles approach with modified spectral resolution of the similarity transformed Hamiltonian. J Chem Phys. 2007 Oct 28; 127(16):164105. PMID: 17979317.
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      45. Groenewold GS, Gianotto AK, Cossel KC, Van Stipdonk MJ, Oomens J, Polfer N, Moore DT, de Jong W, McIlwain ME. Mid-infrared vibrational spectra of discrete acetone-ligated cerium hydroxide cations. Phys Chem Chem Phys. 2007 Feb 07; 9(5):596-606. PMID: 17242741.
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      46. Witek HA, Irle S, Zheng G, de Jong W, Morokuma K. Modeling carbon nanostructures with the self-consistent charge density-functional tight-binding method: vibrational spectra and electronic structure of C(28), C(60), and C(70). J Chem Phys. 2006 Dec 07; 125(21):214706. PMID: 17166039.
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      47. Groenewold GS, Gianotto AK, Cossel KC, Van Stipdonk MJ, Moore DT, Polfer N, Oomens J, de Jong W, Visscher L. Vibrational spectroscopy of mass-selected [UO2(ligand)n]2+ complexes in the gas phase: comparison with theory. J Am Chem Soc. 2006 Apr 12; 128(14):4802-13. PMID: 16594717.
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      48. de Jong W, Aprà E, Windus TL, Nichols JA, Harrison RJ, Gutowski KE, Dixon DA. Complexation of the carbonate, nitrate, and acetate anions with the uranyl dication: density functional studies with relativistic effective core potentials. J Phys Chem A. 2005 Dec 22; 109(50):11568-77. PMID: 16354049.
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      49. Pollack L, Windus TL, de Jong W, Dixon DA. Thermodynamic properties of the C5, C6, and C8 n-alkanes from ab initio electronic structure theory. J Phys Chem A. 2005 Aug 11; 109(31):6934-8. PMID: 16834051.
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      50. Dixon DA, de Jong W, Peterson KA, Christe KO, Schrobilgen GJ. Heats of formation of xenon fluorides and the fluxionality of XeF(6) from high level electronic structure calculations. J Am Chem Soc. 2005 Jun 22; 127(24):8627-34. PMID: 15954767.
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      51. Dixon DA, de Jong W, Peterson KA, McMahon TB. Methyl cation affinities of rare gases and nitrogen and the heat of formation of diazomethane. J Phys Chem A. 2005 May 12; 109(18):4073-80. PMID: 16833729.
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      52. Fanourgakis GS, Aprà E, de Jong W, Xantheas SS. High-level ab initio calculations for the four low-lying families of minima of (H2O)20. II. Spectroscopic signatures of the dodecahedron, fused cubes, face-sharing pentagonal prisms, and edge-sharing pentagonal prisms hydrogen bonding networks. J Chem Phys. 2005 Apr 01; 122(13):134304. PMID: 15847462.
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      53. Cho H, de Jong W, McNamara BK, Rapko BM, Burgeson IE. Temperature and isotope substitution effects on the structure and NMR properties of the pertechnetate ion in water. J Am Chem Soc. 2004 Sep 22; 126(37):11583-8. PMID: 15366905.
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      54. Hirata S, Yanai T, de Jong W, Nakajima T, Hirao K. Third-order Douglas-Kroll relativistic coupled-cluster theory through connected single, double, triple, and quadruple substitutions: applications to diatomic and triatomic hydrides. J Chem Phys. 2004 Feb 15; 120(7):3297-310. PMID: 15268484.
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