Loading...

John Weare

TitleProfessor
InstitutionUniversity of California San Diego
DepartmentChemistry and Biochemistry
Address9500 Gilman Drive #0340
La Jolla CA 92093
Phone858-534-3286
vCardDownload vCard

    Collapse Bibliographic 
    Collapse Publications
    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.
    List All   |   Timeline
    1. Pirojsirikul T, Götz AW, Weare J, Walker RC, Kowalski K, Valiev M. Combined quantum-mechanical molecular mechanics calculations with NWChem and AMBER: Excited state properties of green fluorescent protein chromophore analogue in aqueous solution. J Comput Chem. 2017 Jul 05; 38(18):1631-1639. PMID: 28470855.
      View in: PubMed
    2. Chen Y, Bylaska EJ, Weare J. Weakly bound water structure, bond valence saturation and water dynamics at the goethite (100) surface/aqueous interface: ab initio dynamical simulations. Geochem Trans. 2017 Mar 31; 18(1):3. PMID: 29086806.
      View in: PubMed
    3. Elsässer B, Fels G, Weare J. QM/MM simulation (B3LYP) of the RNase A cleavage-transesterification reaction supports a triester A(N) + D(N) associative mechanism with an O2' H internal proton transfer. J Am Chem Soc. 2014 Jan 22; 136(3):927-36. PMID: 24372083.
      View in: PubMed
    4. Bylaska EJ, Weare JQ, Weare J. Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations. J Chem Phys. 2013 Aug 21; 139(7):074114. PMID: 23968079.
      View in: PubMed
    5. Bogatko S, Cauët E, Bylaska E, Schenter G, Fulton J, Weare J. The aqueous Ca2+ system, in comparison with Zn2+, Fe3+, and Al3+: an ab initio molecular dynamics study. Chemistry. 2013 Feb 25; 19(9):3047-60. PMID: 23315704.
      View in: PubMed
    6. Cauët E, Bogatko SA, Bylaska EJ, Weare J. Ion association in AlCl3 aqueous solutions from constrained first-principles molecular dynamics. Inorg Chem. 2012 Oct 15; 51(20):10856-69. PMID: 23035987.
      View in: PubMed
    7. Fulton JL, Bylaska EJ, Bogatko S, Balasubramanian M, Cauët E, Schenter GK, Weare J. Near-Quantitative Agreement of Model-Free DFT-MD Predictions with XAFS Observations of the Hydration Structure of Highly Charged Transition-Metal Ions. J Phys Chem Lett. 2012 Sep 20; 3(18):2588-93. PMID: 26295879.
      View in: PubMed
    8. Bylaska EJ, Tsemekhman K, Baden SB, Weare J, Jonsson H. Parallel implementation of G-point pseudopotential plane-wave DFT with exact exchange. J Comput Chem. 2011 Jan 15; 32(1):54-69. PMID: 20607748.
      View in: PubMed
    9. Cauët E, Bogatko S, Weare J, Fulton JL, Schenter GK, Bylaska EJ. Structure and dynamics of the hydration shells of the Zn(2+) ion from ab initio molecular dynamics and combined ab initio and classical molecular dynamics simulations. J Chem Phys. 2010 May 21; 132(19):194502. PMID: 20499974.
      View in: PubMed
    10. Cauët E, Valiev M, Weare J. Vertical ionization potentials of nucleobases in a fully solvated DNA environment. J Phys Chem B. 2010 May 06; 114(17):5886-94. PMID: 20394358.
      View in: PubMed
    11. Bogatko SA, Bylaska EJ, Weare J. First principles simulation of the bonding, vibrational, and electronic properties of the hydration shells of the high-spin Fe(3+) ion in aqueous solutions. J Phys Chem A. 2010 Feb 11; 114(5):2189-200. PMID: 20078102.
      View in: PubMed
    12. Bylaska EJ, Holst M, Weare J. Adaptive Finite Element Method for Solving the Exact Kohn-Sham Equation of Density Functional Theory. J Chem Theory Comput. 2009 Apr 14; 5(4):937-48. PMID: 26609603.
      View in: PubMed
    13. Elsässer B, Valiev M, Weare J. A dianionic phosphorane intermediate and transition states in an associative A(N)+D(N) mechanism for the ribonucleaseA hydrolysis reaction. J Am Chem Soc. 2009 Mar 25; 131(11):3869-71. PMID: 19245210.
      View in: PubMed
    14. Valiev M, Yang J, Adams JA, Taylor SS, Weare J. Phosphorylation reaction in cAPK protein kinase-free energy quantum mechanical/molecular mechanics simulations. J Phys Chem B. 2007 Nov 29; 111(47):13455-64. PMID: 17983217.
      View in: PubMed
    15. Bylaska EJ, Valiev M, Rustad JR, Weare J. Structure and dynamics of the hydration shells of the Al3+ ion. J Chem Phys. 2007 Mar 14; 126(10):104505. PMID: 17362073.
      View in: PubMed
    16. Valiev M, Kawai R, Adams JA, Weare J. The role of the putative catalytic base in the phosphoryl transfer reaction in a protein kinase: first-principles calculations. J Am Chem Soc. 2003 Aug 20; 125(33):9926-7. PMID: 12914447.
      View in: PubMed