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John Weare

Title(s)Emeritus Professor, Chemistry and Biochemistry
SchoolVc-academic Affairs
Address9500 Gilman Drive #0340
La Jolla CA 92093
Phone8/5-34--3286
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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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Injury, Illness, and Mental Health Risks in United States Domestic Mariners. J Occup Environ Med. 2020 Aug 05. Lefkowitz RY, Null DB, Slade MD, Redlich CA. PMID: 32769797.
      View in: PubMed   Mentions:    Fields:    
    2. NWChem: Past, present, and future. J Chem Phys. 2020 May 14; 152(18):184102. Aprà E, Bylaska EJ, de Jong WA, Govind N, Kowalski K, Straatsma TP, Valiev M, van Dam HJJ, Alexeev Y, Anchell J, Anisimov V, Aquino FW, Atta-Fynn R, Autschbach J, Bauman NP, Becca JC, Bernholdt DE, Bhaskaran-Nair K, Bogatko S, Borowski P, Boschen J, Brabec J, Bruner A, Cauët E, Chen Y, Chuev GN, Cramer CJ, Daily J, Deegan MJO, Dunning TH, Dupuis M, Dyall KG, Fann GI, Fischer SA, Fonari A, Früchtl H, Gagliardi L, Garza J, Gawande N, Ghosh S, Glaesemann K, Götz AW, Hammond J, Helms V, Hermes ED, Hirao K, Hirata S, Jacquelin M, Jensen L, Johnson BG, Jónsson H, Kendall RA, Klemm M, Kobayashi R, Konkov V, Krishnamoorthy S, Krishnan M, Lin Z, Lins RD, Littlefield RJ, Logsdail AJ, Lopata K, Ma W, Marenich AV, Martin Del Campo J, Mejia-Rodriguez D, Moore JE, Mullin JM, Nakajima T, Nascimento DR, Nichols JA, Nichols PJ, Nieplocha J, Otero-de-la-Roza A, Palmer B, Panyala A, Pirojsirikul T, Peng B, Peverati R, Pittner J, Pollack L, Richard RM, Sadayappan P, Schatz GC, Shelton WA, Silverstein DW, Smith DMA, Soares TA, Song D, Swart M, Taylor HL, Thomas GS, Tipparaju V, Truhlar DG, Tsemekhman K, Van Voorhis T, Vázquez-Mayagoitia Á, Verma P, Villa O, Vishnu A, Vogiatzis KD, Wang D, Weare JH, Williamson MJ, Windus TL, Wolinski K, Wong AT, Wu Q, Yang C, Yu Q, Zacharias M, Zhang Z, Zhao Y, Harrison RJ. PMID: 32414274.
      View in: PubMed   Mentions:    Fields:    
    3. Imaging examination, diagnosis, and control and prevention of nosocomial infection for coronavirus disease 2019: Expert consensus of Hunan radiologist. Zhong Nan Da Xue Xue Bao Yi Xue Ban. 2020 Mar 28; 45(3):221-228. Liu J, Wang W. PMID: 32386011.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCellsPHPublic Health
    4. 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 07 05; 38(18):1631-1639. Pirojsirikul T, Götz AW, Weare J, Walker RC, Kowalski K, Valiev M. PMID: 28470855.
      View in: PubMed   Mentions:    Fields:    
    5. 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. Chen Y, Bylaska EJ, Weare JH. PMID: 29086806.
      View in: PubMed   Mentions:
    6. 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. Elsässer B, Fels G, Weare JH. PMID: 24372083.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    7. 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. Bylaska EJ, Weare JQ, Weare JH. PMID: 23968079.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    8. 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. Bogatko S, Cauët E, Bylaska E, Schenter G, Fulton J, Weare J. PMID: 23315704.
      View in: PubMed   Mentions: 4     Fields:    
    9. Ion association in AlCl3 aqueous solutions from constrained first-principles molecular dynamics. Inorg Chem. 2012 Oct 15; 51(20):10856-69. Cauët E, Bogatko SA, Bylaska EJ, Weare JH. PMID: 23035987.
      View in: PubMed   Mentions:    Fields:    
    10. 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. Fulton JL, Bylaska EJ, Bogatko S, Balasubramanian M, Cauët E, Schenter GK, Weare JH. PMID: 26295879.
      View in: PubMed   Mentions: 1     Fields:    
    11. Parallel implementation of G-point pseudopotential plane-wave DFT with exact exchange. J Comput Chem. 2011 Jan 15; 32(1):54-69. Bylaska EJ, Tsemekhman K, Baden SB, Weare JH, Jonsson H. PMID: 20607748.
      View in: PubMed   Mentions: 2     Fields:    
    12. 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. Cauët E, Bogatko S, Weare JH, Fulton JL, Schenter GK, Bylaska EJ. PMID: 20499974.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    13. Vertical ionization potentials of nucleobases in a fully solvated DNA environment. J Phys Chem B. 2010 May 06; 114(17):5886-94. Cauët E, Valiev M, Weare JH. PMID: 20394358.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    14. 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. Bogatko SA, Bylaska EJ, Weare JH. PMID: 20078102.
      View in: PubMed   Mentions: 1     Fields:    
    15. 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. Bylaska EJ, Holst M, Weare JH. PMID: 26609603.
      View in: PubMed   Mentions: 1     Fields:    
    16. 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. Elsässer B, Valiev M, Weare JH. PMID: 19245210.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    17. Phosphorylation reaction in cAPK protein kinase-free energy quantum mechanical/molecular mechanics simulations. J Phys Chem B. 2007 Nov 29; 111(47):13455-64. Valiev M, Yang J, Adams JA, Taylor SS, Weare JH. PMID: 17983217.
      View in: PubMed   Mentions: 38     Fields:    Translation:Cells
    18. Structure and dynamics of the hydration shells of the Al3+ ion. J Chem Phys. 2007 Mar 14; 126(10):104505. Bylaska EJ, Valiev M, Rustad JR, Weare JH. PMID: 17362073.
      View in: PubMed   Mentions: 4     Fields:    
    19. 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. Valiev M, Kawai R, Adams JA, Weare JH. PMID: 12914447.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    20. Preparation and properties of serum and plasma proteins; crystallization of serum albumins from ethanol water mixtures. J Am Chem Soc. 1947 Jul; 69(7):1753-61. COHN EJ, HUGHES WL, WEARE JH. PMID: 20251413.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
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