John Weare

Title(s)	Emeritus Professor, Chemistry and Biochemistry
School	Vc-academic Affairs
Address	9500 Gilman Drive # La Jolla CA 92093
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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. to make corrections and additions.

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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: 89 Fields:
Bio Biophysics Che Chemistry Phy Physics
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:
Che Chemistry Com Computational Biology
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; PMCID: PMC5374091.

View in: PubMed Mentions: 1
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: 12 Fields:
Che Chemistry
Translation:Animals Cells
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: 3 Fields:
Bio Biophysics Che Chemistry Phy Physics
Translation:Cells
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: 6 Fields:
Che Chemistry
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: 2 Fields:
Che Chemistry
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:
Che Chemistry
Parallel implementation of Γ-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: 3 Fields:
Che Chemistry Com Computational Biology
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: 15 Fields:
Bio Biophysics Che Chemistry Phy Physics
Translation:Cells
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: 7 Fields:
Che Chemistry
Translation:Cells
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: 2 Fields:
Che Chemistry
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: 2 Fields:
Bio Biochemistry Che Chemistry
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: 6 Fields:
Che Chemistry
Translation:Cells
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: 42 Fields:
Che Chemistry
Translation:Cells
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: 6 Fields:
Bio Biophysics Che Chemistry Phy Physics
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: 33 Fields:
Che Chemistry
Translation:Cells
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: 16 Fields:
Che Chemistry
Translation:Humans Cells