Publications

"Design and Implementation of Scientific Software Components to Enable Multi-scale Modeling: The Effective Fragment Potential (QM/EFP) Method", Gaenko, T.L. Windus, M. Sosonkina and M.S. Gordon, J. Chem. Theor. Comp., 2013, 9, 222-231 DOI: 10.1021/ct300614z

"Roles of acetone and diacetone alcohol in coordination and dissociation reactions of uranyl complexes", D. Rios, G. Schoendorff, M.J. Van Stipdonk, M.S. Gordon, T.L. Windus, J.K. Gibson, W.A. de Jong, Inorg. Chem., 2012, 51(23), 12768-12775.

"O + C2H4 potential energy surface: lowest-lying singlet at the multireference level", A. C. West, J. D. Lynch, B. Sellner, H. Lischka, W. L. Hase, T. L. Windus, Theoretical Chemistry Accounts, 2012, 131(10), 1-14.

"O + C2H4 potential energy surface: excited states and biradicals at the multireference level", A. C. West, J. D. Lynch, B. Sellner, H. Lischka, W. L. Hase, T. L. Windus, Theoretical Chemistry Accounts, 2012, 131(3), 1-15.

"Large-scale MP2 calculations on the blue gene architecture using the fragment molecular orbital method", G. D. Fletcher, D. G. Fedorov, G. Dmitri, S. R. Pruitt, T. L. Windus, M. S. Gordon, Journal of Chemical Theory and Computation, 2012, 8(1), 75-79.

"Fragment molecular orbital molecular dynamics with the fully analytic energy gradient", K. R. Brorsen, N. Minezawa, F. Xu, T. L. Windus, M. S. Gordon, Journal of Chemical Theory and Computation, 2012, 8(12), 5008-5012. http://dx.doi.org/10.1021/ct3007869

"Load Balancing of Dynamical Nucleation Theory Monte Carlo Simulations through Resource Sharing Barriers", H. Arafat, J. Dinan, S. Krishnamoorthy, T.L. Windus, and P. Sadayappan, Proc. 26th Intl. Parallel and Distributed Processing Symp. (IPDPS). Shanghai, China. May 2012.

"Direct dynamics simulation of dioxetane formation and decomposition via the singlet O-O-CH2-CH2 biradical: non-RRKM dynamics", R. Sun, K. Park, W. A. de Jong, H. Lischka, T. L. Windus, W. L. Hase, The Journal of Chemical Physics, 2012, 137(4), 044305.

"Can ORMAS be used for nonadiabatic coupling calculations? SiCH4 and butadiene contours", A. C. West, T. L. Windus, Theoretical Chemistry Accounts, 2012, 131(8), 1-11.

"A coarse-grained model for beta-D-glucose based on force matching", S. Markutsya, Y. A. Kholod, A. Devarajan, T. L. Windus, M. S. Gordon and M. H. Lamm, Theoretical Chemistry Accounts, 2012, 131(3), 1-15.

"Large-Scale MP2 Calculations on the Blue Gene Architecture Using the Fragment Molecular Orbital Method", G. D. Fletcher, D. G. Fedorov, S. R. Pruitt, T. L. Windus and M. S. Gordon, J. Chem. Theory Comput., 2012, 8, 75-79.

"Implementation of Dynamical Nucleation Theory Effective Fragment Potentials method for modeling aerosol chemistry", A. Devarajan, T.L. Windus, and M.S. Gordon, J. Phys. Chem. A, 2011, 115(48), 13987-13996.

"On the Formation of "Hypercoordinated" Uranyl Complexes", G. Schoendorff, W.A. de Jong, M.J. Van Stipdonk, J.K. Gibson, D. Rios, M.S. Gordon, T.L. Windus, Inorg. Chem., 2010, 50, 8490-8493.

"NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations", M. Valiev, E.J. Bylaska, D. Wang, K. Kowalski, N. Govind, T.P. Straatsma, J.Nieplocha, E. Apra, T. L. Windus, W. A. de Jong, Comp. Phys. Comm., 2010, 181, 1477-1489.

"Quantum Mechanical Modeling of Sugar Thermochemistry", J. Engelkemier and T.L. Windus in "Computational Modeling in Lignocellulosic Biofuel Production", ACS Symp. Ser., Volume 1052, "Computational Modeling in Lignocellulosic Biofeul Production", eds. M. Nimlos and M Crowley, American Chemical Society: Washington, DC, p. 179-199, 2010.

"Singlet and Triplet Potential Surfaces for the O2 + C2H4 Reaction", K. Park, A.C. West, E. Raheja, B. Sellner, H. Lischka, T.L. Windus, and W.L. Hase, J. Chem. Phys. A, 2010, 133, 184306.

"Steric buttressing in the selective metalation of 4,6-dibromoresorcinol dimethyl ether", G.A. Kraus, I. Jeon, J. Mengwasswer, A.C. West and T.L. Windus, SynLett. 2010, 13, 1955-1958.

"Computational Studies on the Competition Between Nitrile and Water Ligands in Uranyl Complexes", G. Schoendorff, W.A. Wibe, M.S. Gordon, T.L. Windus, J. Chem. Phys. A, 2010, 114, 8902-8912.

"Uncontracted Two-Electron Repulsion Integral Implementation on Multicores and GPUs using the Rys Quadrature Method", A. Asadchev, V. Allada, J. Felder, B. Bode, M.S. Gordon, and T.L. Windus, J. Chem. Theory Comput., 2010, 6, 696-704.

"Development of High Performance Scientific Components for Interoperability of Computing Packages", T.P. Gulabani, M. Sosonkina, M.S. Gordon, C.L. Janssen, J.P. Kenny, H. Netzloff, T.L. Windus, Proceedings of the 2009 Spring Simulation Multiconference (San Diego, California, March 22 - 27, 2009). Society for Computer Simulation International, San Diego, CA, 1-6.

"Non-ancillary achiral tris(oxazolinyl)borate scorpionates Supporting Iridium(I) Complexes", A.V. Pawlikowski, T. Gray, G. Schoendorff, B. Baird, A. Ellern, T. L. Windus, and A.D. Sadow, Inorg. Chim. Acta, 2009, 362, 4517-4525.

"Adaptive Application Composition in Quantum Chemistry", L. Li, J.P. Kenny, M-S. Wu, K. Huck, A. Gaenko, M.S. Gordon, C.L. Janssen, L. Curfman McInnes, H.M. Netzloff, B. Norris, and T.L. Windus, Quality of Software Architectures (QoSA '09) Int. Conf. E. Stroudsburg University, PA, USA, June 22-26, (2009)

"O(3P) + C2H4 Potential Energy Surface: Study at the Multireference Level", A.C. West, J.S. Kretchmer, B. Sellner, K. Park, W.L. Hase, H. Lischka, and T.L. Windus, J. Phys. Chem. A, 2009, 113, 12663-12674. Invited.

"Density Functional Studies on the Complexation and Spectroscopy of Uranyl Ligated with Acetonitrile and Acetone Derivatives", G. Schoendorff, T.L. Windus, and W.A. de Jong, J. Phys. Chem. A, 2009, 113, 12525-12531.

"Nanoscale computations with NWChem", T.L. Windus, E.J. Bylaska, J. Andzelm, N. Govind, J. Comp.and Theor. Nano., 2009, 6, 1297-1304. Invited

"Implementation of Dynamical Nucleation Theory with Quantum Potentials", L.D. Crosby, S.M. Kathmann, T.L. Windus, J. Comp. Chem., 2009, 30, 743-749.

"A Temperature Scaling Method for Markov Chains", L.D. Crosby, T.L. Windus, J. Phys. Chem. A, 2009, 113, 607-616.

"Constructing a performance database for large-scale quantum chemistry packages", M.S. Wu, H. Mori, J. Bentz, T.L. Windus, H. Netzloff, M. Sosonkina, M.S. Gordon, Proceedings of High Performance Computing and Simulation Symposium, 2008, Ottawa, Canada, 393-400.

"A Component Approach to Collaborative Scientific Software Development: Tools and Techniques Utilized by the Quantum Chemistry Science Application Partnership" J.P. Kenny, C.L. Janssen, M.S. Gordon, M. Sosonkina, and T.L. Windus, Scientific Programming, 2008, 16, 287.

"High performance computations using dynamical nucleation theory", T.L. Windus, S.M. Kathmann, L.D. Crosby, J. Phys.: Conf. Ser., 2008, 125, 012017.

"Components for Integral Evaluation in Quantum Chemistry", J.P. Kenny, C.L. Janssen, E.F. Valeev, and T.L. Windus, J. Comp. Chem., 2008, 29, 562-577.

"Tackling Component Interoperability in Quantum Chemistry Software", F. Peng, M.S. Wu, M. Sosonkina, T.L. Windus, J. Bentz, M.S. Gordon, J. Kenny, C.L. Janssen, Proc. of HPC-GECO/CompFrame 2007, 2007, 101-110.

"Direct Dynamics Trajectory Study of F- + CH3OOH Reactive Collisions. An Important Non-IRC Reaction Path", J.G. Lopez, G. Vayner, U. Lourderaj, S.V. Addepalli, S. Kato, W.A. deJong, T.L. Windus, and W.L. Hase, J. Am. Chem. Soc., 2007, 129, 9976-9985.

"Basis Set Exchange: A Community Database for Computational Sciences", K. Schuchardt, B. Didier, T. Elsethagen, L. Sun, V. Gurumoorthi, J. Chase, J. Li, and T.L. Windus, J. Chem. Inf. And Mod., 2007, 47, 1045-1052.

"A Parallel Distributed Data CPHF algorithm for Analytic Hessians", Y. Alexeev, M.W. Schmidt, T.L. Windus, and M.S. Gordon, J. Comp. Chem., 2007, 28, 1685-1694.

"Direct Dynamics Simulations using Hessian-Based Predictor-Corrector Integration Algorithms", U. Lourderaj, K. Song, T.L. Windus, Y. Zhuang, and W.L. Hase, J. Chem. Phys., 2007, 126, 044105.

"Ab Initio and analytic intermolecular potentials for Ar-CH3OH", U. Tasic, Y. Alexeev, G. Vayner, T. D. Crawford, T.L. Windus, and W.L. Hase, Phys.Chem.Chem.Phys., 2006, 8(40), 4678-4684. published with journal cover

"Enabling new capabilities and insights from quantum chemistry by using component architectures", C.L. Janssen, J.P. Kenny, I.M.B. Nielsen, M. Krishnan, V. Gurumoorthi, E.F. Valeev and T.L. Windus, J. Phys.: Conf. Ser., 2006, 46, 220-228.

"Automated Derivation and Parallel Computer Implementation of Renormalized and Active-Space Coupled-Cluster Methods", P. Piecuch, S. Hirata, K. Kowalski, P.-D. Fan, and T.L. Windus, Int. J. Quantum Chem., 2006, 106, 79-97.

"A Component Architecture for High-Performance Scientific Computing", D. E. Bernholdt, B. A. Allan, R. Armstrong, F. Bertrand, K. Chiu, T. L. Dahlgren, K. Damevski, W. R. Elwasif, M. Govindaraju, D. S. Katz, J. A. Kohl, M. Krishnan, G. K. Kumfert, J. Larson, S. Lefantzi, M. J. Lewis, A. D. Malony, L. C. McInnes, J. Nieplocha, B. Norris, S. G. Parker, J. Ray, S. Shende, T. L. Windus, and S. Zhou, Int. J. High Performance Comp. Apps.,2006, 20, 163-202.

"Ab Initio and Analytic Intermolecular Potentials for Ar-CF4", G. Vayner, Y. Alexeev, J. Wang, T.L. Windus, and W.L. Hase, J. Phys. Chem., 2006, 110, 3174-3178.

"Complexation of the Anions Carbonate, Nitrate and Acetate with the Uranyl Dication: Density Functional Studies with Relativistic Effective Core Potentials", W.A. de Jong, E. Apra, T.L. Windus, J.A. Nichols, R.J. Harrison, K. Gutowski and D.A. Dixon, J. Phys. Chem. A, 2005, 109, 11568-11577.

"Multilevel Parallelism in Computational Chemistry using Common Component Architecture", M. Krishnan, Y. Alexeev, T.L. Windus, and J. Nieplocha, Proc. ACM/IEEE Supercomputing 2005 Conference, 2005, 23.

"Component-based software for high-performance scientific computing", Y. Alexeev, B.A. Allan, R.C. Armstrong, D.E. Bernholdt, T.L. Dahlgren, D. Gannon, C.L. Janssen, J.P. Kenny, M. Krishnan, J.A. Kohl, G. Kumfert, L. Curfman McInnes, J. Nieplocha, S.G. Parker, C. Rasmussen, and T.L.Windus, J. Phys.: Conf. Ser., 2005, 16, 536-540.

"Active-space coupled-cluster study of electronic states of Be3 using computer generated programs", K. Kowalski, S. Hirata, M. Wloch, P. Piecuch, and T.L. Windus, J. Chem. Phys., 2005, 123, 074319.

"Thermodynamic Properties of the C5, C6, and C8 n-Alkanes from Ab Initio Electronic Structure Theory", L. Pollack, T.L. Windus, W.A. de Jong, and D.A. Dixon, J. Phys. Chem. A, 2005, 109(31), 6934-6938.

"Accurate Heats of Formation and Acidities for H3PO4, H2SO4, and H2CO3 from Ab Initio Electronic Structure Calculations", Y. Alexeev, T.L. Windus, C. Zhan, D.A. Dixon, Int. J. Quantum Chem., 2005, 102 (5): 775-784.

"Effect of the Ar+Ni(s) Potential on the Cross Section for Ar+CH4/Ni{111} Collision-Induced Desoprtion and the Need for a More Accurate CH4/Ni{111} Potential", L. Sun, K.A. Peterson, Y. Alexeev, T.L. Windus, J. Kindt, and W.L. Hase, J. Chem. Phys., 2005, 122, 44704-44710.

"Component-based integration of chemistry and optimization software", J.P. Kenny, S.J. Benson, Y. Alexeev, J. Sarich, C.L. Janssen, L. Curfman Mcinnes, M. Krishnan, J. Nieplocha, E. Jurrus, C. Fahlstrom, T.L. Windus, J. Comp. Chem., 2004, 25, 1717-1725.

"Very large scale computations of the free energies of eight low-lying structures of arginine in the gas phase", R.J. Gdanitz, W. Cardoen, T.L. Windus, J. Simons, J. Phys. Chem. A, 2004, 108, 515-518

"The energetics of the hydrogenolysis, dehydrohalogenation, and hydrolysis of 4,4-dichloro-diphenyl-trichloroethane from ab initio electronic structure theory," E.J. Bylaska, D.A. Dixon, A.R. Felmy, E. Apra, T.L. Windus, C.G. Zhan, P.G. Tratnyek, J. Phys. Chem. A, 2004, 108, 5883-5893.

"A Collaborative Informatics Infrastructure for Multi-scale Science", J.D. Myers, T.C. Allison, S. Bittner, B. Didier, M. Frenklach, W.H. Green, Jr., Y.L. Ho, J. Hewson, W. Koegler, C. Lansing, D. Leahy, M. Lee, R. McCoy, M. Minkoff, S. Nijsure, G. von Laszewski, D. Montoya, C. Pancerella, R. Pinzon, W. Pitz, L.A. Rahn, B. Ruscic, K. Schuchardt, E. Stephan, A. Wagner, T.L. Windus, C. Yang, Proceedings of the Challenges of Large Applications in Distributed Environments (CLADE) Workshop, 2004, 24-33.

"NWChem: New functionality", T.L. Windus, E.J. Bylaska, M. Dupuis, S. Hirata, L. Pollack, D.M. Smith, T.P. Straatsma, E. Apra, Computational Science ICCS 2003, Pt. IV, Proceedings, Lecture Notes in Computer Science, 2003, 2660, 168-177.

"NWChem for materials science", E. Apra, E.J. Bylaska, D.J. Dean, A. Fortunelli, F. Gao, P.S. Krystic, J.C. Wells, T.L. Windus, Comp. Mat. Sci., 2003, 28, 209-221.

"A new, self-contained asympototic correction scheme to exchange-correlation potentials for time-dependent density functional theory", S. Hirata, C.G. Zhan, E. Apra, T.L. Windus, D.A. Dixon, J. Phys. Chem. A, 2003, 107, 10154-10158.

"Computational Chemistry for Nuclear Waste Characterization and Processing: Relativistic Quantum Chemistry of Actinides", R.J. Harrison, D.E. Bernholdt, B.E. Bursten, W.A. De Jong, D.A. Dixon, K.G. Dyall, W.C. Ermler, G.I. Fann, P.J. Hay, N. Ismail Buchner, R.A. Kendall, J. Li, M.M. Marino, C.J. Marsden, R.L. Martin, M. Minkoff, J.A. Nichols, J. Nieplocha, R.M. Pitzer, L.R. Pratt, H. Schreckenbach, M.C. Seth, R. Shepard, R.L. Stevens, J.L. Tilson, A.F. Wagner, Q. Wang, T.L. Windus, A. Wong, Z. Zhang, Technical Report PNNL-14001, 2002.

"High performance computational chemistry: An overview of NWChem a distributed parallel application", R.A. Kendall, E. Apra, D.E. Bernholdt, E.J. Bylaska, M. Dupuis, G.I. Fann, R.J. Harrison, J.L. Ju, J.A. Nichols, J. Nieplocha, T.P. Straatsma, T.L. Windus, A.T. Wong, Comp. Phys. Comm., 2000, 128, 260-283.

"Internet for the Chemist", K. Flurchick, M. Hurley, J.K. Labanowski, G. Lushington, and T.L. Windus, in preparation for "Computational chemistry : reviews of current trends", Vol. 3, ed. Jerzy Leszczynski, World Scientific 1999.

"6-31G* Basis Set for Atoms K through Zn", V.A. Rassolov, J.A. Pople, M.A. Ratner, T.L. Windus, J. Chem. Phys., 1998, 109, 1223-1229.

"Conformational Study of the Influence of Vibrations on Conduction in Molecular Wires", M. Olson, Y. Mao, T.L. Windus, M. Kemp, M.A. Ratner, N. Leon, V. Mujica, J. Phys. Chem. B, 1998, 102, 941-947.

"Parallel Processing with the Ab Initio Program GAMESS", T.L. Windus, M.W. Schmidt, and M.S. Gordon, Toward Teraflop Computing and New Grand Challenge Applications, Eds. Rajiv K. Kalia and Priya Vashishta, 1995, Nova Science Publishers, Inc., Commack, NY, 189-203.

"Pinnacle: An Approach Toward Object Oriented Quantum Chemistry", T.L. Windus and J.A. Pople, Int. J. Quantum Chem. Symp. Proc., 1995, 29, 485-495.

"Structural Trends in Silicon Atranes", M.W. Schmidt, T.L. Windus, and M.S. Gordon, J. Am. Chem. Soc., 1995, 117, 7480-7486.

"Parallel Implementation of the Electronic Structure Code GAMESS", T.L. Windus, M.W. Schmidt, and M.S. Gordon, ACS Symposium Monograph on Parallel Computing in Chemistry, 1995, 592, 16-28.

"Applications of Parallel GAMESS", K.K. Baldridge, M.S. Gordon, J.H. Jensen, N. Matsunaga, M.W. Schmidt, T.L. Windus, J.A. Boatz, and T.R. Cundari, ACS Symposium Monograph on Parallel Computing in Chemistry, 1995, 592, 29-46.

"Theoretical Investigation of Azaphosphatrane Bases:, T.L. Windus, M.W. Schmidt, and M.S. Gordon, J. Am. Chem. Soc., 1994, 116, 11449-11455.

"Parallel Algorithm for Integral Transformations and GUGA MCSCF", T.L. Windus, M.W. Schmidt, and M.S. Gordon, Theor. Chim. Acta, 1994, 89, 77-88.

"Theoretical Study of Pseudorotation of Pentacoordinated Silicon Anions: SiH5-nXn- (X = F, Cl)", T.L. Windus, M.S. Gordon, L.P. Davis, and L.W. Burggraf, J. Am. Chem. Soc., 1994, 116, 3568-3579.

"Parallel Algorithm for SCF Analytic Hessians I. Small Scale Algorithm', T.L. Windus, M.W. Schmidt, and M.S. Gordon, Chem. Phys. Lett., 1993, 216,375-379.

"Parallel Computing with GAMESS", M.S. Gordon, T.L. Windus, M.W. Schmidt, and N. Matsunaga, CSCC Update, 1993, 13, 6-8.

"General Atomic and Molecular Electronic Structure System GAMESS" M.W. Schmidt, K.K. Baldridge, J.A. Boatz, S.T. Elbert, M.S. Gordon, J.H. Jensen, S. Koseki, N. Matsunaga, K.A. Nguyen, S. Su, T.L. Windus, M. Dupuis, and J.A. Montgomery, Jr., J. Comp. Chem., 1993, 11, 1347-1363.

"Pi-Bond Strengths of H2X=YH2: X = Ge or Sn, and Y = C, Si, Ge, or Sn" T.L. Windus and M.S. Gordon, J. Am. Chem. Soc., 1992, 114, 9559-9568.

"A Detailed Analysis of Pseudorotation in PH4" T.L. Windus and M.S. Gordon, Theor. Chim. Acta, 1992, 83, 21-30.

"Hypercoordination in Group IV MH5 and MH5-" M.T. Carroll, M.S. Gordon, and T.L. Windus, Inorg. Chem., 1992, 31, 825-829.

"A New Twist on Pseudorotation" T.L. Windus, M.S. Gordon, L.W. Burggraf, and L.P. Davis, J. Am. Chem. Soc., 1991, 113, 4356-4357.

"Theoretical Study of Pseudorotation of Pentacoordinated Silicon Anions. 1: The Prototypical SiH5" M.S. Gordon, T.L. Windus, L.P. Davis, and L.W. Burggraf, J. Am. Chem. Soc., 1990, 112, 7167-7171.