Publications of Mark S. Gordon as of 18th Jun. 2013
Supplementary Material for selected publications
490. D.D. Kemp and M.S. Gordon, "Aqueous Solvation of Bihalide Ions", J. Phys. Chem. A, 114, 1298 (2010).
491. D.D. Kemp, J. Rintelman, M.S. Gordon, and J.H. Jensen, "Exchange Repulsion between Effective Fragment Potentials and Ab Initio Molecules", Theor. Chem. Accts., Theor. Chem. Accts., 125, 481 (2010).
492. S.R. Pruitt, D.G. Fedorov, K. Kitaura, and M.S. Gordon, "Open-Shell Formulation of the Fragment Molecular Orbital Method", J. Comp. Theoret. Chem., 6, 1 (2010).
493. C.W. Harmon, R.L. Grimm, T.M. McIntire, M.D. Peterson, B. Njegic, V.M. Angel, A. Alshawa, J.S. Underwood, D.J. Tobias, R.B. Gerber, M.S. Gordon, J.C. Hemminger, and S.A. Nizkorodov, "Hygroscopic Growth and Deliquescence of NaCl Nanoparticles Mixed with Surfactant SDS", J. Phys. Chem. B, 114, 2435 (2010).
494. Y. Ge, M.S. Gordon, F. Battaglia, and R.O. Fox, "Theoretical Study of the Pyrolysis of Methyltrichlorosilane in the Gas Phase. 3. Reaction Rate Constants", J. Phys. Chem. A, 114, 2384 (2010).
495. A. Asadchev, V. Allada, J. Felder, B.M. Bode, T.L. Windus, and M.S. Gordon, "Uncontracted Rys Quadrature Implementation of up to g Functions on Graphical Processing Units", J. Comp. Theor. Chem., 6, 696 (2010).
496. B. Njegic, J.D. Raff, B.J. Finlayson-Pitts, M.S. Gordon, and R.B. Gerber, "A Catalytic Role for Water in Atmospheric Production of ClNO?" J. Phys. Chem. A, 114, 4609 (2010).
497. P. Arora, L.V. Slipchenko, S.P. Webb, A. DeFusco, and M.S. Gordon, "Solvent-Induced Frequency Shifts: Configuration Interaction Singles combined with the Effective Fragment Potential Method, J. Phys. Chem. A, 114, 6742 (2010).
498. L.B. Roskop and M.S. Gordon, "An ORMAS-SCF Study of Silicon (100) Surface Clusters", J. Phys Chem. A, 114, 8817 (2010).
499. P. Arora, W. Li, P. Piecuch, J.W. Evans, M. Albao, and M.S. Gordon, "Diffusion of atomic oxygen on the Si(100) surface", J. Phys. Chem. C, 114, 12649 (2010).
500. G. Schoendorff, W.A. de Jong, M.S. Gordon, and T.L. Windus, "Computational Studies on the Competition Between Nitrile and Water Ligands in Uranyl Complexes", J. Phys. Chem., 114, 8902 (2010).
501. J.L. Hodgson, L.B. Roskop, M.S. Gordon, C.Y. Lin, and M.L. Coote, "Side Reactions of Nitroxide Mediated Polymerization: N-O vs. O-C Cleavage of Alkoxyamines", J. Phys. Chem. A, 114, 10458 (2010).
502. K. Hanson, L. Roskop, P.I. Djurovich, F. Zahariev, M.S. Gordon, and M.E. Thompson, "A paradigm for blue- or red-shifted absorption/emission depending on the site of "~H~Rextension as exemplified in the photophysics of 1,3-bis( 2-pyridylimino)isoindolate Platinum(II) chloride and others?], J. Am. Chem. Soc., 132, 16247 (2010).
503. D. Ghosh, D. Kosenko, V. Vanovschi, C.F. Williams, J.M. Herbert, M.S. Gordon, M.W. Schmidt, L.V. Slipchenko, and A.I. Krylov, "Non-covalent interactions in extended systems described by the Effective Fragment Potential method: The ory and application to nucleobase oligomers", J. Phys. Chem. A, 114, 12739 (2010).
504. T. Nagata, D.G. Fedorov, K. Kitaura, and M.S. Gordon, "A combined effective fragment potential-fragment molecular orbital method. II. Analytic gradient and application to the geometry optimization of solvated tetraglycine and chig nolin", J. Chem. Phys., 134, 034110 (2011).
504. S.S. Xantheas and M.S. Gordon, "A Tribute to Klaus Ruedenberg.", J. Phys. Chem. A, 114, 8489 (2010).
505. T. Nagata, D.G. Fedorov, K. Kitaura, and M.S. Gordon, "A combined effective fragment potential-fragment molecular orbital method. II. Analytic gradient and application to the geometry optimization of solvated tetraglycine and chignolin?", J. Chem. Phys., 134, 034110 (2011).
506. . N. Minezawa, N. De Silva, F. Zahariev, and M.S. Gordon, "Implementation of the analytic energy gradient for the combined time-dependent density functional theory/effective fragment potential method. Application to excited-state molecular dynamics simulations?", J. Chem. Phys., 134, 054111 (2011).
507. . Q.A. Smith and M.S. Gordon, "The Electron Affinity of Al13. A Correlated Electronic Structure Study?", J. Phys. Chem. A, 115, 899 (2011).
508. M.S. Gordon, L. Roskop, and A. Devarajan, "Perspective on The Restricted Active Space Self-Consistent Field Method, Implemented with a Split-Graph Unitary Group Approach?", Int. J. Quantum Chem., in press.
509. T. Kudo, T. Taketsugu, and M.S. Gordon, "Ab Initio Molecular Dynamics Study of H2 Formation Inside POSS Compounds?~@~], J. Phys. Chem. A, 115, 2679 (2011).
510. T. Nagata, K. Brorsen, D.G. Fedorov, K. Kitaura, and M.S. Gordon, "Analytic energy gradient in the fragment molecular orbital method?~@~], J. Chem. Phys., 134, 124115 (2011).
511. N. De Silva, B. Njegic, and M.S. Gordon, "Anharmonicity in M+---H2 Complexes?", J. Phys. Chem., 115, 3272 (2011).
512. A. DeFusco and M.S. Gordon, "Solvent-Induced Shifts in the Electronic Spectra of Uracil?", J. Phys. Chem. A, 115, 4574 (2011).
513. Q.T. Smith, M.S. Gordon, and L.V. Slipchenko, "Benzene-Pyridine Interactions Predicted by the Effective Fragment Potential Method?", J. Phys. Chem. A, 115, 4598 (2011).
514. N. Minezawa and M.S. Gordon, "Photoisomerization of Stilbene: A Spin-Flip Density Functional Approach?", J. Phys. Chem., A115, 7901 (2011).
515. L. Roskop and M.S. Gordon, "Quasi-degenerate second-order perturbation theory for occupation restricted multiple active space self-consistent field reference functions ?", J. Chem. Phys., 135, 044101 (2011).
516. S. Nedd, C.-H. Tsai, I.I. Slowing, M. Pruski, and M.S. Gordon, "Using a Reactive Force Field to Correlate Mobilities Obtained from Solid-State 13C NMR on MesoporousSilica Nanoparticle Systems", J. Phys. Chem. C, 115, 16333 (2011).
517. G. Schoendorff, W.A. de Jong, M.J. Van Stipdonk, J.K. Gibson, D. Rios, M.S. Gordon, and T.L. Windus, "On the Formation of Hypercoordinated Uranyl Complexes", Inorg. Chem., 50, 8490 (2011).
518. S. Sok, S. Y. Willow, F. Zahariev, and M.S. Gordon, "Solvent-Induced Shift of the Lowest Singlet pi-pi* Charge-Transfer Excited State of p-Nitroaniline in Water: An Application of the TDDFT/EFP1 Method", J. Phys. Chem. A, 115, 9801 (2011).
519. Q.A. Smith, M.S. Gordon, and L.V. Slipchenko, "An Effective Fragment Potential Study of the Interaction of DNA Bases", J. Phys. Chem. A, 115, 11269 (2011).
520. A. DeFusco, N. Minezawa, L. Slipchenko, F. Zahariev, and M.S. Gordon, "Modeling Solvent Effects on Electronic Excited States", J. Phys. Chem. Lett. (Invited Perspective), 2, 2184 (2011).
521. A. Devarajan, T.L. Windus, and M.S. Gordon, "Implementation of Dynamical Nucleation Theory Effective Fragment Potentials (DNTEFP) method for modeling aerosol chemistry", J. Phys. Chem. A, 115, 13987 (2011).
522. L. Roskop, J.W. Evans, and M.S. Gordon, "The adsorption and diffusion of gallium adatoms on the Si(100)-2x1 reconstructed surface: An MCSCF study utilizing molecular surface clusters", J. Phys. Chem. C, 115, 23488 (2011).
523. S. Sok and M.S. Gordon, "A dash of protons: A theoretical study on the hydrolysis mechanism of 1-substituted sialtranes and their protonated analogs", Comp. Theor. Chem., 987, 2 (2012).
524. M.S. Gordon, D.G. Fedorov, S.R Pruitt, and L.V. Slipchenko, "Fragmentation Methods: A Route to Accurate Calculations on Large Systems", Chem. Rev, 112, 632 (2012) (INVITED).
525. P.J. Carlson, S. Bose, D.W. Armstrong, T. Hawkins, M.S. Gordon and J.W. Petrich, "Structure and Dynamics of the 1-Hydroxyethyl-4-amino-1,2,4-triazolium Nitrate (HEATN) High Energy Ionic Liquid System", J. Phys. Chem. B, 116, 503 (2012)
526. G.D. Fletcher, D.G. Fedorov, S.R. Pruitt, T.L. Windus and M.S. Gordon, "Large-Scale MP2 Calculations on the Blue Gene Architecture Using the Fragment Molecular Orbital Method", J. Chem. Theor. Comp., 8, 75 (2012).
527. S. Markutsya, Y. Kholod, A. Devarajan, T.L. Windus, M.S. Gordon, and M.H. Lamm, "A coarse-grained model for β-D-glucose based on force matching", Thee or. Chem. Accts., 131, 1 (2012).
528. Sarom Leang, Federico Zahariev, and M.S. Gordon, "Benchmarking the performance of time-dependent density functional methods", J. Chem. Phys., 136, 104101 (2012)==> Most downloaded JCP paper in 2012.
529. S.R. Pruitt, M.A. Addicoat, M.A. Collins, and M.S. Gordon, "Fragment Molecular Orbital and Systematic Molecular Fragmentation Methods Applied to Water Clusters", PCCP, 14, 7752 (2012) (INVITED).
530. A. Asadchev and M.S. Gordon, "Mixed Precision Evaluation of Two-Electron Integrals by Rys Quadrature", Comp. Phys. Comm., 183, 1563 (2012).
531. S. Nedd, N.J. DeYonker, A.K. Wilson, P. Piecuch, and M.S. Gordon, "Incorporating a Completely Renormalized Coupled Cluster Approach into a Composite Method for Thermodynamic Properties and Reaction Paths", J. Chem. Phys., 136, 144109 (2012).
532. K. Hansen, L. Roskop, N. Patel, L. Griffe, P.I. Djurovich, M.S. Gordon, and M.E. Thompson, "Photophysical and Electrochemical Properties of 1,3-bis (2-pyridylimino) isoindolate Platinum(II) Derivatives", JCS Dalton Transactions, 41, 8648 (2012).
533. S.R. Pruitt, D.G. Fedorov, and M.S. Gordon, "Geometry Optimizations of Open Shell Systems with the Fragment Molecular Orbital Method", J. Phys. Chem. A, 116, 4965 (2012).
534. Q.A. Smith, K. Ruedenberg, M.S. Gordon, and L.V. Slipchenko, "The dispersion interaction between quantum mechanics and effective fragment potential molecules", J. Chem. Phys., 136, 244107 (2012).
535. N. Minezawa and M.S. Gordon, "Optimizing conical intersections of solvated molecules: The combined spin-flip density functional theory/effective fragment potential method", J. Chem. Phys., 137, 034116 (2012).
536. A. Asadchev and M.S. Gordon, "New Multithreaded Hybrid CPU/GPU Approach to Hartree-Fock", J. Chem. Theory Comp., 8, 4166 (2012).
537. D.-J. Liu, D.M. Ackerman, X. Guo, M.A. Albao, L. Roskop, M.S. Gordon, and J.W. Evans, "Morphological Evolution during Growth and Erosion on Vicinal Si(100) Surfaces: From Electronic Structure Analyses to Atomistic and Coarse-Grained Modeling", Mater. Res. Soc. Symp. Proc., 1411 (2012)
538. K.Brorsen, N. Minezawa, F. Xu, T.L. Windua, and M.S. Gordon, "Fragment molecular orbital dynamics with the fully analytic gradient.", J. Chem. Comp. Theory, 8, 5008 (2012).
539. A. Gaenko, T.L. Windus, M. Sosonkina and M.S. Gordon, "Design and Implementation of Scientific Software Components to Enable Multi-scale Modeling: The Effective Fragment Potential (QM/EFP) Method", J. Chem. Comp. Theory, 9, 222 (2012).
540. P. Xu, B.T. Nguyen, and M.S. Gordon, "Theoretical Study of the Binding of Silane (SiH4) with Borane (BH3), Diborane (B2H6) and Boron Tricholoride (BCl3): The Role of Core-electron Correlation", J. Phys. Chem A, 116, 11668 (2012).
541. N. De Silva, B. Njegic and M.S. Gordon, "Anharmonicity of Weakly Bound Li+---(H2)n (n=1-3) Complexes", J. Phys. Chem. A, 116, 11248 (2012).
542. D. Rios, G. Schoendorff, M.J. Van Stipdonk, M.S. Gordon, T.L. Windus, J.K. Gibson, and W. A. de Jong, "Roles of Acetone and Diacetone Alcohol In Coordination and Dissociation Reactions of Uranyl Complexes", Inorg. Chem., 51, 12768 (2012).
543. M.S. Gordon, Q.A. Smith, P.Xu, and L.V. Slipchenko, "Accurate First Principles Model Potentials for Intermolecular Interactions", Ann. Rev. Phys Chem., 64, 2013.
544. L. Roskop, D.G. Fedorov, and M.S. Gordon, "Diffusion in silica mesoporous molecular sieves modeled with the fragment molecular orbital method", Mol. Phys., 111, 1622 (2013).
545. S.R. Pruitt, C. Steinmann, J.H. Jensen, and M.S. Gordon, "A Fully Integrated Fragment Molecular Orbital/Effective Fragment Potential Method", J. Chem. Theory Comp., 9, 2235 (2013) → 8th most downloaded paper in 2013
546. M.W. Schmidt and M.S. Gordon, "The Decomposition of Hydrazine in the Gas Phase and over an Iridium Catalyst", Z. Phys. Chem., 227, 1301 (2013).
547. L. Kocia, S. Young, Y. Kholod, M. Gordon, M. Fayer, and A. Rappe, "Theoretical Examination of Picosecond Phenol Migration Dynamics in Phenylacetylene Solution", Chem. Phys., 422, 175 (2013).
548. S. Markutsya, A. Devarajan, J.Y. Baluyut, T.L. Windus,M.S. Gordon, and M.H. Lamm, "Evaluation of Coarse-Grained Mapping Schemes for Polysacchararide Chains in Cellulose", J. Chem. Phys., 138, 214018 (2013).
549. F. Zahariev, S.S. Leang, and M.S. Gordon, "On the functional derivatives of meta-generalized gradient approximation (meta-GGA) typ exchange correlation functionals", J. Chem. Phys., 138, 244108 (2013).
550. N. DeSilva, S.Y. Willow and M.S. Gordon, "Solvent Induced Shifts in the UV Spectrum of Amides", J. Phys. Chem. A, 117, 11847 (2013)
551. N. DeSilva, N. Minezawa, and M.S. Gordon, "Excited State Hydrogen Atom Transfer Reaction in Solvated 7-Hydroxy-4-Methyl Coumarin", J. Phys. Chem. B, 138, 15386 (2013)
552. S.R. Pruitt, S.S. Leang, P. Xu, D.G. Fedorov and M.S. Gordon, "Hexamers and Whichamers: Which Hex do you Choose?", Computational and Theoretical Chemistry, 1021, 70 (2013) (Invited).
553. A. Asadchev and M.S. Gordon, "A Fast and Flexible Coupled Cluster Approach", J. Chem. Theory. Comp., 9, 3385 (2013)
554. A. Devarajan, S. Markutsya, M.H. Lamm, X. Cheng, J.C. Smith, J.Y. Baluyut, Y. Kholod, M.S. Gordon, and T.L. Windus, "Ab Initio Molecular Dynamics Study of Molecular Interactions in a Cellulose Ia Microfiber", J. Phys. Chem. B, 117, 10430(2013)
555. K. Yan, J. Duchimaza Heredia, A. Ellern, M.S. Gordon, and A. Sadow, "Lewis base mediated β-elimination and Lewis acid mediated insertion reactions of disilazido zirconium compounds", J. Am. Chem. Soc., 135, 15225 (2013)
556. P. Xu and M.S. Gordon, ""Charge Transfer Interaction using Quasiatomic Minimal-basis Orbitals in the Effective Fragment Potential Method", J. Chem. Phys., 139, 194104 (2013).
557. A. West, M. Schmidt, M. Gordon, and K. Ruedenberg, "A comprehensive analysis of molecule-intrinsic quasi-atomic, bonding and correlating orbitals. I. Hartree-Fock wave functions", J. Chem. Phys., 139, 234107 (2013)
558. L. Roskop, L. Kong, E.F. Valeev, M.S. Gordon, and T.L. Windus, "Assessment of perturbative explicitly-correlated methods for prototypes of multiconfiguration electronic structure", J. Chem. Theory Comp., 10, 90 (2014)
559. Peng Xu, Federico Zahariev, and Mark S. Gordon, "The R-7 dispersion interaction in the general effective fragment potential method", JCTC, 10, 1576 (2014).
560. S.S. Leang, A. P. Rendell, and M.S. Gordon, "Quantum Chemical Calculations using Accelerators:Migrating Matrix Operations to the NVIDIA Kepler GPU and the Intel Xeon Phi", J. Chem. Theory Comp., 10, 908 (2014).
561. F. Zahariev and M.S. Gordon, "Non-linear Response Time-Dependent Density Functional Theory combined with the Effective Fragment Potential Method", J. Chem. Phys., 140, 18A523 (2014)
562. S.R. Pruitt, C. Bertoni, K. Brorsen, and M.S. Gordon, "Efficient and Accurate Fragmentation Methods", Acc. Chem. Research (INVITED), 47, 2786 (2014)
563. P. Xu and M.S. Gordon, "Renormalized Coupled Cluster Approaches in the Cluster-in-Molecule framework: Predicting vertical electron binding energies of the anionic water clusters", J. Phys. Chem, 118, 7548 (2014).
564. J. Dieterich, D. Krisiloff, A Gaenko, F.Libisch, T. Windus, M. Gordon, E. Carter, " Shared-memory parallelization of a local local correlation multi-reference CI program", Comp. Phys. Comm., 185, 3175 (2014)
565. Y. Shao, ..., M.S. Gordon, ..., J.M. Herbert, A.I. Krylov, P.M.W. Gill, and M.H. Head-Gordon, "Advances in molecular quantum chemistry contained in the Q-Chem 4 program package", Mol. Phys., 113, 184 (2014).
566. Y. Harabuchi, K. Keipert, F. Zahariev, T. Taketsugu and M. S. Gordon, "Dynamics simulations with spin-flip time dependent density functional theory: photoisomerization and photocyclization mechanisms of cis-stilbene in ππ* states", J. Phys. Chem. A, 118, 11987 (2014)
567. H. Nakata, M.W. Schmidt, D.G. Fedorov, K. Kitaura, S. Nakamura, and M.S. Gordon, "Efficient molecular dynamics simulations of multiple radical center systems based on the fragment molecular orbital method", J. Phys. Chem. A, 118, 9762 (2014).
568. A. Gaenko, A. DeFusco, S.A. Varganov, T.J.Martinez, and M.S. Gordon, "Interfacing the Ab initio Multiple Spawning Method with Electronic Structure Methods in GAMESS: Photo-decay of trans-Azomethane", J. Phys. Chem. A, 118, 10902 (2014)
569. K.R. Brorsen, F. Zahariev, H. Nakata, D.G. Fedorov, and M.S. Gordon, "Analytic gradient for density functional theory based on the fragment molecular orbital theory", J. Chem. Theory Comp., 10, 5297 (2014)
570. K.R. Brorsen, S.R. Pruitt, and M.S. Gordon, "Surface affinity of the hydronium ion: The effective fragment potential and umbrella sampling", J. Phys. Chem B., 118, 14382 (2014).
571. J. Wang, A. Garcia, D.M. Ackerman, M.S. Gordon, I.I. Slowing, T. Kobayashi, M. Pruski, and J.W. Evans, "Multi-functionalization of nanoporous catalytic materials to enhance reaction yield: Statistical mechanical modeling for conversion reactions with restricted diffusive transport", Mater. Res. Soc. Symp. Proc. Vol. 1641 (2014)
572. J. Conrad and M.S. Gordon, "Modeling Systems with π-π Interactions using the Hartree Fock Method with an Empirical Dispersion Correction", J. Phys. Chem. A, 119, 5377 (2015)
573. C. Carlin and M.S. Gordon, "Ab Initio Calculation of Anion Proton affinity and Ionization Potential: Sometimes less is more", J. Comp. Chem., 36, 597 (2015)
574. E. Guidez and M.S. Gordon, "A dispersion correction derived from first-principles for density functional theory and Hartree Fock theory", J. Phys. Chem. A, 119, 2161 (2015)
575. S.H. Li, D.G. Truhlar, M.W. Schmidt and M.S. Gordon, "Model State Diabatization for Quantum Chemistry", J. Chem. Phys., 142, 064106 (2015).
576. H. Nakata, D.G. Fedorov, F. Zahariev, M.W. Schmidt, M.S. Gordon, and S. Nakamura, "Analytic second derivative of the energy for density functional theory based on the three-body fragment molecular orbital theory", J. Chem. Phys., 142, 124101 (2015)
577. A. Findlater, F. Zahariev, and M.S. Gordon, "A Combined Fragment Molecular Orbital-Cluster in Molecule Approach to Massively Parallel Electron Correlation Calculations for Large Systems", J. Phys. Chem. A, 119, 3587 (2015)
578. K. Ghandi, A.D. Findlater, Z. Mahimwalla, C.S. MacNeil, A. Awoonor Williams, F. Zahariev and M.S. Gordon, "Ultra-fast electron capture by electrosterically-stabilized gold nanoparticles", Nanoscale, 7, 11545 (2015)
579. N. DeSilva, F. Zahariev, B.P. Hay, M.S. Gordon and T.L. Windus, "Conformations of Organophosphine Oxides", J. Phys. Chem. A, 119, 8765 (2015).
580. K.R. Brorsen, S.Y. Willow, S.S. Xantheas, and M.S. Gordon, "The melting temperature of liquid water with the effective fragment potential", J. Phys. Chem. Lett., 6, 3555 (2015).
581. A. C. West, M. W. Schmidt, M. S. Gordon, and K. Ruedenberg, "A comprehensive analysis in terms of molecule-intrinsic, quasi-atomic orbitals. II. Strongly correlated wave functions", J. Phys. Chem., 119, 10360 (2015).
582. A. C. West, M. W. Schmidt, M. S. Gordon, and K. Ruedenberg, "A comprehensive analysis in terms of molecule-intrinsic, quasi-atomic orbitals. III. The covalent bonding structure of urea", J. Phys. Chem., 119, 10368 (2015).
583. A. C. West, M. W. Schmidt, M. S. Gordon, and K. Ruedenberg, "A comprehensive analysis in terms of molecule-intrinsic, quasi-atomic orbitals. IV. Bond breaking and bond forming along the dissociative reaction path of dioxetane", J. Phys. Chem., 119, 10376 (2015).
584. S.R. Pruitt, K. Brorsen and M.S. Gordon, " Ab Initio Investigation of the Aqueous Solvation of Nitrate Ion", Phys. Chem. Chem Phys, 17, 27027 (2015)
585. K. Keipert, G. Mitra, V. Sunriyal, S.S. Leang, M. Sosonkina, A. Rendell, and M.S. Gordon, "Energy Efficient Computational Chemistry: Comparison of X86 and ARM Systems", J. Chem. Theory Comp., 11, 5055 (2015)
586. Y. Harabuchi, Y. Ono, S. Maeda, T. Taketsugu, K. Keipert, and M.S. Gordon, "Non-Totally Symmetric Trifurcation of an SN2 Reaction", J. Comp. Chem., 37, 487 (2016).
587. Ana P. de Lima Batista, Federico Zahariev, Igor I. Slowing, Ataualpa A. C. Braga, Fernando R. Ornellas, Mark S. Gordon, "Silanol-Assisted Carbinolamine Formation in an Amine-Functionalized Mesoporous Silica Surface: Theoretical Investigation by Fragmentation Methods", J. Phys. Chem. B, 120, 1660 (2016).
588. Emilie Guidez, Peng Xu and Mark S. Gordon, "Derivation and Implementation of the Gradient of the R-7 Dispersion Interaction in the Effective Fragment Potential Method", J. Phys. Chem. A., 120, 639 (2016).
589. D.G. Tomlinson, A. Asadchev, and M.S. Gordon, "A New Approach to Second Order Perturbation Theory", J. Chem. Theory Comp., 37, 1274 (2016).
590. B.W. McCann, N. DeSilva, T.L. Windus, M.S. Gordon, B. Moyer, V.S. Bryantsev and B.P. Hay, Computer-Aided Molecular Design of Bis-Phosphene Oxide Lanthanide Extractants, Inorg. Chem., 55, 5787 (2016)
591. S.R. Pruitt, H. Nakata, T. Nagata, M. Mayes, Y. Alexeev, G.D. Fletcher, D.G. Fedorov, K. Kitaura, and M.S. Gordon, "The Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water", J. Chem. Theory Comp., 12, 1423 (2016)
592. D.A. Fedorov, S.R. Pruitt, K. Keipert, M.S. Gordon, and S.A. Varganov, "Ab Initio Multiple Spawning Method for Intersystem Crossing Dynamics: Spin-Forbidden Transitions Between 3B1 and 1A1 States", J. Phys. Chem. A, 120, 2911 (2016)
593. L.B. Roskop, E.F. Valeev, E.A. Carter, M.S. Gordon, and T.L. Windus, "A Spin-Free [2]R12 Basis Set Incompleteness Correction to the Local Multi-Reference Configuration Interaction and the Local Multi-Reference Average Coupled Pair Funtional Methods", J. Chem. Theory. Comp., 12, 3176 (2016)
594. C. Carlin and M.S. Gordon, "Ab Initio Investigation of Cation Proton Affinity and Proton Transfer Ability for Energetic Ionic Liquids", J. Phys. Chem A, 120, 6059 (2016)
595. C. Bertoni and M.S. Gordon, "Analytic gradients for the Effective Fragment Molecular Orbital Method", J. Chem. Theory Comp., 12, 4743 (2016)
596. A. Tiwari, K. Keipert, A. Jundt, S. Leang, M. Laurenzano, M. Gordon, and L. Carrington, "Performance and Energy Analysis of 64-bit ARM Using GAMESS", Proceedings of the Second Annual Workshop on Hardware-Software Co-Design for High Performance Computing, 2015, Article # 8, doi:10.1145/2834899.2834905, 2016.
597. Y. Zhang, M. W. Schmidt, S. Kumari, M. S. Gordon, and D.-S. Yang, "Threshold Ionization and Spin-Orbit Coupling of Ceracyclopropene Formed by Ethylene Dehydrogenation", J. Phys. Chem. A, 120, 6963 (2016)
598. T. Kudo, T. Taketsugu, and M.S. Gordon, "An Ab Initio Molecular Dynamics Study of H2 Formation Inside POSS Compounds. 2. The Effect of an Encapsulated Hydrogen Molecule", J. Phys. Chem A, 120, 8699 (2016)
599. B.Q. Pham and M.S. Gordon, "Thermodynamics and Kinetics of Graphene Chemistry: A Graphene Hydrogenation Prototype Study", Physical Chemistry Chemical Physics, 18, 33274 (2016)
600. D.-J. Liu, F. Zahariev, M.S. Gordon and J.W. Evans, "Predictive Beyond Mean-FieldRate Equations for Multisite Lattice-Gas Models of Catalytic Surface Reactions: CO-Oxidation on Pd(100)", J. Phys. Chem. C, 120, 28639 (2016)
601. K. Yanai, K. Ishimura, A. Nakayama, M.W. Schmidt, M.S. Gordon, and J. Hasegawa, "Electronic Polarization of the Water Environment in Charge-Separated Donor-Acceptor Systems: An Effective Fragment Potential Model System", J. Phys. Chem. A, 120, 10273 (2016)
602. A.C. West, M.W. Schmidt, M.S. Gordon and K. Ruedenberg, "Intrinsic Resolution of Molecular Electronic Wave Functions and energies in terms of Quasi-Atoms and Their Interactions", J. Phys. Chem. A, 121, 1086 (2017). DOI: 10.1021/acs.jpca.6b10911
603. F. Zahariev, N. DeSilva, M.S. Gordon, T.L. Windus, and M. Dick-Perez, "ParFit: A Python-based object oriented program for fitting molecular mechanics parameters to ab-initio data", J. Chem. Inform. Modeling, 57, 391 (2017). DOI: 10.1021/acs.jcim.6b00654
604. C. Bertoni , L.V. Slipchenko, A. Misquitta, and M.S. Gordon, "Multipole moments in the Effective Fragment Potential method", J. Phys. Chem. A, 121, 2056 (2017). DOI: http://dx.doi.org/10.1021/acs.jpca.7b00682
605. J. Mato, K. Keipert, and M.S. Gordon, "Excited state properties of 5-formylcytosine and 5-hydroxymethylcytosine", Mol. Phys., in press.
606. E. Guidez and M.S. Gordon, "Dispersion interactions in water clusters", J. Phys. Chem. A, 121, 3736 (2017) (http://dx.doi.org/10.1021/acs.jpca.6b11403).
607. G.S. Schoendorff, A.C. West, M.W. Schmidt, K. Ruedenberg, A.K. Wilson, and M.S. Gordon "Relativistic Ab Initio Accurate Minimal Basis Sets: Quantitative LUMOs and Oriented Quasi-atomic Orbitals for the Elements Li-Xe", 121, 3588 (2017), in press.
608. B.Q. Pham and M.S. Gordon, " Can Orbitals Really be Observed in STM Expderiments?", J. Phys. Chem. A, in press [DOI: 10.1021/acs.jpca.7b05789]
609. A. Devarajan, A. Gaenko, M.S. Gordon and T.L. Windus, “Nucleation Using the Effective Fragment Potential and Two-Level Parallelism”, in Fragmentation: Toward Accurate Calculations on Complex Molecular Systems, M.S. Gordon Editor, Wiley, 2017.
610. M. W. Schmidt and M.S. Gordon, “The Effect of Boron Clusters on the Ignition Reaction of HNO3 and Dicynanamide-based Ionic Liquids”, J. Phys. Chem. A, 121, 8003 (2017).
611. A. West, J. Duchimaza-Heredia, M.S. Gordon and K. Ruedenberg, “Identification and characterization of molecular bonding structures by ab initio quasi-atomic orbital analyses”, J. Phys Chem. A, 121, 8884 (2017).
612. L.V. Slipchenko, M.S. Gordon and K. Ruedenberg, “Dispersion interactions in QM/EFP”, J. Phys. Chem A., 121, 9495 (2017)
613. V. Mironov, Y. Alexeev, K. Keipert, M. D’Mello, A. Moskovsky and M.S. Gordon, “An Efficient MPI/OpenMPParallelization of the Hartree-Fock Method for the Second Generation of Intel Xeon Processor”, SC17, Salt Lake City, 2017
614. V. Sundriyal, M. Sosonkina, and M.S. Gordon, “Runtime Power Limiting in GAMESS on Dual-Socket Nodes," 2017 International Conference on Computational Science and Computational Intelligence (CSCI), Las Vegas, NV, USA, 2017, pp. 1594-1599. doi: 10.1109/CSCI.2017.277
615. J. Mato and M.S. Gordon, “A general spin-complete spin-flip configuration interaction method”, Phys. Chem. Chem. Phys., 20, 2615 (2018)
616. P. Xu, E.B. Guidez, C. Bertoni and M.S. Gordon, “Perspective: Ab Initio Force Field Methods Derived From Quantum Mechanics”, J. Chem. Phys., 148, 090901 (2018).
617. J. Duchimaza Heredia, K. Ruedenberg and M.S. Gordon, “Quasi-Atomic Bonding Analysis of X-Containing Compounds”, J. Phys. Chem. A, 122, 3442 (2018).
618. V. Sundriyal, K. Keipert, M.Sosonkina, and M.S. Gordon, “Effect of Frequency Scaling Granularity on Energy-Saving Strategies”, Int. J. High Performance Computing: https://doi.org/10.1177/1094342018774405
619. S. Kim, C.M. Kaliszewski, E.B. Guidez and M.S. Gordon, “Benchmarking the Effective Fragment Potential Dispersion Correction on the S22 test set”, J. Phys. Chem. A, 122, 4076 (2018).
620. F. Zahariev, M.S. Gordon, and Mel Levy, “Nodal Variational Principle for Excited States”, Phys. Rev. A, 98, 012144 (2018)
621. L. Schoeberle, E.B. Guidez, and M.S. Gordon, “Benchmarking of the R-7 Anisotropic Dispersion Energy Term on the S22 Dimer Test Set”, J. Phys. Chem. A, 122, 6100 (2018)
622. B. Chan, J. Rintelman, G.P.F. Wood, L. Radom, and M.S. Gordon, “Solvation of the Glycyl Radical”, J. Phys. Chem. A, 122, 7212 (2018)
623. J. Conrad, S.R. Pruitt and M.S. Gordon, “Proton Transfer in 1,2,4-Triazolium Dinitramide: Effect of Microsolvation”, J. Phys. Chem. A, 122, 7443 (2018)
624. N. DeSilva and M.S. Gordon, "Application of an Empirical Dispersion Correction for Modeling Water Clusters", J. Comp. Chem., 40, 310 (2018): DOI:10.1002/jcc.25596
625. J. Duchimaza Heredia, A. D. Sadow, and M.S. Gordon, “A quasi-atomic analysis of three-center two-electron Zr-H-Si interactions”, J. Phys. Chem A, 122, 9563 (2018)
626. V. Sundriyal, M. Sosonkina, B. Westheimier and M.S. Gordon, “Core and Uncore Joint Frequency Scaling Strategy”, J. Computer & Communcations, 6, 2018: 1730892
627. J. Mato and M.S. Gordon, “Analytic Gradients for the Spin-Flip ORMAS-CI Method: Optimizing Minima, Saddle Points, and Conical Intersections, J. Phys. Chem A, 123, 1260 (2019). DOI: 10.1021/acs.jpca.8b11569; publication date (web) 1/15/2019
628. F. Zahariev and M.S. Gordon, “Development of a Combined Quantum Monte Carlo-Effective Fragment Molecular Orbital Method”, Mol. Phys., published onloine, 2/20/2019.
629. S. Koseki, N. Matsunaga, T. Asada, M.W. Schmidt and M.S. Gordon, “Spin-Orbit Coupling Constants in Atoms and Ions of Transition Elements: Comparison of Effective Core Potentials, Model Core Potentials, and All-Electron Methods”, J. Phys. Chem. A, in press.
630. B.Q. Pham and M.S. Gordon, “Compressing the Four-Index Two-Electron Repulsion Integral Matrix Using the Resolution-of-the-Identity Approximation Combined with the Rank Factorization Approximtion”, J. Comp. Theor. Chem., in press
631. D.G. Truhlar, S. Shaik, M.S. Gordon, D. Danovich, and P.C. Hiberty, “Interpretation of Photoelectron Spectroscopy Experiments and (e,2e) Experiments”, Angew. Chem., 58, 12332 (2019)
632. G.S. Schoendorff, A.C. West, M.W. Schmidt, K. Ruedenberg and M.S. Gordon, “Quasi-atomic bond analyses in the sixth period. I. Relativistic accurate atomic minimal basis sets for the elements cesium to radon”, J. Phys. Chem., 123, 5242 (2019)
633. G.S. Schoendorff, M.W. Schmidt, K. Ruedenberg and M.S. Gordon, “Quasi-atomic bond analyses in the sixth period. II. Bond Analysis of cerium oxides”, J. Phys. Chem, 123, 5249 (2019)
634. Y. Harabuchi, R. Tani, N. DeSilva, B. Njegic, M.S. Gordon, and T. Taketsugu, “Anharmonic Vibrational Computations with Quartic Force Field for Curvilinear Vibrational Modes”, J. Chem. Phys., 151, 064104 (2019)
635. J. Conrad, S. Kim, and M.S. Gordon, “Ionic Liquids from a Fragmented Perspective”, PCCP, 21, 16878 (2019).
636. T. Sattasathuchana, P. Xu and M.S. Gordon, “An Accurate Quantum-Based Approach to Explicit Solvent Effects: Interfacing the general effective fragment potential method with ab initio electronic structure theory, J. Phys. Chem. A, 123, 8460 (2019).
637. B.Q. Pham and M.S. Gordon, “A Hybrid Distributed/Shared Memory Model for the RI-MP2 Method in the Fragment Molecular Orbital Method”, J. Chem. Theory Comp., 15, 10 (2019)
638. M. Alkan, P. Xu, and M.S. Gordon, “Many-Body Dispersion in Molecular Clusters”, J. Phys. Chem. A, 123, 8406 (2019).
639. J. Mato and M.S. Gordon, “Analytic Nonadiabatic Coupling Matrix Elements for the Spin-Flip ORMAS Method”, Phys. Chem. Chem. Phys., 22, 1475 (2020)
640. B.Q. Pham and M.S. Gordon, “Development of the FMO/RI-MP2 Fully Analytic Gradient Using a Hybrid Distributed/Shared Memory Programming Model”, J. Chem. Theory Comp., 16, 1039 (2020). DOI: 10.1021/acs.jctc.9b01082
641. Francis Alexander, Ann Almgren, John Bell, Amitava Bhattacharjee, Jacqueline Chen, Phil Colella, David Daniel, Jack DeSlippe, Lori Diachin, Erik Draeger, Anshu Dubey, Thom Dunning, Thomas Evans, Ian Foster, Marianne Francois, Tim Germann, Mark S. Gordon, Salman Habib, Mahantesh Halappanavar, Steven Hamilton, William Hart, Zhenyu (Henry) Huang, Aimee Hungerford, Daniel Kasen, Paul R. C. Kent, Tzanio Kolev, Douglas B. Kothe, Andreas Kronfeld, Ye Luo, Paul Mackenzie, David McCallen, Bronson Messer, Sue Mniszewski, Chris Oehmen, Amedeo Perazzo, Danny Perez, David Richards, William J. Rider, Rob Rieben, Kenneth Roche, Andrew Siegel, Michael Sprague, Carl Steefel, Rick Stevens, Madhava Syamlal, Mark Taylor, John Turner, Jean-Luc Vay, Artur F. Voter, Theresa L. Windus, and Katherine Yelick, “Exascale Computing: Skin in the game”, Phil. Trans.A, 378, 20190056 (2020) https://doi.org/10.1098/rsta.2019.0056
642. Giuseppe M. J. Barca, Colleen Bertoni, Laura Carrington, Dipayan Datta, Nuwan DeSilva, J. Emiliano Deustua, Dmitri G. Fedorov, Jeffrey R. Gour, Anastasia O. Gunina, Emilie Guidez, Taylor Harville, Stephan Irle, Joe Ivanic, Karol Kowalski, Sarom S. Leang, Hui Li, Wei Li, Jesse J. Lutz, Ilias Magoulas, Joani Mato, Vladimir Mironov, Hiroya Nakata, Buu Q. Pham, Piotr Piecuch, David Poole, Spencer R. Pruitt, Alistair P. Rendell, Luke B. Roskop, Klaus Ruedenberg, Tosaporn Sattasathuchana, Michael W. Schmidt, Jun Shen, Lyudmila Slipchenko, Masha Sosonkina, Vaibhav Sundriyal, Ananta Tiwari, Jorge L. Galvez Vallejo, Bryce Westheimer, Marta Włoch, Peng Xu, Federico Zahariev, and Mark S. Gordon, “Recent Developments in the General Atomic and Molecular Electronic Structure System”, J. Chem. Phys., 152, 154201 (2020). https://doi.org/10.1063/5.0005188
643. V. Sundriyal, M.Sosonkina, D. Poole, and M.S. Gordon, “Runtime Power Allocation Approach for GAMESS Hybrid CPU/GPU Implementation”, Concurrency and Computation, 32, e5917 (2020): DOI: 10.1002/cpe.5917
644. M.S. Gordon, G. Barca, S.S. Leang, D. Poole, A.P. Rendell, J.L. Galvez Vallejo, and B. Westheimer, “Novel Computer Architectures and Quantum Chemistry”, J. Phys. Chem. A (invited feature Article), 124, 4557 (2020). DOI: 10.1021/acs.jpca.0c02249
645. D. L. Poole, J.L. Galvez Vallejo and M.S. Gordon, “A New Kid on the Block: Application of Julia to Hartree-Fock Calculations”, J. Chem. Theory Comp., 16, 5006 (2020) DOI: 0.1021/acs.jctc.0c00337
646. G.M.J. Barca, D.L. Poole, J.L. Galvez Vallejo, M. Alkan, C. Bertoni, A.P. Rendell, and M.S. Gordon, “Scaling the Hartree-Fock Matrix Build on Summit”, Supercomputing 2020. DOI:10.1109/SC41405.2020.00085
647. M.S. Gordon and T.L. Windus, “Editorial: Modern Architectures and Their Impact on Electronic Structure Theory”, Chem. Rev., 120, 9015 (2020).
648. E.B. Guidez, A.C. West, M.S. Gordon and K. Ruedenberg, “Why is Si2H2 not linear? An intrinsic quasi-atomic bonding analysis”, J Am. Chem. Soc., 142, 13729 (2020): https://doi.org/10.1021/jacs.0c03082
649. J. Mato, D. Poole, and M.S. Gordon, “The stability and dissociation of ethylenedione (OCCO)”, J. Phys. Chem A, 124, 8209 (2020).
650. P. Xu, Melisa Alkan and M.S. Gordon, “Focus Review: Many-Body Dispersion”, Chem. Rev., Invited, 120, 12343 (2020); DOI 10.1021/acs.chemrev.0c00216
651. G.M.J Barca, J.L. Galvez Vallejo, D.L. Poole, A.P. Rendell, and M.S. Gordon, “A high-perfomance GPU-accelerated Fock build algorithm”, J. Chem. Theor. Comp., 16, 7232 (2020); DOI: 10.1021/acs.jctc.0c00768
652. D. Poole, F. Zahariev, M. Isay-DelViscio, M. Gordon, T, Windus, M. Perez Garcia, “Computational Modeling of diphosphine oxide and glycolimide complexation to lanthanides and extraction from acidic media”, ACS Symposium Series, in press.
653. P.Xu, T. Sattasathuchana, E. Guidez, S.P. Webb, K. Montgomery, H. Yasini, I.F.M. Pedreira and M.S. Gordon, “Computation of Host-Guest Binding Free Energies with a New Quantum Mechanics Based Mining Minima Algorithm”, J. Chem. Phys. (INVITED: Special Collection in Honor of Women in Chemical Physics and Physical Chemistry), in press
654. Yu Lim Kim, Yong Han, James W. Evans, and Mark S. Gordon, “Effective Fragment Potential based Molecular Dynamics Studies of Diffusion in Acetone and Hexane”, J. Phys. Chem. A (Ng special issue), in press. DOI: 10.1021/acs.jpca.1c01865
655. I.G. Gerasimov, F. Zahariev, S.S. Leang, A. Tesliuk, M.S. Gordon, and M.G. Medvedev, “Introducing LibXC into GAMESS(US)”, Mendeleev Letters, in press.
656. G. Schoendorff, K. Ruedenberg, and M.S. Gordon, “Multiple bonding in rhodium monoboride. Quasi-atomic analyses of the ground and low-lying excited states”, J. Phys Chem. A, in press.
657. F. Zahariev and M.S. Gordon, “Combined Quantum Monte Carlo – Effective Fragment Molecular Orbital Method: Fragmentation Across Covalent Bonds”, Phys Chem Chem Phys, 23, 14308 – 14314 (2021). DOI: 10.1039/D0CP06528E
658. V. Brenner, T. Véry, M.W. Schmidt, M.S. Gordon, S. Hoyau, and N. Ben Amor, “Model proteins excited states: MRCI calculations with large active spaces versus CC2 method”, J. Chem. Phys., 154, 214105 (2021) DOI: https://doi.org/10.1063/5.0048146
659. S. Pophale, B. Chapman, B. Pham, C. Yang, C. Daley, C. Bertoni, D. Kulkarni, D. Oryspayev, E. D'Azevedo, H. He, J. Doerfert, K. Zhou, K. Ravikumar, M. Gordon, M. Del Ben, M. Lin, M. Alkan, M. Kruse, O. Hernandez, P. K. Yeung, P. Lin, P. Xu, T. Sattasathuchana, V. Kale and W. Huhn, “Outcomes of OpenMP Hackathon: OpenMP Application Experiences with the Offloading Model (Part I)”, Proceedings of the International Workshop on OpenMP, 2021, accepted for Springer book.
660. S. Pophale, B, Chapman, B. Pham, C. Yang, C. Daley, C. Bertoni, D. Oryspayev, E. D'Azevedo, H. He, J. Doerfert, K. Zhou, K. Ravikumar, M. S. Gordon, M. Del Ben, M. Lin, M. Alkan, M. Kruse, O. Hernandez, P.-K Yeung, P. Lin, P. Xu, T. Sattasathuchana, V. Kale, W. Huhn and D. Kulkarni, “Outcomes of OpenMP Hackathon: OpenMP Application Experiences with the Offloading Model (Part I)”, Proceedings of the International Workshop on OpenMP, 2021, accepted for Springer book.
661. D. Datta and M.S. Gordon, “A Massively Parallel Implementation of the CCSD(T) Method Using the Resolution-of-the-Identity Approximation and a Hybrid Distributed/Shared Memory Parallelization Model”, J. Chem. Theory Comp., in press; DOI: 10.1021/acs.jctc.1c00389
662. F. Zahariev, M.S. Gordon, and M. Levy, “Energy Components in Spin Density Functional Theory”, Phys. Rev. A, 104, 022815 (2021). DOI: https://doi.org/10.1103/PhysRevA.104.022815
663. J.L. Galvez Vallejo, J. Duchimaza Heredia, and M.S. Gordon, “Bonding Analysis of Water Clusters Using Quasi-Atomic Orbitals”, Phys. Chem. Chem.Phys., in press. DOI: 10.1039/D1CP02301B