Publications of Mark S. Gordon as of 5th Apr. 2007

Supplementary Material for selected publications

303. M.W. Schmidt, M.S. Gordon, and J.A. Boatz, “Cubic Fuels?”, Int. J. Quantum Chemistry, 76, 434 (2000).

304.P.N. Day, R. Pachter, M.S. Gordon and G.N. Merrill, “A Study of Water Clusters Using the Effective Fragment Potential and Monte Carlo Simulated Annealing”, J. Chem. Phys., 112, 2063 (2000)

305. M.S. Gordon and J.H. Jensen, “Perspective on “The Physical Nature of the Chemical Bond”, by Klaus Ruedenberg”, Theor. Chem. Acc., 103, 248 (2000).

306. J. Shoemaker, L.W. Burggraf, and M.S. Gordon, “An Ab Initio Study of the Structure of the Si(100) Surface”, J. Chem. Phys., 112, 2994 (2000).

307. D.G. Fedorov and M.S. Gordon, “A Study of the Relative Importance of One and Two Electron Contributions to Spin-Orbit Coupling”, J. Chem. Phys., 112, 5611 (2000).

308. M.W. Schmidt, G.D. Fletcher, B.M. Bode and M.S. Gordon, “The Distributed Data Interface in GAMESS”, Computer Physics Comm., 128, 190 (2000).

309.    D. Fedorov and M.S. Gordon, “A Theoretical Study of the Reaction Path for Cobalt Cation with Propane”, J. Phys. Chem., 104, 2253 (2000).

310.    T. Kudo and M.S. Gordon, “Theoretical Studies of the Mechanism for the Synthesis of Silsesquioxanes. 2. Cyclosiloxanes (D3 and D4)”, J. Phys. Chem., A104, 4058 (2000).

311. M.A. Freitag, M.S. Gordon, J.H. Jensen and W.J. Stevens, “Evaluation of charge penetration between distributed multipolar expansions”, J. Chem. Phys., 112, 7300 (2000).

312. J. Moc, D.G. Fedorov and M.S. Gordon, “A Theoretical Study of the Reaction of Ti+ with Ethane”, J. Chem. Phys., 112, 10247 (2000).

313. K.R Glaesemann and M.S. Gordon, “Auxiliary basis sets for grid-free density functional theory”, J. Chem. Phys., 112, 10738 (2000).

314 G. Chung, M.W. Schmidt and M.S. Gordon, “An Ab Initio Study of Potential Energy Surfaces for N8 Isomers”, J. Phys. Chem. A, 104, 5647 (2000)

315P. Bandyopadhyay and M.S. Gordon, “A Combined Discrete/Continuum Solvation Model: Application to Glycine”, J. Chem. Phys., 113, 1104 (2000).

316. K. Yagi, T. Taketsugu, K. Hirao and M.S. Gordon, “Direct Vibrational Self-Consistent Field Method: Applications to H2O and H2CO”, J. Chem. Phys., 113, 1005 (2000).

317. M. Pak and M.S. Gordon, “Full CI and CASSCF spin density in boron and carbon atoms”, J. Chem. Phys., 113, 4238 (2000).

318. G. Chung, M. V. Pak, M.S. Gordon, and S. Kass,“Theoretical Study of 2-oxo-3,5- and 4-oxo-2,5-cyclohexadienylidene: Molecular and Electronic Structures”, J. Phys. Chem., A104, 11822 (2000).

319. M.S. Gordon, J. Shoemaker and L.W. Burggraf, “Reply to ‘Comment on “An ab initio cluster study of the structure of the Si(100) surface” [J. Chem. Phys., 112, 2994 (2000)” ‘,J. Chem. Phys., 113, 9355 (2000).

320. M.S. Gordon, S.P. Webb, T. Kudo, B.M. Bode, J. Moc, D.G. Fedorov, and G. Chung, “Titanium Chemistry”, Computational Organometallic Chemistry, T.R. Cundari, Ed., Marcel-Dekker, Inc. NY, 2001

321. M.S. Gordon, M.A. Freitag, P.Bandyopadhyay, J.H. Jensen, V. Kairys, and W.J. Stevens, “The Effective Fragment Potential Method: A QM-Based MM Approach to Modelling Environmental Effects in Chemistry”, J. Phys. Chem. (Feature Article), A105, 293 (2001).

322. C.H. Choi, L. Ruedenberg and M.S. Gordon, “A new parallel optimal-parameter fast multipole method”, J. Comp. Chem., 22, 1484 (2001).

323. Y. Jung, C.H. Choi and M.S. Gordon, “Adsorption of water on the Si(100) surface: An ab initio and QM/MM cluster study”, J. Phys. Chem., 105, 4039 (2001).

324. C.H. Choi and M.S. Gordon, “Chemistry on Silicon Surfaces”, The Chemistry of Organic Silicon Compounds, Vol. 3, Z. Rappaport and Y. Apeloig, Eds., p. 821 (2001).

325. A. Yoshikawa, M.S. Gordon, V.F. Sidorkin and V.A. Pestunovich, “Proton Affinity of the Silatranes and Their Analogs”, Organomet., 20, 927 (2001).

326.M.V. Pak and M.S. Gordon, “The Potential Energy Surfaces for AlO2 using Multi-reference Wave Functions”, Chem. Phys. Lett., 344, 236(2001).

327. A. Datta, P. Bandyopadhyay, Jin Wen, Jacob W. Petrich, and Mark S. Gordon, “Coupling of Large-Amplitude Side Chain Motions to the Excited-State H-Atom Transfer of Perylene Quinones:Application of Theory and Experiment to Calphostin C”, J. Phys. Chem. A, 105, 1057 (2001).

328. D. G. Fedorov, M. S. Gordon, Y. Song, and C. Y. Ng, “A Theoretical Study of Spin-Orbit Coupling Constants for O2+(A2Π3/2,1/2u, v+=0-17 and a4∏5/2,3/2,1/2,-1/2u, v+=0-25)”, J. Chem. Phys., 115, 9606 (2001).

329. J. Rintelman and M.S. Gordon, “Structure and Energetics of the Silicon Carbide Clusters SiC3 and Si2C2”, J. Chem. Phys., 115, 1795 (2001).

330. B.M. Showalter, A. Datta, P.K. Chowdhury, J. Park, P. Bandyopadhyay, S. Kesavan, G.A. Kraus, M.S. Gordon and J. Petrich, “Identification of a Vibrational Frequency Corresponding to H-Atom Translocation in Hypericin”, Photochem. Photobiol., 74, 157 (2001).

331. S. Koseki, D.G. Fedorov, M.W. Schmidt and M.S. Gordon,“Spin-Orbit Splittings in the Third-Row Transition Elements: Comparison of Effective Nuclear Charge and Full Breit-Pauli Calculations”, J. Phys. Chem., A105, 8262 (2001).

332. T.I. Solling, D.M. Smith, L. Radom, M.A. Freitag, and M.S. Gordon, “Multi-reference equivalents of the G2 and G3 methods using reduced Moller-Plesset orders, J. Chem. Phys., 115, 8758 (2001).

333. T. Kudo and M.S. Gordon, “Structures and Stabilities of Titanium Silsesquioxanes”, J. Phys. Chem. A, 105, 11276 (2001).

334. D.G. Fedorov and M.S. Gordon, “Speeding Up Spin-Orbit Calculations”, ACS Symposium Series 828, Low-Lying Potential Energy Surfaces, M.R. Hoffmann and K.G. Dyall, Ed., Oxford Press, 2002.

335. G.D. Fletcher, M.S. Gordon and R.S. Bell, “Gradient of the ZAPT2 Energy”, Theor. Chem. Accts., 107, 57 (2002).

336. Y. Alexeev, R.A. Kendall and M.S. Gordon, “The Distributed Data SCF”, Computer Physics Commun., 143, 69 (2002)

337. S. Koseki, Y. Ishihara, H. Umeda, D.G. Fedorov, and M.S. Gordon, “Dissociation Potential Curves of Low-Lying States in Transition Metal Hydrides. I. Hydrides of Group IV”, J. Phys. Chem., 106, 785 (2002).

338. P. Bandyopadhyay, B. Mennucci, J. Tomasi, and M.S. Gordon“An Effective Fragment – Polarizable Continuum Approach to Solvation: Theory and Application to Glycine”, J. Chem. Phys., 116, 5023 (2002).

339. V.-A. Glezakou, J.A. Boatz, and M.S. Gordon, “Structure and thermodynamics of Carbon- and Carbon/Silicon-precursors to nanostructures”, J. Am. Chem. Soc., 124, 6144 (2002).

340. C.H. Choi, D.-J. Liu, J.W. Evans, and M.S. Gordon, “Passive and Active Oxidation of Si(100) by Atomic Oxygen: A Theoretical Study of Possible Reaction Mechanisms”, J. Am. Chem. Soc., 124, 8730 (2002).

341. C. H. Choi and Mark S. Gordon, “Cycloaddition Reactions of Acrylonitrile on the Si(100) Surface”, J. Am. Chem. Soc., 124, 8730 (2002)..

342. M. Freitag and M.S. Gordon, “On the Electronic Structure of Bis(η5−Cyclopentadienyl) Titanium”, J. Phys. Chem., 106, 7921 (2002).

343. G. Mills, M.S. Gordon and H. Metiu, The Adsorption of oxygen on neutral and negative Aun clusters (n = 2-5), Chem. Phys. Lett., 359, 493 (2002).

344.T. Kudo and M.S. Gordon, “Exploring the Mechanism for the Synthesis of Silsesquioxanes. 3. The Effect of Substituents and Water”, J. Phys. Chem., 106, 11347 (2002).

345. S. A. Varganov, P.V. Avramov, S.G. Ovchinnikov, and M.S. Gordon, “A study of the isomers of C36 fullerene using single and multireference MP2 perturbation theory”, Chem. Phys. Lett., 362, 380 (2002).

346. B. Tejerina and M.S. Gordon, “Insertion Mechanism of N2 and O2 into Tn (n = 8, 10, 12)-Silsesquioxane Framework”, J. Phys. Chem., A106, 11764 (2002).

347. Y. Jung, Y. Akinaga, K.D. Jordan, and M.S. Gordon, “An ab initio study of the structure of two-, three- and five-dimer silicon clusters: An approach to the Si(100) surface”, Theoret. Chem. Accts., 109, 268 (2003).

348. G. Chung and M.S. Gordon, “MCSCF Study of Multiple Bonding between Ti and Main Group Elements C, Si, N and P”, Organometallics, 22, 42 (2003).

349. M.V. Pak and Mark S. Gordon, “Hyperfine coupling tensors for multi-configurational quasi-degenrate perturbation theory (MCQDPT)”, J. Chem. Phys., 118, 40 (2003).

350. C. Aikens and M.S. Gordon, “Electronic Structure and Properties of Y2Ti(μ-X)2TiY2 (X,Y = H, F, Cl, Br) Isomers”, J. Phys. Chem., 107, 104 (2003).

351. S.A. Varganov, R.M. Olson, M.S. Gordon, G. Mills and H. Metiu, “Oxygen adsorption on Au clusters: A Reply to a comment by W.T. Wallace, A.J. Leavitt and R.J. Whetten, Chem. Phys. Lett., 368, 778 (2003).

352. W.L. Hase, K. Song and M.S. Gordon, “Direct Dynamics Simulations”, Computing in Science & Engineering, 5, 36 (2003).

353. M.V. Pak and M.S. Gordon, “Potential energy surfaces for the Al + O2 reaction”, J. Chem. Phys., 118, 4471 (2003).

354. Dana R. Reed, Michael C. Hare, Alireza Fattahi, Gyusung Chung, Mark S. Gordon and Steven R. Kass,

“α,2-, α,3-, and α,4-Dehydrophenol Radical Anions:Formation, Reactivity, and Energetics Leading to the Heats of Formation of α,2-, α,3-, and α,4-Oxocyclohexadienylidene”, J. Am. Chem. Soc., 125, 4643 (2003)

355. I. Adamovic, M.A. Freitag and M.S. Gordon, “Density Functional Theory Based Effective Fragment Potential”, J. Chem. Phys., 118, 6725 (2003).

356. M.S. Gordon, “Theory (Energies and Potential Energy Surfaces)”, in The Encyclopedia of Mass Spectrometry, Vol. 1, Theory and Ion Chemistry, P.B. Armentrout, Ed., Elsevier, Amsterdam, 2003.

357. S.A. Varganov, R.M. Olson, M.S. Gordon, and H. Metiu, “The interaction of oxygen with small gold clusters”,J. Chem. Phys., 119, 2531 (2003).

358. C. M. Aikens, S. P. Webb, R. Bell, G.D. Fletcher, M.W. Schmidt, and M.S. Gordon, “A derivation of the frozen-orbital unrestricted open shell and restricted closed shell MP2 analytic gradient expressions”, Theor. Chem. Accts., 110, 233 (2003).

359. Z. Gan, Y. Alexeev, R.A. Kendall, and M.S. Gordon, “The Parallel Implementation of a Full CI Program”, J. Chem. Phys., 119, 47 (2003).

360. G. Mills, M.S. Gordon, and H. Metiu, “Oxygen adsorption on Au clusters and rough Au(111) surface: The role of surface flatness, electron confinement, excess electrons and band gap”, J. Chem. Phys., 118, 4198 (2003).

361. H.M. Netzloff, M.S. Gordon, K. Christe, A. Vij, W.W. Wilson, V. Vij, and J.A. Boatz, “On the Existence of FN5: A Theoretical and Experimental Study”, J. Phys. Chem. A107, 6638 (2003).

362. Y. Alexeev and M.S. Gordon, “A theoretical study of the bis-silylation reaction of ethylene catalyzed by titanium dichloride”, Organomet., 22, 4111 (2003).

363. D.G. Fedorov, S. Koseki, M.W. Schmidt and M.S. Gordon, “Spin-orbit coupling in Molecules: Chemistry beyond the adiabatic approximation”, Int. Revs. Phys. Chem., 22, 551 (2003).

364. Y. Jung, Y. Shao, M.S. Gordon, D. Doren, and M. Head-Gordon, “Are both symmetric and buckled on Si(100) minima? Density functional and multi-reference perurbation theory calculations”, J. Chem. Phys., 119, 10917 (2003).

365. W.C. Lu, C.Z. Wang, V. Nguyen, M.W. Schmidt, M.S. Gordon and K.M. Ho, “Structures and Fragmentation of Small Silicon Oxide Clusters by ab initio Calculations, J. Phys. Chem., A107, 6936 (2003).

366. D. A. Dixon, D. Feller, K. O. Christe, W. W. Wilson,‡ A. Vij, V. Vij, H. D. B. Jenkins, R. M. Olson, and M. S. Gordon, “Enthalpies of Formation of Gas Phase N3, N3-, N5+, and N5- from Ab Initio Molecular Orbital Theory, Stability Predictions for N5+N3- and N5+N5-, and Experimental Evidence for the Instability of N5+N3-“, J. Am. Chem. Soc., 126, 834 (2003).

367. T. Kudo and M.S. Gordon, “Ab initio Study of the Catalytic Reactivity of Titanosilsesquioxanes and Titanosiloxanes”, J. Phys. Chem. A107, 8756 (2003).

368. H. Tamura and M.S. Gordon, “Multi-configurational SCF study of the SiC (001) surface”, J. Chem. Phys., 119, 10318 (2003).

369. R.M. Olson, M.W. Schmidt, M.S. Gordon, and A.P. Rendell, “Enabling the Efficient Use of SMP Clusters: The GAMESS/DDI Model”, Proc. Supercomputing, 2003

370. D. Fedorov, M.W. Schmidt, S. Koseki, and M.S. Gordon, “Spin-Orbit Coupling and Applications to Chemistry”, “Recent Advances in Relativistic Molecular Theory”, Vol. 5, K. Hirao and Y. Ishikawa, Eds., World Scientific, Singapore, pp. 107-136, 2004.

371. D.G. Fedorov, R.M. Olson, K. Kitaura, M.S. Gordon, and S. Koseki, “A new hierarchical parallelization scheme: Generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO)”, J. Comp. Chem., 25, 872 (2004).

372. M.A. Freitag, B. Hillman, and M.S. Gordon, “Predicting shielding constants in solution using gauge-invariant atomic orbital theory and the effective fragment potential method”, J. Chem. Phys., 120, 1197 (2004).

373. C.H. Choi and M.S. Gordon, “Theoretical Studies of Silicon Surface Reactions with Main Group Adsorbates”, in Computational Materials Chemistry: Methods and Applications, L.A. Curtiss and M.S. Gordon, Eds., pp. 125-190 (2004).

374. P. Zapol, L.A. Curtiss, H. Tamura and M.S. Gordon, “Theoretical Studies of growth Reactions on Diamond Surfaces”, in Computational Materials Chemistry: Methods and Applications, L.A. Curtiss and M.S. Gordon, Eds., pp. 266-307 (2004).

375. M.A. Albao, D.-J. Liu, C.H. Choi, M.S. Gordon, and J.W. Evans, “Atomistic Modeling of Morphological Evolution Due to Competition Between Oxidation and Etching of Si(100)”, Suface Science, 555, 51 (2004).

376. C.M. Aikens and M.S. Gordon, “Parallel Unrestricted MP2 Analytic Gradients using the Distributed Data Interface”, J. Phys. Chem., A108, 3103 (2004).

377. S.A. Varganov, R.M. Olson, M.S. Gordon, G. Mills, and H. Metiu, “A Study of the Reactions of Molecular Hydrogen with Small Gold Clusters”, J. Chem. Phys., 120, 5169 (2004).

379. I. Adamovic and M.S. Gordon, “Potential energy surfaces for the reactions Si + O2”, J. Phys. Chem., A108, 8395 (2004).

380. J.M. Rintelman and M.S. Gordon, “Adsorption of Acetylene on Si(100)-(2x1)”, J. Phys. Chem., B108, 7820 (2004).

381. S. Koseki, Y. Ishihara, D.G. Fedorov, M.W. Schmidt and M.S. Gordon, “Dissociation Potential Curves of Low-Lying States in Transitions Metals. II. Hydrides of Groups 3 and 5”, J. Phys. Chem., 108, 4707 (2004).

382. S. Chretien, M.S. Gordon, and H. Metiu, “Binding of propene on small gold clusters and on Au(111): simple rules for binding sites and relative binding energies”, J. Chem. Phys., 121, 3756 (2004).

383. K. Yagi, K. Hirao, T. Taketsugu, M.W. Schmidt, and M.S. Gordon, “Ab initio vibrational state calculations with a quartic force field: Applications to H2CO, C2H2, CH3OH, CH3CCH, and C6H^”, J. Chem. Phys., 120, 1383 (2004).

384. H.M. Netzloff and M.S. Gordon, “The Effective Fragment Potential: Small Clusters and Radial Distribution Function”, J. Chem. Phys., 121, 2711 (2004).

385. J. Song, M.S. Gordon, C.A. Deakyne, and W. Zheng, “Theoretical Investigation of Acetylcholine (ACh) and Acetylthiocholine (ATCh) Using ab initio and Effective Fragment Potential Methods”, J. Phys. Chem., 108, 11419 (2004)..

386. H. Netzloff and M.S. Gordon, “Fast Fragments: The Development of a Parallel Effective Fragment Potential Method”, J. Comp. Chem., 25, 1926 (2004).

387. I. Adamovic and M. S. Gordon, “Molecular structures and potential energy surfaces for IHI-·Arn (n=1-7)”, J. Phys. Chem., 108, 11042 (2004).

388. S. Chretien, M.S. Gordon, and H. Metiu, “Density functional study of the adsorption of propene on silver clusters, Agmq (m = 1-5; q = 0,1)”, J. Chem. Phys., 121, 9925 (2004).

389. S. Chretien, M.S. Gordon, and H. Metiu, “Density functional study of the adsorption of propene on mixed gold-silver clusters AunAgm: Propensity rules for binding”, J. Chem. Phys., 121, 9931 (2004).

390. Z.M. Loh, R.L. Wilson, D.A. Wild, E.J. Bieske, and M.S. Gordon, “Structures of F—(CH4)n and Cl—(CH4)n (n = 1,2) Anion Clusters Elucidate Through Ab Initio Calculatios and Infrared Spectra”, Aust. J. Chem., 57, 1157 (2004).

391. R.M. Olson, S. Varganov, M.S. Gordon, H. Metiu, S. Chretien, P. Piecuch, K. Kowalski, S. Kucharski, and M. Musial, “Where Does the Planar-to-Nonplanar Turnover Occur in Small Gold Clusters?”, J. Am. Chem. Soc., 127, 1047 (2005).

392. J.M. Rintelman, I. Adamovic, S. Varganov, and M.S. Gordon, “Multi-Reference Second-Order Perturbation Theory: How Size Consistent is ‘Almost Size Consistent’”?, J. Chem. Phys., 122, 044105 (2005).

393. I. Adamovic and M. S. Gordon, “Dynamic polarizability, dispersion coefficient C6, and dispersion energy in the effective fragment potential method”, Mol. Phys., 103, 379 (2005).

394. Y. Jung and M.S. Gordon, “Cycloaddition of benzene on Si(100) and its Surface Conversion”, J. Am. Chem. Soc., 127, 3131 (2005).

395. I. Adamovic and M.S. Gordon, “Solvent Effects on the SN2 Reaction: Application of the Density Functional Theory-Based Effective Fragment Potential Method, J. Phys. Chem., 109, 1629 (2005).

396. K. Das , M. Halder , P. K. Chowdhury , J. Park, Y. Alexeev, M. S. Gordon, and J. W. Petrich, “Hypericin and its perylene quinone analogs:Probing structure, dynamics, and interactions with the environment”, Adv. Photochem., 28, 1 (2005).

397. M.S. Gordon and M.W. Schmidt, “Advances in Electronic Structure Theory: GAMESS a Decade Later”, Theory and Applications of Computational Chemistry, Ch.. 41, C. E. Dykstra, G. Frenking, K.S. Kim, G.E. Scuseria, Eds., Elsevier, 2005.

398. H.S. Lee, C.H. Choi, and M.S. Gordon, “Comparative Study of Surface Cycloadditions of Ethylene and 2-Butene on the Si(100)-2x1 Surface, J. Am. Chem. Soc., 109, 5067 (2005).

399. M.A. Albao, M.M.R. Evans, J. Nogami, D. Zorn, M.S. Gordon, and J.W. Evans, “Monotonically decreasing size distributions for one-dimensional Ga Rows on Si(100)”, Phys. Rev. B, 72, 035426 (2005).

400. H. Tamura and M.S. Gordon, “Ab initio study of nucleation on the diamond (100) surface during chemical vapor deposition with methyl and H radicals”, Chem. Phys. Lett., 406, 197 (2005).

401. D.D. Kemp and M.S. Gordon, “Theoretical Study of the Solvation of Fluorine and Chlorine Anions by Water”, J. Phys. Chem A109, 7688 (2005). [13th most downloaded paper july-sept 2005]

402. Marvin A. Albao, Da-Jiang Liu, Cheol H. Choi, Mark S. Gordon, and J. W. Evans,

“Competitive Etching and Oxidation of Vicinal Si(100) Surfaces”, MRS Proceedings Vol. 859E (2005) JJ3.6

403. T. Taketsugu, K. Yagi, and M.S. Gordon, “A Vibrational Analysis of the 7-Azaindole-Water Complex: Anharmonicities Using the Quartic Force Field, Int. J. Quantum Chem., 104, 758 (2005).

404. T. Kudo, K. Machada, and M.S. Gordon, “Exploring the Mechanism for the Synthesis of Silsesquioxanes. 4. The Synthesis of T8”, J. Phys. Chem., A109, 5424 (2005).

405. H.S. Lee, C.H. Choi, and M.S. Gordon, “Cycloaddition Isomerizations of Adsorbed 1,3-Cyclohexadiene on the Si(100)-2x1 Surface: First Neighbor Interactions”, J. Am. Chem. Soc., 127, 8485 (2005).

406. P.V. Avramov, I. Adamovic, K.-M. Ho, C.Z. Wang, W.C. Lu, and M.S. Gordon, “Potential Energy Surfaces of SimOn Cluster Formation and Isomerization”, J. Phys. Chem., A109, 6294 (2005).

407. G. Krishnamoorthy, S. P. Webb, T. Nguyen, P. K. Chowdhury, M. Halder, N. J. Wills, S. Carpenter, G. A. Kraus, M.S. Gordon, and J. W. Petrich, “Synthesis of Hydroxy and Methoxy Perylene Quinones, Their Spectroscopic and Computational Characterization, and Their Antiviral Activity”, Photochemistry and Photobiology, 81, 924 (2005).

408. R. Becera, S.-J. Bowes, J.S. Ogden, J.P. Cannady, I. Adamovic, M.S. Gordon, M.J. Almond, and R. Walsh, “Time-Resolved Gas-Phase Kinetic and quantum chemical studies of the reaction of silylene with oxygen, PCCP, 7, 2900 (2005).

409. Michael W. Schmidt, Mark S. Gordon, and Jerry A. Boatz, “Triazolium-Based Energetic Ionic Liquids”, J. Phys. Chem., A109, 7285 (2005).

410. Z. M. Loh, R.L. Wilson, D.A. Wild, E. Bieske, and M.S. Gordon, “Infrared Spectra and Ab Initio Calculations for the Cl—(CH4)n (n=1,10) Anion Clusters”, J. Phys. Chem., A109, 8481 (2005).

411. M. Albao, D.-J. Liu, M.S. Gordon, and J.W. Evans, “Simultaneous Etching and Oxidation of Vicinal Si(100) Surfaces: Atomistic Lattice-Gas Modeling of Morphological Evolution”, Phys. Rev. B, 72, 195420 (2005).

412. C.M. Aikens and M.S. Gordon, “Influence of multi-atom bridging ligands on the electronic structure and magnetic properties of homodinuclear titanium molecules:, J. Phys. Chem., 109, 11885 (2005).

413. R.M. Olson, S. Varganov, M.S. Gordon, and H. Metiu, “The Binding of the Noble Metals Au+ and Ag+ to Propene”, Chem. Phys. Lett., 412, 416 (2005).

414. T.J. Dudley and M.S. Gordon, “Theoretical Study of the Formation and Isomerization of Al2H2”, Mol. Phys., 104, 751 (2006).

415. H. Li and M.S. Gordon, “Gradients of the Exchange-Repulsion Energy in the Effective Fragment Potential Method”, Theor. Chem. Accts., 115, 385 (2006).

416. C.M. Aikens, G.D Fletcher, M.W. Schmidt, and M.S. Gordon, “Scalable Implementation Of Analytic Gradients For Second-Order Z-Averaged Perturbation Theory Using The Distributed Data Interface”, J. Chem. Phys., 124, 014107 (2006).

417. T.J. Dudley, R.M. Olson, M.W. Schmidt, and M.S. Gordon, “Parallel Coupled Perturbed CASSCF Equations and Analytic CASSCF Second Derivatives”, J. Comp. Chem., 27, 353 (2006).

418. J.M. Rintelman, M.S. Gordon, G.D. Fletcher, and J. Ivanic, “Reinvestigation of SiC3 with multireference perturbation theory”, J. Chem. Phys., 124, 034303 (2006).

419. S. Koseki, T. Matsushita, and M.S. Gordon, “Dissociation Potential Curves of Low-Lying States in Transition Metal Hydrides. III. Hydrides of Groups 6 and 7”, J. Phys. Chem, A110, 2560 (2006).

420. S. Varganov and M.S. Gordon, “Effects of Strong Correlations in Ti8C12 Met-Car”, Chem. Phys., 326, 97 (2006).

421. I. Adamovic, H. Li, M.H. Lamm, and M. S. Gordon, “Modeling Styrene-Styrene Interactions”, J. Phys. Chem., A110, 519 (2006).

422. R.M. Olson and M.S. Gordon, “The structure of the Si9H12 cluster: A coupled cluster and muti-reference perturbation theory study”, J. Chem. Phys., 124, 081105 (2006).

423. D.G. Fedorov, K. Kitaura, H. Li, J.H. Jensen, and M.S. Gordon, “The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO)”, J. Comp. Chem., 27, 976 (2006).

424. H.M. Netzloff, M.A. Collins, and M.S. Gordon, “Growing Multi-Configurational Potential Energy Surfaces with Applications to X + H2 (X = C, N, O) Reactions”, J. Chem. Phys., 124, 154104 (2006)..

425. I. Adamovic and M.S. Gordon, “Methanol-water mixtures: A microsolvation study using the effective fragment potential method, J. Phys. Chem, A110, 10267 (2006).

426. H. Li, M.S. Gordon, and J.H. Jensen, “Charge Transfer Interaction in the Effective Fragment Potential Method”, J. Chem. Phys., 124, 214108 (2006).

427. D.D. Zorn, J.A. Boatz and M.S. Gordon, “Tetrazolium-Based Energetic Ionic Liquids”, J. Phys. Chem., B110, 11110 (2006).

428. C.M. Aikens and M.S. Gordon, “Incremental Solvation of Nonionized and Zwitterionic Glycine”, J. Am. Chem. Soc., 128, 12835 (2006).

429. B. Njegic and M.S. Gordon, “Exploring the Effect of Anharmonicity of Molecular Vibrations on Thermodynamic Properties”, J. Chem. Phys., 125, 224102 (2006).

430. S. Varganov, T.J. Dudley, and M.S. Gordon,“Predicted IR spectra of Ti8C12 and Ti8C12+”, Chem. Phys. Lett., 429, 49 (2006).

431. M.A. Albao, M.M.R. Evans, J. Nogami, D. Zorn, M.S. Gordon, and J.W. Evans, Reply to ‘Comment on “Monotonicall decreasing size distributions for one-dimensional Ga rows on Si(100)”’, Phys. Rev. B, 74, 1 (2006).

432. H. Li and M.S. Gordon, “Gradients of the Polarization Energy in the Effective Fragment Potential Method”, J. Chem. Phys., 125, 194103 (2006).

433. M.S. Gordon, K. Ruedenberg, M.W. Schmidt, L. Bytautas, T.J. Dudley, T. Nagata, R. Olson, and S. varganov, “Scalable correlated electronic structure theory”, J. Phys Conf Series, 46, 229 (2006)

434. Z. M. Loh, R. L. Wilson, D. A. Wild, E. J. Bieske, J. M. Lisy, B. Njegic, and M. S. Gordon, “Infrared Spectra and Ab Initio Calculations for the F--(CH4)n (n = 1-8) Anion Clusters”, J. Phys. Chem A, 110, 13736 (2006)

435. L. Slipchenko and M.S. Gordon, “Electrostatic Energy in the Effective Fragment Potential (EFP) Method. Theory and Application to Benzene Dimer”, J. Comp. Chem., 28, 276 (2007).

436. Y. Alexeev, M.W. Schmidt, T.L. Windus, M.S. Gordon, “A Parallel Distributed Data CPHF Algorithm for Analytic Hessians, J. Comp. Chem., 28, 1685, (2007).

437. Y. Ge, M.S. Gordon, F. Battaglia, and R.O. Fox, Theoretical Study of the Pyrolyisis of Methyltrichlorosilane in the Gas Phase. I. Thermodynamics”, J. Phys. Chem., A111, 1462 (2007).

438. Y. Ge, M.S. Gordon, F. Battaglia, and R.O. Fox, Theoretical Study of the Pyrolyisis of Methyltrichlorosilane in the Gas Phase. II. ”Reaction Paths and Transition States”, J. Phys. Chem., A111, 1475 (2007).

439. I.S.O Pimienta, S. Elzey, J.A. Boatz and M.S. Gordon, “Pentzole-Based Energetic Ionic Liquids: A Computational Study”, J. Phys. Chem. A, 111, 691 (2007).

440. R. Becerra, I. W. Carpenter, M. S. Gordon, L. Roskop, and R. Walsh, “Gas-phase kinetic and quantum chemical studies of the reactions of silylene with the methylsilanes. Absolute Rate Constants, Temperature Dependences, RRKM modelling and Potential Energy surfaces”, PCCP, 9, 2817 (2007).

441. H. Li and M.S. Gordon, “Polarization Energy Gradients in Combined Quantum Mechanics, Effective Fragment Potential and Polarizable Continuum Model Calculations”, J. Chem. Phys., 126, 124112 (2007).

442. Ryan M. Olson, Jonathan L. Bentz, Ricky A. Kendall, Michael W. Schmidt, and Mark S. Gordon, “A Novel Approach to Parallel Coupled Cluster Calculations: Combining Distributed and Shared Memory Techniques for Modern Cluster Based Systems”, J. Comp. Theoret. Chem., 3, 1312 (2007)

443. R.M. Olson and M.S. Gordon, “The Isomers of Au8”, J. Chem. Phys., 126, 214310 (2007)

444. M.S. Gordon, L. Slipchenko, H. Li, and J.H. Jensen, “The Effective Fragment Potential: A General Method for Predicting Intermolecular Forces”, Ann. Rep. Comp. Chem., 3, 177 (2007).

445. P.A. Avramov, L.A. Chernozatonskii, P.B. Sorokin, and M.S. Gordon, "Multiterminal Nanowire Junctions of Silicon: A Theoretical Prediction of Atomic Structure and Electronic Properties", Nano Letters, 7, 2063 (2007).

446. V.F. Sidorkin, E.F Belogolova, M.S. Gordon, M.I. Lazarevich, and N.F. Lazareva, "Hypercorrdinated Carbon in 2,8,9-Sila- and Thia-Substituted Carbatranes", Organometallics, 26, 4568 (2007).

447. L. Bytautas, T. Nagata, M.S. Gordon, and K. Ruedenberg, "Accurate ab initio potential energy curve of F2.I. Non-relativistic full valence CI energies by the CEEIS method", J. Chem. Phys., 127, 164317 (2007).

448. L. Bytautas, N. Matsunaga, T. Nagata, M.S. Gordon, and K. Ruedenberg, "Accurate ab initio potential energy curve of F2.II.Core-valence correlations, relativistic contributions and long-range interactions", J. Chem. Phys., 127, 204301 (2007)

449. L. Bytautas, N. Matsunaga, T. Nagata, M.S. Gordon, and K. Ruedenberg, "Accurate ab initio potential energy curve of F2.III.The Vibration rotation spectrum", J. Chem. Phys., 127, 204313 (2007).

450. P.V. Avramov, D.G. Fedorov, P.V. Sorokin, L.A. Chernozatonskii, and M.S. Gordon, "Atomic and electronic structure of new hollow-based symmetric families of silicon nanoclusters", J. Phys. Chem. C, 111, 18824 (2007).

451. Y. Ge, M.S. Gordon, and P. Piecuch, "Breaking Bonds with the Left Eigenstate Completely Renormalized Coupled Cluster Method", J. Chem. Phys., 127, 174106 (2007).

452. B.J. Tejerina, and M.S. Gordon, “The Addition of POSS-T8 to the Si(100) Surface”, J. Phys. Chem., 112, 754 (2008).

453. Takako Kudo, Mitsutoshi Akasaka and Mark S. Gordon, “Ab Inito Molecular Orbital Study of the Insertion of H2 Into POSS”, Theor. Chem. Accts., 120, 155 (2008).

454. J. Moc and M.S. Gordon, “A Theoretical Study of the Reaction of Ti+ with Propane”, Theor. Chem. Acc., 120, 243 (2008).

455. T. Kudo, M. Akasaka, and M.S. Gordon, “Ab initio molecular orbital study on the Ge-, Sn-, Zr-, and Si/Ge- mixed Silsesquioxanes”, J. Phys. Chem. A, 112, 4836 (2008).

456. D. D. Kemp and M.S. Gordon, “An Interpretation of the Enhancement of the Water Dipole Moment Due to the Presence of Other Water Molecules”, J. Phys. Chem., 112, 4885 (2008)

457. T. Smith, L.V. Slipchenko, and M.S. Gordon, “Modeling π-π interactions with the effective fragment potential method: The benzene dimer and substituents”, J. Phys. Chem. A, 112, 5286 (2008).

458. D. Shemesh, J. Mullin, M.S. Gordon, and R.B. Gerber, “Vibrational Spectroscopy for Glycine adsorbed on Silicon Clusters: Harmonic and Anharmonic Models of the Si(100)-2x1 Surface”, Chem. Phys., in press.

459. H. Li, J.A. Boatz, and M.S. Gordon, “Π−Π stacking in small ionic clusters of 1,2,4-triazolium”, J. Am. Chem. Soc., in press.

460. K.C. Sears, J.W. Ferguson, T.J. Dudley, R.S. Houk, and M.S. Gordon, “Theoretical Investigation of Small Polyatomic Ions Observed in Inductively Coupled Plasma – Mass Spectrometry: HxCO+ and HxN2+ (x=1,2,3)”, J. Phys. Chem., in press.

461. J. Velasquez, III B. Njegic, M. S. Gordon and M. A. Duncan, “IR Photodissociation Spectroscopy and Theory of Au+(CO)n Complexes: Nonclassical Carbonyls in the Gas Phase”, J. Phys. Chem A, in press.

462. D. Zorn, V. S.-Y. Lin, M. Pruski, and M.S. Gordon, “Comparison of Nitroaldol Reaction Mechanisms Using Accurate Ab Initio Calculations, J. Phys. Chem. A, 112, 10635 (2008).

463. D. Kina, A. Nakayama, T. Noro, T. Taketsugu and M.S. Gordon, “Ab initio QM/MM molecular dynamics study on the excited state proton transfer of 7-azaindole in water solution”, J. Phys. Chem., 112, 9675 (2008)”.

464. W.D. Luedtke, Uzi. Landman, Y.-H. Chiu, D. J. Levandier, R. A. Dressler, S. Sok and M. S. Gordon, “Nanojets, Electrospray, and Field-Ion Evaporation: Molecular Dynamics Simulations and Laboratory Experiments”, J. Phys. Chem. A, 112, 9628 (2008) (Feature Article).

465. D. Zorn, V.S.-Y. Lin, M. Pruski and M.S. Gordon, “An Interface Between the Universal Force Field and the Effective Fragment Potential Method”, J. Phys. Chem. B, 112, 12753 (2008).

466. G.P.F. Wood, M.S. Gordon, L. Radom, and D.M. Smith, “The Nature of Glycine and its α-Carbon Radical in Aqueous Solution: A Theoretical Investigation”, J. Phys. Chem., in press.

467. B. Njegic and M.S. Gordon, “Reaction mechanism of the directgas phase synthesis of H2O2 catalyzed by Au3”, J. Chem. Phys., in press.

468. B. Njegic and M.S. Gordon, “Predicting accurate vibrational frequencies for highly anharmonic systems”, J. Chem. Phys., in press.

469. Y. Ge, M.S. Gordon, P. Piecuch, M. Wloch, and J.R. Gour, “Breaking bonds of open-shell species with the restricted open-shell size extensive left eigenstate completely renormalized coupled-cluster method”, J. Chem. Phys., 112, 11873 (2008).

470. S. Yoo, F. Zahariev, S. Sok, and M.S. Gordon, “Solvent Affects on Optical Properties of Molecules: A Combined Time-Dependent Density Functional Theory/Effective Fragment Potential Approach”, J. Chem. Phys., 129, 144112 (2008).

471. A. Asadchev, B.M. Bode, and M.S. Gordon, “Performance of Electronic Structure Calculations on Blue Gene and Cray XT4 Computers”, J. Comput. Theoret. Nanoscience, in press.

472. J. W. Ferguson, T. J. Dudley, K. C. Sears, M. S. Gordon, and R. S. Houk, “A Study of Polyatomic Ions in Inductively Coupled Plasma – Mass Spectrometry. Part II: Novel Calculations of Unusual Ions”, Spectrochim. Acta B, submitted.

473. Z. Gao, F. Battaglia, R.O. Fox, Y. Ge, and M.S. Gordon, “Theoretical Study of the Pyrolysis of Methyltrichlorosilane in the Gas Phase III. Reduced Mechanism”, J. Phys. Chem C, submitted.

474. D.D. Zorn, M.A. Albao, J.W. Evans, and M.S. Gordon, “Binding and Diffusion of Al Adatoms and Dimers, on the Si(100)-2x1 Reconstructed Surface: A Hybrid QM/MM Embedded Cluster Study, J. Phys. Chem. C, submitted.

475. L. Slipchenko and M.S. Gordon, “Damping functions in the Effective Fragment Potential”, Mol. Phys., submitted.