Martinez Group reprints (1996-2004)

Reprints and Preprints (1996-Present)

Titles are hyperlinked to HTML abstracts
References are hyperlinked to PDF reprints

Papers and Chapters

78. Electrostatic Control of Photoisomerization in the Photactive Yellow Protein Chromophore: Ab Initio Multiple Spawning Dynamics
C. Ko, A. M. Virshup, and T. J. Martinez
Chem. Phys. Lett., in press

77. Graphical Processing Units for Quantum Chemistry
I. S. Ufimtsev and T. J. Martinez
Comp. in Sci. and Eng., in press

76. Pseudospectral Time-Dependent Density Functional Theory
C. Ko, D. K. Malick, D. A. Braden, R. . Friesner, and T. J. Martinez
J. Chem. Phys., 128, 104103 (2008)

75. Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation
I. S. Ufimtsev and T. J. Martinez
J. Chem. Theo. Comp., 4, 222-231 (2008)

74. Implementation of Ab Initio Multiple Spawning in the MolPro Quantum Chemistry Package
B. G. Levine, J. D. Coe, A. M. Virshup, and Todd J. Martinez
Chem. Phys., 347, 3-16 (2008)

73. Ab Initio Multiple Spawning Dynamics of Excited State Intramolecular Proton Transfer: The Role of Spectroscopically Dark States
J. D. Coe and T. J. Martinez
Mol. Phys., 106, 537-545 (2008)

72. Optimizing Conical Intersections Without Derivative Coupling Vectors: Application to Multi-State Multireference Second Order Perturbation Theory (CASPT2)
B. G. Levine, J. D. Coe, and T. J. Martinez
J. Phys. Chem., 112B, 405-413 (2008)
Supporting Information

71. Comparative Genomics and Site-Directed Mutagenesis Suport the Existence of Only One Input Channel for Protons in the C-Family (cbb3) Oxidase of Heme-Copper Oxygen Reductases
J. Hemp, H. Han, J. H. Roh, S. Kaplan, T. J. Martinez, and R. B. Gennis
Biochemistry 46, 9963-9972 (2007)

70. Ab Initio Molecular Dynamics and Time-Resolved Photoelectron Spectroscopy of Electronically Excited Uracil and Thymine
H. R. Hudock, B. G. Levine, A. L. Thompson, H. Satzger, D. Townsend, N. Gador, S. Ullrich, A. Stolow, and T. J. Martinez
J. Phys. Chem. 111A, 8500-8508 (2007)
Supporting Information

69. First Principles Dynamics of Photoexcited DNA and RNA Bases
H. R. Hudock, B. G. Levine, A. L. Thompson, and T. J. Martinez
AIP Conf. Proc., 963, 219-222 (2007)

68. Optimization of Semiempirical Quantum Chemistry Methods via Multiobjective Genetic Algorithms: Accurate Photodynamics for Larger Molecules and Longer Time Scales
K. Sastry, D. D. Johnson, A. . Thompson, D. E. Goldberg, T. J. Martinez, J. Leiding, and J. Owens
Mat. Manuf. Proc., 22, 553-561 (2007)

67. Substituent Effects on Dynamics at Conical Intersections: a,b enones
A. M. D. Lee, J. D. Coe, S. Ullrich, M.-L. Ho, S.-J. Lee, B.-M. Cheng, M. Z. Zgierski, I.-C. Chen, T. J. Martinez, and A. Stolow
J. Phys. Chem., 111A, 11948-11960 (2007)
Supporting Information

66. A Continuous Spawning Method for Nonadiabatic Dynamics and Validation for the Zero Temperature Spin Boson Problem
M. Ben-Nun and T. J. Martinez
Isr. J. Chem., 47, 75-88 (2007)

65. The Vibrationally Adiabatic Torsional Potential Energy Surface of trans-Stilbene
P. D. Chowdary, T. J. Martinez, and M. Gruebele
Chem. Phys. Lett. 440, 7-11 (2007)

64. A Charged Ring Model for Classical OH-(aq) Simulations
I. S. Ufimtsev, A. G. Kalinichev, T. J. Martinez, and R. J. Kirkpatrick
Chem. Phys. Lett. 442, 128-133 (2007)

63. Ab Initio Molecular Dynamics of Excited State Intramolecular Proton Transfer Using Multireference Perturbation Theory
J. D. Coe, B. G. Levine, and T. J. Martinez
J. Phys. Chem., 111, 11302-11310 (2007)
Supporting Information

62. Conformationally controlled chemistry: Excited state dynamics dictate ground state dissociation
M. H. Kim, L. Shen, H. Tao, T. J. Martinez and A. G. Suits
Science, 315, 1561-1565 (2007)
Supporting Information

61. QTPIE: Charge Transfer with Polarization Current Equalization. A fluctuating charge model with correct asymptotics
J. Chen and T. J. Martinez
Chem. Phys. Lett., 438, 315-320 (2007)

60. Isomerization Through Conical Intersections
B. G. Levine and T. J. Martinez
Ann. Rev. Phys. Chem., 58 613-634 (2007)

59. The Evolutionary Migration of a Post-Translationally Modified Active-Site Residue in the Proton-Pumping Heme-Copper Oxygen Reductases
J. Hemp, D. E. Robinson, T. J. Martinez, N. L. Kelleher, and R. B. Gennis
Biochemistry, 45, 15405-15410 (2006)

58. Multiobjective genetic algorithms for multiscaling excited state direct dynamics in photochemistry
K. Sastry, D. D. Johnson, A. L. Thompson, D. E. Goldberg, T. J. Martinez, J. Leiding, and J. Owens
Proceedings of the 8th Annual Conference on Genetic and Evolutionary Computation, 1745-1752 (2006)

57. Multicentered Valence Electron Effective Potentials: A Solution to the Link Atom Problem for Ground and Excited Electronic States
P. Slavicek and T. J. Martinez
J. Chem. Phys., 124, 084107 (2006)

56. Ab Initio Molecular Dynamics of Excited State Intramolecular Proton Transfer Around a Three-State Conical Intersection in Malonaldehyde
J. D. Coe and T. J. Martinez
J. Phys. Chem.,110, 618-630 (2006)
Supplementary Information

55. Insights for Light-Driven Molecular Devices from Ab Initio Multiple Spawning Dynamics
T. J. Martinez
Acc. Chem. Res., 39, 119-125 (2006)

54. Conical Intersections and Double Excitations in Time-Dependent Density Functional Theory
B. G. Levine, C. Ko, J. Quenneville, and T. J. Martinez
Mol. Phys., 104, 1039-1051 (2006)

53. Computation of Reaction Mechanisms and Dynamics in Photobiology
S. Olsen, A. Toniolo, C. Ko, L. Manohar, K. Lamothe, and T. J. Martinez
in Computational Photochemistry, Ed. M. Olivucci, (Amsterdam, Elsevier, 2005)

52. Simulation of the Photodynamics of Azobenzene on its First Excited State: Comparison of Full Multiple Spawning and Surface Hopping Treatments
A. Toniolo, C. Ciminelli, M. Persico, and T. J. Martinez
J. Chem. Phys., 123, 234308 (2005)

51. Competitive Decay at Two and Three-State Conical Intersections in Excited State Intramolecular Proton Transfer
J. D. Coe and T. J. Martinez
J. Amer. Chem. Soc., 127, 4560 (2005)
Supplementary Information

50. Using Meta Conjugation to Enhance Charge Separation versus Charge Recombination in Phenylacetylene Donor-Bridge-Acceptor Complexes
A. L. Thompson, K. R. J. Thomas, T. J. Martinez, C. J. Bardeen, and S. Thayumanavan
J. Amer. Chem. Soc., 127, 16348-16349 (2005)
Supporting Information

49. Helix Switching of a Key Active Site Residue in Cytochrome cbb3 Oxidases
J. Hemp, C. Christian, B. Barquera, R. B. Gennis, and T. J. Martinez
Biochemistry, 44, 10766 (2005)
Supporting Information

48. Photochemistry from First Principles and Direct Dynamics
A. Toniolo, B. Levine, A. Thompson, J. Quenneville, M. Ben-Nun. J. Owens, S. Olsen, L. Manohar, and T. J. Martinez
in Computational Methods in Organic Photochemistry, Ed. A. Kutateladze (New York, Marcel-Dekker, 2005)

47. First Principles Ab Initio Multiple Spawning Dynamics of Electronically Excited trans-1,3-Butadiene with Wavefunction and Density Functional Theory
B. Levine and T. J. Martinez
in Quantum Dynamics and Conical Intersections, Ed. G. A. Worth and S. C. Allthorpe, (Daresbury, CCP6, 2004)

46. Ab Initio Equation-of-Motion Coupled-Cluster Molecular Dynamics with "On-the-Fly" Diabatization: The Doublet-like Feature in the Photoabsorption Spectrum of Ethylene
A. Toniolo, A. L. Thompson, and T. J. Martinez
Chem. Phys. Lett., 398, 407-413 (2004)

45. Excited State Direct Dynamics of Benzene with Reparameterized Multireference Semiempirical Configuration Interaction Methods
A. Toniolo, A. L. Thompson, and T. J. Martinez
Chemical Physics, 304, 133 (2004)
Supplementary Information By Request

44. Conical Intersection Dynamics in Solution: The Chromophore of Green Fluorescent Protein
A. Toniolo, S. Olsen, L. Manohar, and T. J. Martinez
Faraday Discussions, 127, 149 (2004)
Supplementary Information By Request

43. Azobenzene photoisomerization: Two states and two relaxation pathways explain the violation of Kasha's rule
T. Schultz, S. Ullrich, J. Quenneville, T. J. Martinez, M. Z. Zgierski, and A. Stolow
in Femtochemistry and Femtobiology: Ultrafast Events in Molecular Science, Ed. M. Martin and J. T. Hynes, (Amsterdam, Elsevier, 2004)

42. Ultrafast Excited State Dynamics in Green Fluorescent Protein Chromophore
A. Toniolo, S. Olsen, L. Manohar, and T. J. Martinez
in Femtochemistry and Femtobiology: Ultrafast Events in Molecular Science, Ed. M. Martin and J. T. Hynes, (Amsterdam, Elsevier, 2004)

41. A New Approach to Reactive Potentials with Fluctuating Charges: The Quadratic Valence Bond Model
J. Morales and T. J. Martinez
J. Phys. Chem., 108A, 3076 (2004)

40. Variable Electronic Coupling in Phenylacetylene Dendrimers: The Role of Forster, Dexter, and Charge-Transfer Interactions
A. L. Thompson, K. M. Gaab, J. Xu, C. J. Bardeen, and T. J. Martinez
J. Phys. Chem., 108A, 671 (2004)
Supplementary Information

39. Ab Initio Excited State Dynamics of the Photoactive Yellow Protein Chromophore
C. Ko, B. Levine, A. Toniolo, L. Manohar, S. Olsen, H.-J. Werner, and T. J. Martinez
J. Amer. Chem. Soc., 125, 12710 (2003)
Supplementary Information

38. Quantum Energy Flow and trans-Stilbene Photoisomerization: An Example of a non-RRKM Reaction
D. M. Leitner, J. Quenneville, B. Levine, T. J. Martinez, and P. G. Wolynes
J. Phys. Chem., 107, 10706 (2003)
Supplementary Information

37. The Construction of Semi-diabatic Potential Energy Surfaces of Excited States for Use in AIMD Studies by the Equation-of-Motion Coupled-Cluster Method
K. K. Baeck and T. J. Martinez
Bull. Kor. Chem. Soc., 24, 712 (2003)

36. Ab Initio Molecular Dynamics with Equation-of-Motion Coupled-Cluster Theory: Electronic Absorption Spectrum of Ethylene
K. K. Baeck and T. J. Martinez
Chem. Phys. Lett., 375, 299 (2003)

35. Meta-conjugation and Excited State Coupling in Phenylacetylene Dendrimers
K. M. Gaab, A. L. Thompson, J. Xu, T. J. Martinez, and C. J. Bardeen
J. Amer. Chem. Soc., 125, 9288 (2003)
Supplementary Information

34. Mechanism and Dynamics of Azobenzene Photoisomerization
T. Schultz, J. Quenneville, B. Levine, A. Toniolo, T. J. Martinez, S. Lochbrunner, M. Schmitt, J. P. Shaffer, M. Z. Zgierski, and A. Stolow
J. Amer. Chem. Soc., 125, 8098 (2003)
Supplementary Information

33. Conical Intersections in Solution: A QM/MM Study Using Floating Occupation Semiempirical Configuration Interaction Wavefunctions
A. Toniolo, G. Granucci, and T. J. Martinez
J. Phys. Chem., 107A, 3822 (2003)
Supplementary Information
Supplementary Information By Request

32. Electronic Structure of Solid 1,3,5-triamino-2,4,6-trinitrobenzene Under Uniaxial Compression: On the Possible Role of Pressure Induced Metallization in Energetic Materials
C. J. Wu, L. H. Yang, L. E. Fried, J. Quenneville, and T. J. Martinez
Phys. Rev. B, 67, 235101 (2003)

31. Ab Initio Study of cis-trans Photoisomerization in Stilbene and Ethylene
J. Quenneville and T. J. Martinez
J. Phys. Chem., 107A, 829 (2003)
Supplementary Information